Starting phenix.real_space_refine on Fri Jul 3 08:58:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp6_36469/07_2026/8jp6_36469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp6_36469/07_2026/8jp6_36469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jp6_36469/07_2026/8jp6_36469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp6_36469/07_2026/8jp6_36469.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp6_36469/07_2026/8jp6_36469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp6_36469/07_2026/8jp6_36469.cif" } resolution = 3.29 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= 0.012 sd= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 Zn 4 6.06 5 S 36 5.16 5 C 8466 2.51 5 N 2346 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13500 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "B" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "E" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2619 Classifications: {'peptide': 326} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 309} Chain: "F" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2517 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 1 Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 2.90, per 1000 atoms: 0.21 Number of scatterers: 13500 At special positions: 0 Unit cell: (120.516, 118.524, 127.488, 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) Zn 4 29.99 Ca 16 19.99 S 36 16.00 O 2632 8.00 N 2346 7.00 C 8466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 506.8 milliseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 33.5% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.696A pdb=" N ASP A 181 " --> pdb=" O HIS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.681A pdb=" N LYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.509A pdb=" N ILE A 322 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.628A pdb=" N ASP B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 311 removed outlier: 3.765A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 365 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.886A pdb=" N ILE C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 80 removed outlier: 3.582A pdb=" N HIS C 80 " --> pdb=" O TYR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 Processing helix chain 'C' and resid 113 through 129 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 48 through 57 removed outlier: 4.129A pdb=" N ILE D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET D 53 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 113 through 129 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.711A pdb=" N ASP E 181 " --> pdb=" O HIS E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 309 removed outlier: 3.682A pdb=" N LYS E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU E 306 " --> pdb=" O LYS E 302 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE E 307 " --> pdb=" O LYS E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.510A pdb=" N ILE E 322 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 338 through 367 Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.624A pdb=" N ASP F 181 " --> pdb=" O HIS F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 311 removed outlier: 3.765A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 365 Processing helix chain 'G' and resid 42 through 47 Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.885A pdb=" N ILE G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 80 removed outlier: 3.587A pdb=" N HIS G 80 " --> pdb=" O TYR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 98 Processing helix chain 'G' and resid 113 through 129 Processing helix chain 'G' and resid 137 through 142 Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'H' and resid 48 through 57 removed outlier: 3.670A pdb=" N ILE H 52 " --> pdb=" O ASP H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 113 through 129 Processing helix chain 'H' and resid 137 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 53 removed outlier: 3.845A pdb=" N HIS A 43 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS A 257 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 53 removed outlier: 3.845A pdb=" N HIS A 43 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR A 264 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS A 49 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N PHE A 262 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 10.920A pdb=" N SER A 51 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 11.705A pdb=" N LEU A 260 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N LYS A 53 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N ASP A 258 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS A 257 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N THR A 113 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL A 259 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG A 111 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE A 216 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE A 229 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 71 removed outlier: 5.652A pdb=" N PHE A 244 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.622A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.891A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.388A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS B 257 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 43 through 53 removed outlier: 4.622A pdb=" N THR B 264 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N LYS B 49 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N PHE B 262 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 10.983A pdb=" N SER B 51 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N LEU B 260 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 11.891A pdb=" N LYS B 53 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 14.388A pdb=" N ASP B 258 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N HIS B 257 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR B 113 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL B 259 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ARG B 111 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE B 216 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE B 229 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 71 removed outlier: 5.747A pdb=" N PHE B 244 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 43 through 46 removed outlier: 3.845A pdb=" N HIS E 43 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N HIS E 257 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 43 through 46 removed outlier: 3.845A pdb=" N HIS E 43 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS