Starting phenix.real_space_refine on Tue Nov 18 15:33:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ljv_4062/11_2025/5ljv_4062.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ljv_4062/11_2025/5ljv_4062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ljv_4062/11_2025/5ljv_4062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ljv_4062/11_2025/5ljv_4062.map" model { file = "/net/cci-nas-00/data/ceres_data/5ljv_4062/11_2025/5ljv_4062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ljv_4062/11_2025/5ljv_4062.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 72 5.16 5 C 9474 2.51 5 N 2580 2.21 5 O 2856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15000 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "B" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "C" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "E" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "F" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2472 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 306} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.85, per 1000 atoms: 0.26 Number of scatterers: 15000 At special positions: 0 Unit cell: (97.82, 92.46, 187.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 12 15.00 Mg 6 11.99 O 2856 8.00 N 2580 7.00 C 9474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.34 Conformation dependent library (CDL) restraints added in 672.2 milliseconds 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 46.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.541A pdb=" N LYS A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.895A pdb=" N GLU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.893A pdb=" N ARG A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.551A pdb=" N ALA A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 257 through 270 removed outlier: 3.702A pdb=" N ILE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 282 removed outlier: 4.718A pdb=" N ALA A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.528A pdb=" N LYS B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 84 through 100 removed outlier: 3.906A pdb=" N GLU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 188 through 204 removed outlier: 3.916A pdb=" N ARG B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.584A pdb=" N ALA B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 Processing helix chain 'B' and resid 257 through 270 removed outlier: 3.703A pdb=" N ILE B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 282 removed outlier: 4.707A pdb=" N ALA B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.530A pdb=" N LYS C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 Processing helix chain 'C' and resid 84 through 100 removed outlier: 3.899A pdb=" N GLU C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 188 through 204 removed outlier: 3.884A pdb=" N ARG C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.563A pdb=" N ALA C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 255 Processing helix chain 'C' and resid 257 through 270 removed outlier: 3.714A pdb=" N ILE C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 282 removed outlier: 4.715A pdb=" N ALA C 278 " --> pdb=" O PRO C 274 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THR C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'D' and resid 44 through 52 removed outlier: 3.537A pdb=" N LYS D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 64 Processing helix chain 'D' and resid 84 through 100 removed outlier: 3.900A pdb=" N GLU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 132 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.891A pdb=" N ARG D 203 " --> pdb=" O ALA D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 222 removed outlier: 3.575A pdb=" N ALA D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 257 through 270 removed outlier: 3.708A pdb=" N ILE D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 282 removed outlier: 4.716A pdb=" N ALA D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 293 Processing helix chain 'D' and resid 295 through 304 Processing helix chain 'D' and resid 305 through 308 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'E' and resid 44 through 52 removed outlier: 3.537A pdb=" N LYS E 49 " --> pdb=" O VAL E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 64 Processing helix chain 'E' and resid 84 through 100 removed outlier: 3.912A pdb=" N GLU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 143 through 150 Processing helix chain 'E' and resid 188 through 204 removed outlier: 3.914A pdb=" N ARG E 203 " --> pdb=" O ALA E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 222 removed outlier: 3.595A pdb=" N ALA E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 255 Processing helix chain 'E' and resid 257 through 270 removed outlier: 3.695A pdb=" N ILE E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 282 removed outlier: 4.709A pdb=" N ALA E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 293 Processing helix chain 'E' and resid 295 through 304 Processing helix chain 'E' and resid 305 through 308 Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'F' and resid 44 through 52 removed outlier: 3.549A pdb=" N LYS F 49 " --> pdb=" O VAL F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 64 Processing helix chain 'F' and resid 84 through 100 removed outlier: 3.898A pdb=" N GLU F 88 " --> pdb=" O ASP F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'F' and resid 143 through 150 Processing helix chain 'F' and resid 188 through 204 removed outlier: 3.894A pdb=" N ARG F 203 " --> pdb=" O ALA F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 222 removed outlier: 3.569A pdb=" N ALA F 216 " --> pdb=" O ASN F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 255 Processing helix chain 'F' and resid 257 through 270 removed outlier: 3.693A pdb=" N ILE F 261 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 282 removed outlier: 4.720A pdb=" N ALA F 278 " --> pdb=" O PRO F 274 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N THR F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 293 Processing helix chain 'F' and resid 295 through 304 Processing helix chain 'F' and resid 305 through 308 Processing helix chain 'F' and resid 320 through 331 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.132A pdb=" N LEU A 12 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 112 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 14 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY A 114 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 16 " --> pdb=" O GLY A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 185 removed outlier: 6.591A pdb=" N ILE A 158 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA A 287 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 160 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.335A pdb=" N ARG A 236 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 32 through 36 removed outlier: 6.113A pdb=" N LEU B 12 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL B 112 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 14 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY B 114 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL B 16 " --> pdb=" O GLY B 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 185 Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.341A pdb=" N ARG B 236 " --> pdb=" O GLN B 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 32 through 36 removed outlier: 6.117A pdb=" N LEU C 12 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL C 112 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 14 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLY C 114 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 16 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 57 Processing sheet with id=AB2, first strand: chain 'C' and resid 182 through 185 Processing sheet with id=AB3, first strand: chain 'C' and resid 207 through 208 removed outlier: 4.361A pdb=" N ARG C 236 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 32 through 36 removed outlier: 6.115A pdb=" N LEU D 12 " --> pdb=" O CYS D 110 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL D 112 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D 14 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY D 114 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL D 16 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 57 Processing sheet with id=AB6, first strand: chain 'D' and resid 182 through 185 Processing sheet with id=AB7, first strand: chain 'D' and resid 207 through 208 removed outlier: 4.371A pdb=" N ARG D 236 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 36 removed outlier: 6.116A pdb=" N LEU E 12 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL E 112 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU E 14 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY E 114 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL E 16 " --> pdb=" O GLY E 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 57 Processing sheet with id=AC1, first strand: chain 'E' and resid 182 through 185 Processing sheet with id=AC2, first strand: chain 'E' and resid 207 through 208 removed outlier: 4.359A pdb=" N ARG E 236 " --> pdb=" O GLN E 208 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 32 through 36 removed outlier: 6.130A pdb=" N LEU F 12 " --> pdb=" O CYS F 110 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL F 112 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU F 14 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY F 114 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL F 16 " --> pdb=" O GLY F 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AC5, first strand: chain 'F' and resid 182 through 185 removed outlier: 6.589A pdb=" N ILE F 158 " --> pdb=" O VAL F 285 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA F 287 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL F 160 " --> pdb=" O ALA F 287 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 207 through 208 removed outlier: 4.353A pdb=" N ARG F 236 " --> pdb=" O GLN F 208 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2112 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: 2.72 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 2365 1.26 - 1.42: 3797 1.42 - 1.57: 8777 1.57 - 1.72: 211 1.72 - 1.87: 108 Bond restraints: 15258 Sorted by residual: bond pdb=" CA HIS A 22 " pdb=" C HIS A 22 " ideal model delta sigma weight residual 1.520 1.374 0.146 1.21e-02 6.83e+03 1.46e+02 bond pdb=" CA VAL C 160 " pdb=" C VAL C 160 " ideal model delta sigma weight residual 1.527 1.426 0.101 8.50e-03 1.38e+04 1.41e+02 bond pdb=" CA HIS F 22 " pdb=" C HIS F 22 " ideal model delta sigma weight residual 1.520 1.377 0.144 1.21e-02 6.83e+03 1.41e+02 bond pdb=" CA VAL D 160 " pdb=" C VAL D 160 " ideal model delta sigma weight residual 1.527 1.429 0.097 8.50e-03 1.38e+04 1.31e+02 bond pdb=" CA VAL D 183 " pdb=" CB VAL D 183 " ideal model delta sigma weight residual 1.550 1.435 0.115 1.03e-02 9.43e+03 1.25e+02 ... (remaining 15253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.27: 18285 4.27 - 8.55: 2169 8.55 - 12.82: 222 12.82 - 17.09: 45 17.09 - 21.36: 15 Bond angle restraints: 20736 Sorted by residual: angle pdb=" C VAL E 147 " pdb=" CA VAL E 147 " pdb=" CB VAL E 147 " ideal model delta sigma weight residual 111.97 98.86 13.11 1.28e+00 6.10e-01 1.05e+02 angle pdb=" C VAL B 147 " pdb=" CA VAL B 147 " pdb=" CB VAL B 147 " ideal model delta sigma weight residual 111.97 99.07 12.90 1.28e+00 6.10e-01 1.01e+02 angle pdb=" C VAL D 147 " pdb=" CA VAL D 147 " pdb=" CB VAL D 147 " ideal model delta sigma weight residual 111.97 99.35 12.62 1.28e+00 6.10e-01 9.73e+01 angle pdb=" C VAL C 147 " pdb=" CA VAL C 147 " pdb=" CB VAL C 147 " ideal model delta sigma weight residual 111.81 99.72 12.09 1.25e+00 6.40e-01 9.35e+01 angle pdb=" C VAL F 147 " pdb=" CA VAL F 147 " pdb=" CB VAL F 147 " ideal model delta sigma weight residual 111.97 100.08 11.89 1.28e+00 6.10e-01 8.63e+01 ... (remaining 20731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.13: 7969 20.13 - 40.27: 1016 40.27 - 60.40: 269 60.40 - 80.53: 20 80.53 - 100.67: 14 Dihedral angle restraints: 9288 sinusoidal: 3708 harmonic: 5580 Sorted by residual: dihedral pdb=" C MET D 258 " pdb=" N MET D 258 " pdb=" CA MET D 258 " pdb=" CB MET D 258 " ideal model delta harmonic sigma weight residual -122.60 -142.76 20.16 0 2.50e+00 1.60e-01 6.50e+01 dihedral pdb=" C MET C 258 " pdb=" N MET C 258 " pdb=" CA MET C 258 " pdb=" CB MET C 258 " ideal model delta harmonic sigma weight residual -122.60 -142.34 19.74 0 2.50e+00 1.60e-01 6.23e+01 dihedral pdb=" C MET E 258 " pdb=" N MET E 258 " pdb=" CA MET E 258 " pdb=" CB MET E 258 " ideal model delta harmonic sigma weight residual -122.60 -142.24 19.64 0 2.50e+00 1.60e-01 6.17e+01 ... (remaining 9285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 2035 0.192 - 0.384: 340 0.384 - 0.576: 49 0.576 - 0.768: 6 0.768 - 0.960: 6 Chirality restraints: 2436 Sorted by residual: chirality pdb=" CA MET F 258 " pdb=" N MET F 258 " pdb=" C MET F 258 " pdb=" CB MET F 258 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" CA MET E 258 " pdb=" N MET E 258 " pdb=" C MET E 258 " pdb=" CB MET E 258 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CA MET A 258 " pdb=" N MET A 258 " pdb=" C MET A 258 " pdb=" CB MET A 258 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.25e+01 ... (remaining 2433 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 67 " 0.069 2.00e-02 2.50e+03 4.21e-02 3.55e+01 pdb=" CG TYR F 67 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR F 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 67 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR F 67 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR F 67 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR F 67 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR F 67 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 286 " -0.063 2.00e-02 2.50e+03 4.45e-02 3.47e+01 pdb=" CG PHE E 286 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 PHE E 286 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 286 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE E 286 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 286 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE E 286 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " 0.064 2.00e-02 2.50e+03 3.90e-02 3.04e+01 pdb=" CG TYR A 67 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " -0.005 2.00e-02 2.50e+03 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 828 2.64 - 3.20: 15328 3.20 - 3.77: 25228 3.77 - 4.33: 35377 4.33 - 4.90: 55138 Nonbonded interactions: 131899 Sorted by model distance: nonbonded pdb=" NZ LYS A 49 " pdb=" OH TYR C 149 " model vdw 2.070 3.120 nonbonded pdb=" OH TYR D 149 " pdb=" NZ LYS F 49 " model vdw 2.075 3.120 nonbonded pdb=" OH TYR A 149 " pdb=" NZ LYS B 49 " model vdw 2.106 3.120 nonbonded pdb=" NZ LYS E 49 " pdb=" OH TYR F 149 " model vdw 2.132 3.120 nonbonded pdb=" O THR D 20 " pdb=" OG1 THR D 20 " model vdw 2.181 3.040 ... (remaining 131894 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.820 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.030 0.189 15258 Z= 2.067 Angle : 2.849 21.364 20736 Z= 1.714 Chirality : 0.155 0.960 2436 Planarity : 0.016 0.126 2676 Dihedral : 18.809 100.668 5700 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 2.89 % Allowed : 7.38 % Favored : 89.73 % Rotamer: Outliers : 11.82 % Allowed : 13.25 % Favored : 74.94 % Cbeta Deviations : 4.74 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.82 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.53 (0.15), residues: 1938 helix: -3.57 (0.11), residues: 870 sheet: -0.64 (0.27), residues: 306 loop : -3.16 (0.18), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 203 TYR 0.083 0.015 TYR F 67 PHE 0.093 0.013 PHE E 286 HIS 0.016 0.006 HIS E 22 Details of bonding type rmsd covalent geometry : bond 0.03037 (15258) covalent geometry : angle 2.84871 (20736) hydrogen bonds : bond 0.17586 ( 762) hydrogen bonds : angle 8.47996 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 507 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7885 (p90) REVERT: A 63 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: A 84 ASP cc_start: 0.8938 (m-30) cc_final: 0.8416 (t0) REVERT: A 100 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.9002 (t) REVERT: A 112 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.8843 (p) REVERT: A 126 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8191 (tp) REVERT: A 136 HIS cc_start: 0.8070 (p90) cc_final: 0.7799 (p90) REVERT: A 166 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9027 (p) REVERT: A 180 GLU cc_start: 0.8894 (mp0) cc_final: 0.8650 (tp30) REVERT: A 185 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7961 (mm) REVERT: A 209 MET cc_start: 0.8559 (mtm) cc_final: 0.8089 (mtm) REVERT: A 249 PRO cc_start: 0.8970 (Cg_exo) cc_final: 0.8729 (Cg_endo) REVERT: A 302 GLU cc_start: 0.8662 (tp30) cc_final: 0.8434 (tp30) REVERT: A 331 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8968 (tp30) REVERT: B 84 ASP cc_start: 0.8701 (m-30) cc_final: 0.8372 (t0) REVERT: B 109 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7385 (mm) REVERT: B 180 GLU cc_start: 0.9280 (mp0) cc_final: 0.9045 (tp30) REVERT: B 194 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7900 (tt0) REVERT: B 202 GLU cc_start: 0.8659 (tt0) cc_final: 0.8358 (mt-10) REVERT: B 209 MET cc_start: 0.8639 (mtm) cc_final: 0.8004 (mtm) REVERT: B 259 PRO cc_start: 0.8362 (OUTLIER) cc_final: 0.8094 (Cg_exo) REVERT: B 270 ARG cc_start: 0.8521 (ptt180) cc_final: 0.7943 (mmt180) REVERT: B 317 ASP cc_start: 0.7993 (t0) cc_final: 0.7184 (p0) REVERT: C 26 MET cc_start: 0.8722 (mtp) cc_final: 0.8486 (mtm) REVERT: C 51 LEU cc_start: 0.9260 (tp) cc_final: 0.8637 (tp) REVERT: C 59 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8283 (t70) REVERT: C 64 MET cc_start: 0.7739 (mtt) cc_final: 0.7506 (mtt) REVERT: C 75 GLN cc_start: 0.8702 (pm20) cc_final: 0.8449 (pt0) REVERT: C 109 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7876 (mp) REVERT: C 112 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 126 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8495 (mt) REVERT: C 146 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8483 (ptt) REVERT: C 154 LEU cc_start: 0.8347 (mt) cc_final: 0.8008 (mp) REVERT: C 180 GLU cc_start: 0.9122 (mp0) cc_final: 0.8758 (tp30) REVERT: C 240 LYS cc_start: 0.7704 (mttt) cc_final: 0.7420 (tptt) REVERT: C 249 PRO cc_start: 0.9129 (Cg_exo) cc_final: 0.8880 (Cg_endo) REVERT: C 275 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8769 (tm-30) REVERT: D 26 MET cc_start: 0.8569 (mtp) cc_final: 0.8326 (mtm) REVERT: D 32 LYS cc_start: 0.8682 (mttt) cc_final: 0.8290 (mtpp) REVERT: D 51 LEU cc_start: 0.9279 (tp) cc_final: 0.8662 (tp) REVERT: D 59 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8244 (t70) REVERT: D 72 TYR cc_start: 0.8898 (m-80) cc_final: 0.8670 (m-80) REVERT: D 74 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8849 (mt) REVERT: D 109 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7977 (mp) REVERT: D 112 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9046 (m) REVERT: D 126 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8467 (tt) REVERT: D 146 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8380 (ptt) REVERT: D 149 TYR cc_start: 0.9047 (t80) cc_final: 0.8833 (t80) REVERT: D 154 LEU cc_start: 0.8270 (mt) cc_final: 0.7990 (mp) REVERT: D 180 GLU cc_start: 0.9127 (mp0) cc_final: 0.8724 (tp30) REVERT: D 194 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8051 (tt0) REVERT: D 198 ASN cc_start: 0.8982 (m-40) cc_final: 0.8748 (m110) REVERT: D 220 GLN cc_start: 0.8791 (tt0) cc_final: 0.8475 (tt0) REVERT: D 240 LYS cc_start: 0.7724 (mttt) cc_final: 0.7436 (tptt) REVERT: D 275 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8836 (tm-30) REVERT: E 69 ASP cc_start: 0.8908 (t0) cc_final: 0.8514 (p0) REVERT: E 109 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7299 (mm) REVERT: E 112 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9061 (t) REVERT: E 167 THR cc_start: 0.9237 (m) cc_final: 0.8794 (p) REVERT: E 180 GLU cc_start: 0.9271 (mp0) cc_final: 0.9014 (tm-30) REVERT: E 187 LYS cc_start: 0.8689 (mttt) cc_final: 0.8393 (mtmt) REVERT: E 195 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8050 (tpt-90) REVERT: E 204 HIS cc_start: 0.8279 (m90) cc_final: 0.8045 (m90) REVERT: E 209 MET cc_start: 0.8676 (mtm) cc_final: 0.8292 (mtm) REVERT: E 229 GLU cc_start: 0.8556 (pt0) cc_final: 0.8254 (pm20) REVERT: E 252 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8448 (mm) REVERT: E 259 PRO cc_start: 0.8492 (OUTLIER) cc_final: 0.8257 (Cg_exo) REVERT: E 270 ARG cc_start: 0.8504 (ptt180) cc_final: 0.7892 (mtt180) REVERT: E 302 GLU cc_start: 0.8927 (tp30) cc_final: 0.8688 (tp30) REVERT: E 317 ASP cc_start: 0.7863 (t0) cc_final: 0.6951 (p0) REVERT: F 13 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8057 (p90) REVERT: F 20 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8785 (t) REVERT: F 51 LEU cc_start: 0.8861 (tp) cc_final: 0.8648 (tp) REVERT: F 55 TYR cc_start: 0.8923 (p90) cc_final: 0.8470 (p90) REVERT: F 81 GLU cc_start: 0.8403 (tt0) cc_final: 0.8004 (tp30) REVERT: F 84 ASP cc_start: 0.8998 (m-30) cc_final: 0.8583 (t0) REVERT: F 100 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.8995 (t) REVERT: F 112 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.8818 (m) REVERT: F 136 HIS cc_start: 0.8038 (p90) cc_final: 0.7735 (p90) REVERT: F 137 THR cc_start: 0.9074 (m) cc_final: 0.8765 (p) REVERT: F 143 GLU cc_start: 0.8742 (tt0) cc_final: 0.8020 (tp30) REVERT: F 166 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9117 (p) REVERT: F 168 ASP cc_start: 0.8731 (m-30) cc_final: 0.8488 (m-30) REVERT: F 180 GLU cc_start: 0.8911 (mp0) cc_final: 0.8640 (tp30) REVERT: F 185 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8233 (mm) REVERT: F 209 MET cc_start: 0.8543 (mtm) cc_final: 0.8075 (mtm) REVERT: F 249 PRO cc_start: 0.8988 (Cg_exo) cc_final: 0.8783 (Cg_endo) outliers start: 190 outliers final: 36 residues processed: 627 average time/residue: 0.1304 time to fit residues: 119.2646 Evaluate side-chains 351 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 259 PRO Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 259 PRO Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 PRO Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 259 PRO Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 195 ARG Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 259 PRO Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 259 PRO Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 267 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 136 HIS A 198 ASN B 92 HIS B 132 GLN B 198 ASN B 212 ASN C 92 HIS C 198 ASN C 212 ASN D 92 HIS D 132 GLN D 136 HIS D 198 ASN D 212 ASN E 92 HIS E 132 GLN E 136 HIS E 198 ASN E 212 ASN F 92 HIS F 136 HIS F 198 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098304 restraints weight = 20385.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102059 restraints weight = 10381.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104521 restraints weight = 6042.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106124 restraints weight = 3861.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107215 restraints weight = 2671.938| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15258 Z= 0.216 Angle : 0.879 7.935 20736 Z= 0.433 Chirality : 0.050 0.181 2436 Planarity : 0.007 0.067 2676 Dihedral : 11.615 96.411 2283 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.97 % Allowed : 19.47 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.17), residues: 1938 helix: -1.42 (0.15), residues: 906 sheet: -0.79 (0.24), residues: 330 loop : -1.90 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 118 TYR 0.020 0.002 TYR A 191 PHE 0.015 0.002 PHE B 272 HIS 0.011 0.002 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00473 (15258) covalent geometry : angle 0.87866 (20736) hydrogen bonds : bond 0.04707 ( 762) hydrogen bonds : angle 5.22968 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 391 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6264 (mm-30) REVERT: A 136 HIS cc_start: 0.7852 (p-80) cc_final: 0.5963 (p-80) REVERT: A 146 MET cc_start: 0.6766 (ptt) cc_final: 0.6449 (ptt) REVERT: A 194 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6925 (mp0) REVERT: A 276 TYR cc_start: 0.7539 (m-80) cc_final: 0.7163 (m-80) REVERT: A 303 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8742 (mmtt) REVERT: A 329 LEU cc_start: 0.9053 (tp) cc_final: 0.8826 (tp) REVERT: B 41 TYR cc_start: 0.8709 (m-80) cc_final: 0.8456 (m-10) REVERT: B 48 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9034 (mt) REVERT: B 220 GLN cc_start: 0.8270 (tt0) cc_final: 0.7900 (mm-40) REVERT: B 329 LEU cc_start: 0.9115 (tp) cc_final: 0.8839 (tt) REVERT: C 64 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7345 (mtm) REVERT: C 94 LEU cc_start: 0.9139 (mt) cc_final: 0.8901 (mt) REVERT: C 112 VAL cc_start: 0.9319 (t) cc_final: 0.8996 (p) REVERT: C 193 ASP cc_start: 0.7653 (m-30) cc_final: 0.7369 (m-30) REVERT: C 211 VAL cc_start: 0.8887 (m) cc_final: 0.8304 (t) REVERT: C 220 GLN cc_start: 0.8376 (tt0) cc_final: 0.7777 (mt0) REVERT: C 240 LYS cc_start: 0.8548 (mttt) cc_final: 0.8121 (tptt) REVERT: D 51 LEU cc_start: 0.8937 (tp) cc_final: 0.8712 (tp) REVERT: D 64 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7308 (mtt) REVERT: D 72 TYR cc_start: 0.8642 (m-80) cc_final: 0.8269 (m-80) REVERT: D 94 LEU cc_start: 0.9097 (mt) cc_final: 0.8833 (mt) REVERT: D 149 TYR cc_start: 0.8621 (t80) cc_final: 0.8197 (t80) REVERT: D 186 THR cc_start: 0.8619 (p) cc_final: 0.8379 (p) REVERT: D 193 ASP cc_start: 0.7562 (m-30) cc_final: 0.7239 (m-30) REVERT: D 220 GLN cc_start: 0.8333 (tt0) cc_final: 0.7716 (mt0) REVERT: D 240 LYS cc_start: 0.8598 (mttt) cc_final: 0.8177 (tptt) REVERT: D 275 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7059 (mp0) REVERT: E 41 TYR cc_start: 0.8640 (m-80) cc_final: 0.8415 (m-10) REVERT: E 48 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8814 (mt) REVERT: E 252 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8562 (mm) REVERT: E 275 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: F 100 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8496 (t) REVERT: F 110 CYS cc_start: 0.7370 (m) cc_final: 0.7048 (m) REVERT: F 112 VAL cc_start: 0.9340 (t) cc_final: 0.9076 (m) REVERT: F 194 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6853 (mp0) REVERT: F 212 ASN cc_start: 0.8440 (m-40) cc_final: 0.8011 (t0) REVERT: F 276 TYR cc_start: 0.7580 (m-80) cc_final: 0.7206 (m-80) REVERT: F 292 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8037 (mpp80) REVERT: F 329 LEU cc_start: 0.9071 (tp) cc_final: 0.8869 (tp) outliers start: 112 outliers final: 40 residues processed: 467 average time/residue: 0.1165 time to fit residues: 82.3721 Evaluate side-chains 340 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 77 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 182 GLN B 132 GLN B 282 GLN E 132 GLN E 136 HIS E 212 ASN E 282 GLN F 132 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098865 restraints weight = 20581.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102702 restraints weight = 10560.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105173 restraints weight = 6148.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106809 restraints weight = 3944.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107829 restraints weight = 2728.184| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15258 Z= 0.176 Angle : 0.774 8.054 20736 Z= 0.374 Chirality : 0.049 0.180 2436 Planarity : 0.006 0.054 2676 Dihedral : 8.803 87.976 2189 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.35 % Allowed : 22.70 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.18), residues: 1938 helix: -0.53 (0.16), residues: 912 sheet: -0.36 (0.24), residues: 306 loop : -1.20 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 118 TYR 0.015 0.001 TYR A 191 PHE 0.011 0.001 PHE D 235 HIS 0.011 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00405 (15258) covalent geometry : angle 0.77437 (20736) hydrogen bonds : bond 0.03891 ( 762) hydrogen bonds : angle 4.78413 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 0.824 Fit side-chains REVERT: A 136 HIS cc_start: 0.8036 (p-80) cc_final: 0.7057 (p-80) REVERT: A 185 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8202 (mm) REVERT: A 194 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6844 (mp0) REVERT: A 270 ARG cc_start: 0.7512 (ptp90) cc_final: 0.7248 (ptp90) REVERT: A 276 TYR cc_start: 0.7481 (m-80) cc_final: 0.7135 (m-80) REVERT: B 48 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8851 (mt) REVERT: B 194 GLU cc_start: 0.7524 (tt0) cc_final: 0.6908 (mt-10) REVERT: B 202 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7407 (mt-10) REVERT: B 220 GLN cc_start: 0.8258 (tt0) cc_final: 0.7917 (mm-40) REVERT: C 64 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7270 (mtm) REVERT: C 112 VAL cc_start: 0.9305 (t) cc_final: 0.9099 (p) REVERT: C 208 GLN cc_start: 0.8223 (mt0) cc_final: 0.7704 (pp30) REVERT: C 211 VAL cc_start: 0.8841 (m) cc_final: 0.8297 (t) REVERT: C 220 GLN cc_start: 0.8359 (tt0) cc_final: 0.7762 (mt0) REVERT: C 240 LYS cc_start: 0.8574 (mttt) cc_final: 0.8096 (tptt) REVERT: C 252 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8518 (mm) REVERT: C 276 TYR cc_start: 0.7441 (m-80) cc_final: 0.7164 (m-80) REVERT: D 64 MET cc_start: 0.7547 (mtt) cc_final: 0.7330 (mtm) REVERT: D 86 ASP cc_start: 0.8189 (m-30) cc_final: 0.7890 (m-30) REVERT: D 149 TYR cc_start: 0.8530 (t80) cc_final: 0.8271 (t80) REVERT: D 208 GLN cc_start: 0.8058 (mt0) cc_final: 0.7629 (pp30) REVERT: D 211 VAL cc_start: 0.8547 (m) cc_final: 0.7968 (t) REVERT: D 220 GLN cc_start: 0.8324 (tt0) cc_final: 0.7697 (mt0) REVERT: D 252 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8505 (mm) REVERT: E 48 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8922 (mt) REVERT: E 252 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8571 (mm) REVERT: F 112 VAL cc_start: 0.9305 (t) cc_final: 0.9068 (m) REVERT: F 136 HIS cc_start: 0.8196 (p-80) cc_final: 0.7315 (p-80) REVERT: F 185 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8085 (mm) REVERT: F 194 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6819 (mp0) REVERT: F 212 ASN cc_start: 0.8465 (m-40) cc_final: 0.8097 (m-40) REVERT: F 224 VAL cc_start: 0.7974 (m) cc_final: 0.7764 (m) REVERT: F 276 TYR cc_start: 0.7528 (m-80) cc_final: 0.7200 (m-80) REVERT: F 292 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7725 (mtt180) outliers start: 70 outliers final: 35 residues processed: 380 average time/residue: 0.1116 time to fit residues: 65.4742 Evaluate side-chains 324 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 280 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 152 optimal weight: 0.1980 chunk 64 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 48 optimal weight: 0.0020 chunk 175 optimal weight: 1.9990 overall best weight: 1.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN B 208 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 208 GLN F 132 GLN F 182 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095870 restraints weight = 20914.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099527 restraints weight = 10943.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101961 restraints weight = 6529.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103568 restraints weight = 4257.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104681 restraints weight = 3005.029| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15258 Z= 0.242 Angle : 0.758 6.735 20736 Z= 0.369 Chirality : 0.049 0.169 2436 Planarity : 0.006 0.053 2676 Dihedral : 8.121 84.708 2183 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.79 % Allowed : 23.63 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 1938 helix: -0.42 (0.16), residues: 900 sheet: -0.24 (0.26), residues: 306 loop : -1.11 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 118 TYR 0.011 0.001 TYR D 55 PHE 0.012 0.002 PHE A 307 HIS 0.011 0.002 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00560 (15258) covalent geometry : angle 0.75801 (20736) hydrogen bonds : bond 0.03827 ( 762) hydrogen bonds : angle 4.70734 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 194 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7041 (mp0) REVERT: A 276 TYR cc_start: 0.7444 (m-80) cc_final: 0.7203 (m-80) REVERT: B 194 GLU cc_start: 0.7527 (tt0) cc_final: 0.7001 (mt-10) REVERT: B 202 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7279 (mt-10) REVERT: B 220 GLN cc_start: 0.8166 (tt0) cc_final: 0.7807 (mm-40) REVERT: B 261 ILE cc_start: 0.9025 (mt) cc_final: 0.8744 (tt) REVERT: C 64 MET cc_start: 0.7606 (mtt) cc_final: 0.7373 (mtm) REVERT: C 112 VAL cc_start: 0.9302 (t) cc_final: 0.9087 (p) REVERT: C 149 TYR cc_start: 0.8363 (t80) cc_final: 0.7986 (t80) REVERT: C 208 GLN cc_start: 0.8131 (mt0) cc_final: 0.7678 (pp30) REVERT: C 220 GLN cc_start: 0.8287 (tt0) cc_final: 0.7787 (mt0) REVERT: C 240 LYS cc_start: 0.8744 (mttt) cc_final: 0.8269 (mmtt) REVERT: C 252 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8610 (mm) REVERT: C 276 TYR cc_start: 0.7486 (m-80) cc_final: 0.7149 (m-80) REVERT: D 64 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7423 (mtm) REVERT: D 149 TYR cc_start: 0.8584 (t80) cc_final: 0.8361 (t80) REVERT: D 208 GLN cc_start: 0.8093 (mt0) cc_final: 0.7616 (pp30) REVERT: D 220 GLN cc_start: 0.8291 (tt0) cc_final: 0.7781 (mt0) REVERT: D 252 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8574 (mm) REVERT: D 276 TYR cc_start: 0.7450 (m-80) cc_final: 0.7170 (m-80) REVERT: E 168 ASP cc_start: 0.7607 (m-30) cc_final: 0.7334 (m-30) REVERT: E 252 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8621 (mm) REVERT: E 261 ILE cc_start: 0.9016 (mt) cc_final: 0.8771 (tt) REVERT: F 64 MET cc_start: 0.7420 (mtt) cc_final: 0.7137 (mtm) REVERT: F 194 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6900 (mp0) REVERT: F 276 TYR cc_start: 0.7419 (m-80) cc_final: 0.7144 (m-80) REVERT: F 292 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7712 (mtt180) outliers start: 77 outliers final: 47 residues processed: 335 average time/residue: 0.1038 time to fit residues: 55.2473 Evaluate side-chains 318 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 64 MET Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 108 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 208 GLN F 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100677 restraints weight = 20396.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104458 restraints weight = 10441.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.106922 restraints weight = 6078.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108556 restraints weight = 3871.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109615 restraints weight = 2665.026| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15258 Z= 0.137 Angle : 0.690 7.628 20736 Z= 0.330 Chirality : 0.046 0.146 2436 Planarity : 0.005 0.052 2676 Dihedral : 7.619 76.349 2183 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.04 % Allowed : 23.94 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 1938 helix: 0.09 (0.17), residues: 876 sheet: -0.05 (0.26), residues: 348 loop : -0.83 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 270 TYR 0.011 0.001 TYR F 41 PHE 0.014 0.001 PHE B 320 HIS 0.010 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00326 (15258) covalent geometry : angle 0.69049 (20736) hydrogen bonds : bond 0.03324 ( 762) hydrogen bonds : angle 4.49124 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 313 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASP cc_start: 0.6247 (m-30) cc_final: 0.6032 (m-30) REVERT: A 146 MET cc_start: 0.6652 (ptt) cc_final: 0.6435 (ptt) REVERT: A 185 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7933 (mm) REVERT: A 194 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7011 (mp0) REVERT: A 276 TYR cc_start: 0.7338 (m-80) cc_final: 0.7127 (m-80) REVERT: B 48 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8863 (mt) REVERT: B 194 GLU cc_start: 0.7438 (tt0) cc_final: 0.6940 (mt-10) REVERT: B 202 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7371 (mt-10) REVERT: B 220 GLN cc_start: 0.8165 (tt0) cc_final: 0.7843 (mm-40) REVERT: B 261 ILE cc_start: 0.8958 (mt) cc_final: 0.8748 (tt) REVERT: B 263 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 72 TYR cc_start: 0.8662 (m-80) cc_final: 0.8404 (m-80) REVERT: C 118 ARG cc_start: 0.7806 (tpp80) cc_final: 0.7286 (mtm-85) REVERT: C 149 TYR cc_start: 0.8382 (t80) cc_final: 0.7985 (t80) REVERT: C 193 ASP cc_start: 0.7522 (m-30) cc_final: 0.7303 (m-30) REVERT: C 194 GLU cc_start: 0.7400 (tt0) cc_final: 0.7013 (mt-10) REVERT: C 220 GLN cc_start: 0.8184 (tt0) cc_final: 0.7692 (mt0) REVERT: C 240 LYS cc_start: 0.8802 (mttt) cc_final: 0.8359 (mmtt) REVERT: C 276 TYR cc_start: 0.7350 (m-80) cc_final: 0.6930 (m-80) REVERT: D 74 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8505 (mt) REVERT: D 118 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7169 (mtm-85) REVERT: D 208 GLN cc_start: 0.7940 (mt0) cc_final: 0.7708 (pp30) REVERT: D 220 GLN cc_start: 0.8157 (tt0) cc_final: 0.7690 (mt0) REVERT: D 276 TYR cc_start: 0.7357 (m-80) cc_final: 0.6981 (m-80) REVERT: E 48 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8898 (mt) REVERT: F 59 ASP cc_start: 0.6321 (m-30) cc_final: 0.6038 (m-30) REVERT: F 64 MET cc_start: 0.7369 (mtt) cc_final: 0.6993 (mtm) REVERT: F 185 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8001 (mm) REVERT: F 194 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6975 (mp0) REVERT: F 292 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7711 (mtt180) outliers start: 65 outliers final: 42 residues processed: 353 average time/residue: 0.1056 time to fit residues: 58.5461 Evaluate side-chains 314 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 61 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 208 GLN C 123 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 208 GLN F 182 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099555 restraints weight = 20590.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103107 restraints weight = 10996.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105480 restraints weight = 6602.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107073 restraints weight = 4308.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108187 restraints weight = 3023.525| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15258 Z= 0.167 Angle : 0.692 7.958 20736 Z= 0.332 Chirality : 0.046 0.150 2436 Planarity : 0.005 0.071 2676 Dihedral : 7.439 76.440 2177 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.10 % Allowed : 24.81 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 1938 helix: 0.22 (0.17), residues: 864 sheet: 0.04 (0.27), residues: 348 loop : -0.71 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 118 TYR 0.011 0.001 TYR E 67 PHE 0.009 0.001 PHE B 320 HIS 0.010 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00396 (15258) covalent geometry : angle 0.69219 (20736) hydrogen bonds : bond 0.03276 ( 762) hydrogen bonds : angle 4.45761 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 146 MET cc_start: 0.6759 (ptt) cc_final: 0.6546 (ptt) REVERT: A 185 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7924 (mm) REVERT: A 194 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7017 (mp0) REVERT: B 194 GLU cc_start: 0.7508 (tt0) cc_final: 0.6976 (mt-10) REVERT: B 220 GLN cc_start: 0.8151 (tt0) cc_final: 0.7873 (mm-40) REVERT: B 261 ILE cc_start: 0.8967 (mt) cc_final: 0.8745 (tt) REVERT: B 263 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7489 (tm-30) REVERT: C 118 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7222 (mtm-85) REVERT: C 149 TYR cc_start: 0.8391 (t80) cc_final: 0.7980 (t80) REVERT: C 194 GLU cc_start: 0.7444 (tt0) cc_final: 0.7022 (mt-10) REVERT: C 220 GLN cc_start: 0.8196 (tt0) cc_final: 0.7677 (mt0) REVERT: C 276 TYR cc_start: 0.7506 (m-80) cc_final: 0.7047 (m-80) REVERT: D 118 ARG cc_start: 0.7841 (tpp80) cc_final: 0.7159 (mtm-85) REVERT: D 208 GLN cc_start: 0.8072 (mt0) cc_final: 0.7726 (pp30) REVERT: D 220 GLN cc_start: 0.8117 (tt0) cc_final: 0.7584 (mt0) REVERT: D 224 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8384 (m) REVERT: D 276 TYR cc_start: 0.7415 (m-80) cc_final: 0.7098 (m-80) REVERT: E 48 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8732 (mt) REVERT: F 59 ASP cc_start: 0.6277 (m-30) cc_final: 0.5986 (m-30) REVERT: F 64 MET cc_start: 0.7340 (mtt) cc_final: 0.7046 (mtm) REVERT: F 185 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8010 (mm) REVERT: F 194 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6982 (mp0) REVERT: F 292 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7703 (mtt180) outliers start: 66 outliers final: 46 residues processed: 324 average time/residue: 0.1082 time to fit residues: 54.4816 Evaluate side-chains 316 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 136 HIS Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 0.0970 chunk 187 optimal weight: 0.8980 chunk 134 optimal weight: 0.3980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN E 212 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103116 restraints weight = 20031.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106832 restraints weight = 10402.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109323 restraints weight = 6141.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110913 restraints weight = 3951.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112132 restraints weight = 2765.954| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15258 Z= 0.129 Angle : 0.664 7.609 20736 Z= 0.316 Chirality : 0.045 0.140 2436 Planarity : 0.005 0.051 2676 Dihedral : 7.196 72.033 2175 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.98 % Allowed : 25.81 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 1938 helix: 0.42 (0.18), residues: 870 sheet: 0.22 (0.27), residues: 348 loop : -0.53 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 270 TYR 0.011 0.001 TYR B 67 PHE 0.009 0.001 PHE C 145 HIS 0.010 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00308 (15258) covalent geometry : angle 0.66363 (20736) hydrogen bonds : bond 0.03044 ( 762) hydrogen bonds : angle 4.40107 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 297 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 146 MET cc_start: 0.6655 (ptt) cc_final: 0.6419 (ptt) REVERT: A 185 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7828 (mm) REVERT: A 194 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6991 (mp0) REVERT: B 194 GLU cc_start: 0.7386 (tt0) cc_final: 0.6832 (mt-10) REVERT: B 220 GLN cc_start: 0.8176 (tt0) cc_final: 0.7856 (mm-40) REVERT: B 263 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 118 ARG cc_start: 0.7820 (tpp80) cc_final: 0.7245 (mtm-85) REVERT: C 149 TYR cc_start: 0.8390 (t80) cc_final: 0.7960 (t80) REVERT: C 220 GLN cc_start: 0.8126 (tt0) cc_final: 0.7626 (mt0) REVERT: C 276 TYR cc_start: 0.7424 (m-80) cc_final: 0.6982 (m-80) REVERT: D 118 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7104 (mtm-85) REVERT: D 193 ASP cc_start: 0.7471 (m-30) cc_final: 0.7257 (m-30) REVERT: D 208 GLN cc_start: 0.8065 (mt0) cc_final: 0.7798 (pp30) REVERT: D 220 GLN cc_start: 0.8003 (tt0) cc_final: 0.7490 (mt0) REVERT: D 224 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8342 (m) REVERT: D 276 TYR cc_start: 0.7437 (m-80) cc_final: 0.7031 (m-80) REVERT: E 48 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8691 (mt) REVERT: E 75 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7556 (tp-100) REVERT: F 59 ASP cc_start: 0.6354 (m-30) cc_final: 0.6064 (m-30) REVERT: F 64 MET cc_start: 0.7326 (mtt) cc_final: 0.6996 (mtm) REVERT: F 185 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7961 (mm) REVERT: F 194 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6973 (mp0) REVERT: F 292 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7569 (mtt180) outliers start: 64 outliers final: 47 residues processed: 340 average time/residue: 0.1133 time to fit residues: 59.8396 Evaluate side-chains 326 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 274 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101683 restraints weight = 20449.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105395 restraints weight = 10637.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107852 restraints weight = 6260.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109486 restraints weight = 4019.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110585 restraints weight = 2780.944| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15258 Z= 0.151 Angle : 0.678 7.324 20736 Z= 0.324 Chirality : 0.045 0.144 2436 Planarity : 0.005 0.066 2676 Dihedral : 7.090 70.943 2175 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.73 % Allowed : 26.74 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1938 helix: 0.49 (0.18), residues: 858 sheet: 0.23 (0.28), residues: 348 loop : -0.35 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 270 TYR 0.017 0.001 TYR D 149 PHE 0.019 0.001 PHE F 223 HIS 0.008 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00358 (15258) covalent geometry : angle 0.67835 (20736) hydrogen bonds : bond 0.03093 ( 762) hydrogen bonds : angle 4.38508 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 286 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.6660 (ptt) cc_final: 0.6413 (ptt) REVERT: A 185 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 194 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7025 (mp0) REVERT: B 194 GLU cc_start: 0.7402 (tt0) cc_final: 0.6900 (mt-10) REVERT: B 220 GLN cc_start: 0.8137 (tt0) cc_final: 0.7843 (mm-40) REVERT: B 263 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7433 (tm-30) REVERT: C 118 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7219 (mtm-85) REVERT: C 220 GLN cc_start: 0.8038 (tt0) cc_final: 0.7531 (mt0) REVERT: C 276 TYR cc_start: 0.7447 (m-80) cc_final: 0.6982 (m-80) REVERT: D 118 ARG cc_start: 0.7743 (tpp80) cc_final: 0.7093 (mtm-85) REVERT: D 149 TYR cc_start: 0.8471 (t80) cc_final: 0.8186 (t80) REVERT: D 208 GLN cc_start: 0.8007 (mt0) cc_final: 0.7791 (pp30) REVERT: D 220 GLN cc_start: 0.8022 (tt0) cc_final: 0.7559 (mt0) REVERT: D 224 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8330 (m) REVERT: D 276 TYR cc_start: 0.7454 (m-80) cc_final: 0.7062 (m-80) REVERT: E 75 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7698 (tp-100) REVERT: E 282 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: F 59 ASP cc_start: 0.6244 (m-30) cc_final: 0.5990 (m-30) REVERT: F 64 MET cc_start: 0.7400 (mtt) cc_final: 0.7103 (mtm) REVERT: F 102 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7353 (tm-30) REVERT: F 185 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.7997 (mm) REVERT: F 194 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7015 (mp0) REVERT: F 292 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7591 (mtt180) outliers start: 60 outliers final: 49 residues processed: 322 average time/residue: 0.1108 time to fit residues: 55.1787 Evaluate side-chains 327 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 276 TYR Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 0.1980 chunk 181 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101463 restraints weight = 20412.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.105163 restraints weight = 10621.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107567 restraints weight = 6255.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109206 restraints weight = 4028.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110237 restraints weight = 2787.892| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15258 Z= 0.156 Angle : 0.682 8.238 20736 Z= 0.328 Chirality : 0.045 0.145 2436 Planarity : 0.005 0.050 2676 Dihedral : 6.978 69.383 2175 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.67 % Allowed : 26.99 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 1938 helix: 0.46 (0.18), residues: 864 sheet: 0.14 (0.27), residues: 360 loop : -0.48 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 270 TYR 0.015 0.001 TYR C 72 PHE 0.018 0.001 PHE F 223 HIS 0.008 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00372 (15258) covalent geometry : angle 0.68236 (20736) hydrogen bonds : bond 0.03079 ( 762) hydrogen bonds : angle 4.39665 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 292 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 146 MET cc_start: 0.6680 (ptt) cc_final: 0.6441 (ptt) REVERT: A 194 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6998 (mp0) REVERT: B 194 GLU cc_start: 0.7411 (tt0) cc_final: 0.6903 (mt-10) REVERT: B 220 GLN cc_start: 0.8165 (tt0) cc_final: 0.7932 (mm-40) REVERT: B 263 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7463 (tm-30) REVERT: C 118 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7215 (mtm-85) REVERT: C 157 THR cc_start: 0.8421 (m) cc_final: 0.8175 (p) REVERT: C 220 GLN cc_start: 0.8008 (tt0) cc_final: 0.7513 (mt0) REVERT: C 276 TYR cc_start: 0.7466 (m-80) cc_final: 0.7008 (m-80) REVERT: D 118 ARG cc_start: 0.7777 (tpp80) cc_final: 0.7148 (mtm-85) REVERT: D 149 TYR cc_start: 0.8471 (t80) cc_final: 0.7928 (t80) REVERT: D 194 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6824 (mp0) REVERT: D 208 GLN cc_start: 0.8069 (mt0) cc_final: 0.7784 (pp30) REVERT: D 220 GLN cc_start: 0.8036 (tt0) cc_final: 0.7577 (mt0) REVERT: D 224 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8344 (m) REVERT: D 276 TYR cc_start: 0.7441 (m-80) cc_final: 0.7012 (m-80) REVERT: E 26 MET cc_start: 0.7665 (ptp) cc_final: 0.7407 (mtm) REVERT: F 59 ASP cc_start: 0.5967 (m-30) cc_final: 0.5744 (m-30) REVERT: F 64 MET cc_start: 0.7331 (mtt) cc_final: 0.7046 (mtm) REVERT: F 102 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7347 (tm-30) REVERT: F 118 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.8075 (mmm-85) REVERT: F 185 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.7995 (mm) REVERT: F 194 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7024 (mp0) REVERT: F 292 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7602 (mtt180) outliers start: 59 outliers final: 48 residues processed: 328 average time/residue: 0.1128 time to fit residues: 56.9959 Evaluate side-chains 332 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 281 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 276 TYR Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 114 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 102 optimal weight: 0.0370 chunk 119 optimal weight: 1.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 208 GLN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102787 restraints weight = 20266.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106493 restraints weight = 10487.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108916 restraints weight = 6173.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110558 restraints weight = 3960.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111567 restraints weight = 2719.859| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15258 Z= 0.139 Angle : 0.685 8.661 20736 Z= 0.329 Chirality : 0.045 0.141 2436 Planarity : 0.005 0.047 2676 Dihedral : 6.788 66.142 2175 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.54 % Allowed : 27.67 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.19), residues: 1938 helix: 0.55 (0.18), residues: 852 sheet: 0.20 (0.28), residues: 360 loop : -0.50 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 270 TYR 0.015 0.001 TYR C 72 PHE 0.018 0.001 PHE F 223 HIS 0.008 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00335 (15258) covalent geometry : angle 0.68517 (20736) hydrogen bonds : bond 0.02987 ( 762) hydrogen bonds : angle 4.36534 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 298 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8534 (p90) cc_final: 0.7821 (p90) REVERT: A 146 MET cc_start: 0.6609 (ptt) cc_final: 0.6378 (ptt) REVERT: A 194 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6988 (mp0) REVERT: B 26 MET cc_start: 0.7260 (ptp) cc_final: 0.7028 (mtm) REVERT: B 194 GLU cc_start: 0.7382 (tt0) cc_final: 0.6884 (mt-10) REVERT: B 263 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7477 (tm-30) REVERT: C 118 ARG cc_start: 0.7699 (tpp80) cc_final: 0.7158 (mtm-85) REVERT: C 220 GLN cc_start: 0.8032 (tt0) cc_final: 0.7542 (mt0) REVERT: C 276 TYR cc_start: 0.7435 (m-80) cc_final: 0.6972 (m-80) REVERT: D 118 ARG cc_start: 0.7711 (tpp80) cc_final: 0.7090 (mtm-85) REVERT: D 149 TYR cc_start: 0.8446 (t80) cc_final: 0.7872 (t80) REVERT: D 157 THR cc_start: 0.8409 (m) cc_final: 0.8137 (p) REVERT: D 208 GLN cc_start: 0.8041 (mt0) cc_final: 0.7778 (pp30) REVERT: D 220 GLN cc_start: 0.8031 (tt0) cc_final: 0.7572 (mt0) REVERT: D 276 TYR cc_start: 0.7413 (m-80) cc_final: 0.6998 (m-80) REVERT: E 26 MET cc_start: 0.7632 (ptp) cc_final: 0.7387 (mtm) REVERT: F 55 TYR cc_start: 0.8514 (p90) cc_final: 0.7829 (p90) REVERT: F 64 MET cc_start: 0.7332 (mtt) cc_final: 0.6999 (mtm) REVERT: F 102 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 118 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.8028 (mmm-85) REVERT: F 185 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7959 (mm) REVERT: F 194 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7008 (mp0) REVERT: F 292 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7353 (mtt180) outliers start: 57 outliers final: 45 residues processed: 335 average time/residue: 0.1138 time to fit residues: 58.9373 Evaluate side-chains 325 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 136 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 136 HIS Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 13 PHE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 136 HIS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 136 HIS Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 276 TYR Chi-restraints excluded: chain F residue 292 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 166 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 134 optimal weight: 0.0040 chunk 160 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN F 156 ASN ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102327 restraints weight = 20281.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105986 restraints weight = 10643.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108326 restraints weight = 6291.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109864 restraints weight = 4068.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111008 restraints weight = 2854.110| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15258 Z= 0.152 Angle : 0.689 8.966 20736 Z= 0.331 Chirality : 0.045 0.151 2436 Planarity : 0.005 0.048 2676 Dihedral : 6.713 64.037 2175 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.17 % Allowed : 27.99 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1938 helix: 0.57 (0.18), residues: 858 sheet: 0.13 (0.28), residues: 360 loop : -0.43 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 270 TYR 0.015 0.001 TYR C 72 PHE 0.018 0.001 PHE F 223 HIS 0.008 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00366 (15258) covalent geometry : angle 0.68909 (20736) hydrogen bonds : bond 0.03003 ( 762) hydrogen bonds : angle 4.37013 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2334.79 seconds wall clock time: 41 minutes 24.24 seconds (2484.24 seconds total)