E 257 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR E 113 " --> pdb=" O HIS E 257 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL E 259 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG E 111 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE E 216 " --> pdb=" O PHE E 229 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE E 229 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.653A pdb=" N PHE E 244 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.612A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.384A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS F 257 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 43 through 53 removed outlier: 4.612A pdb=" N THR F 264 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LYS F 49 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N PHE F 262 " --> pdb=" O LYS F 49 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N SER F 51 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N LEU F 260 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N LYS F 53 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 14.384A pdb=" N ASP F 258 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS F 257 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR F 113 " --> pdb=" O HIS F 257 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL F 259 " --> pdb=" O ARG F 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG F 111 " --> pdb=" O VAL F 259 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE F 216 " --> pdb=" O PHE F 229 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE F 229 " --> pdb=" O ILE F 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 71 removed outlier: 5.747A pdb=" N PHE F 244 " --> pdb=" O THR F 95 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1857 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: 2.03 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4572 1.34 - 1.46: 2472 1.46 - 1.58: 6686 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 13794 Sorted by residual: bond pdb=" CA GLN F 173 " pdb=" CB GLN F 173 " ideal model delta sigma weight residual 1.527 1.570 -0.042 2.48e-02 1.63e+03 2.93e+00 bond pdb=" CA GLN B 173 " pdb=" CB GLN B 173 " ideal model delta sigma weight residual 1.527 1.570 -0.042 2.48e-02 1.63e+03 2.90e+00 bond pdb=" N TYR A 127 " pdb=" CA TYR A 127 " ideal model delta sigma weight residual 1.464 1.444 0.020 1.36e-02 5.41e+03 2.07e+00 bond pdb=" C ASN E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.338 1.362 -0.024 1.90e-02 2.77e+03 1.65e+00 bond pdb=" CB GLN A 290 " pdb=" CG GLN A 290 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 13789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18366 2.09 - 4.18: 230 4.18 - 6.26: 27 6.26 - 8.35: 5 8.35 - 10.44: 2 Bond angle restraints: 18630 Sorted by residual: angle pdb=" CA GLU F 292 " pdb=" CB GLU F 292 " pdb=" CG GLU F 292 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA GLU B 292 " pdb=" CB GLU B 292 " pdb=" CG GLU B 292 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA LEU G 72 " pdb=" CB LEU G 72 " pdb=" CG LEU G 72 " ideal model delta sigma weight residual 116.30 126.74 -10.44 3.50e+00 8.16e-02 8.89e+00 angle pdb=" CA LEU C 72 " pdb=" CB LEU C 72 " pdb=" CG LEU C 72 " ideal model delta sigma weight residual 116.30 126.73 -10.43 3.50e+00 8.16e-02 8.88e+00 angle pdb=" C GLY B 132 " pdb=" N LEU B 133 " pdb=" CA LEU B 133 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.53e+00 ... (remaining 18625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7148 17.79 - 35.59: 815 35.59 - 53.38: 200 53.38 - 71.18: 78 71.18 - 88.97: 7 Dihedral angle restraints: 8248 sinusoidal: 3432 harmonic: 4816 Sorted by residual: dihedral pdb=" CA ASN E 162 " pdb=" C ASN E 162 " pdb=" N PRO E 163 " pdb=" CA PRO E 163 " ideal model delta harmonic sigma weight residual 0.00 23.75 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA TRP B 126 " pdb=" C TRP B 126 " pdb=" N TYR B 127 " pdb=" CA TYR B 127 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TRP F 126 " pdb=" C TRP F 126 " pdb=" N TYR F 127 " pdb=" CA TYR F 127 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1203 0.035 - 0.070: 476 0.070 - 0.104: 158 0.104 - 0.139: 72 0.139 - 0.174: 7 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA VAL G 100 " pdb=" N VAL G 100 " pdb=" C VAL G 100 " pdb=" CB VAL G 100 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CA VAL C 100 " pdb=" N VAL C 100 " pdb=" C VAL C 100 " pdb=" CB VAL C 100 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA VAL F 93 " pdb=" N VAL F 93 " pdb=" C VAL F 93 " pdb=" CB VAL F 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1913 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 162 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ASN E 162 " 0.057 2.00e-02 2.50e+03 pdb=" O ASN E 162 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO E 163 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 135 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO A 136 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 135 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO E 136 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 136 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 136 " 0.024 5.00e-02 4.00e+02 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 76 2.36 - 2.99: 6501 2.99 - 3.63: 20026 3.63 - 4.26: 31129 4.26 - 4.90: 53204 Nonbonded interactions: 110936 Sorted by model distance: nonbonded pdb=" OD1 ASP B 155 " pdb=" OD1 ASN B 162 " model vdw 1.720 3.040 nonbonded pdb=" OD1 ASP F 155 " pdb=" OD1 ASN F 162 " model vdw 1.723 3.040 nonbonded pdb=" CE1 HIS D 51 " pdb="ZN ZN D 703 " model vdw 1.915 2.450 nonbonded pdb=" CE1 HIS H 51 " pdb="ZN ZN H 703 " model vdw 1.950 2.450 nonbonded pdb=" NE2 HIS H 101 " pdb="ZN ZN H 703 " model vdw 2.004 2.310 ... (remaining 110931 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'B' selection = (chain 'E' and (resid 42 through 312 or resid 324 through 365 or resid 601 throu \ gh 602)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 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 : 0.003 0.042 13798 Z= 0.153 Angle : 0.595 10.438 18638 Z= 0.318 Chirality : 0.046 0.174 1916 Planarity : 0.004 0.044 2510 Dihedral : 16.633 88.970 5140 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.14 % Allowed : 14.38 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.12 (0.21), residues: 1650 helix: 1.65 (0.23), residues: 512 sheet: 1.00 (0.31), residues: 324 loop : -1.41 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 360 TYR 0.014 0.001 TYR A 127 PHE 0.015 0.001 PHE F 52 TRP 0.013 0.002 TRP A 104 HIS 0.008 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (13794) covalent geometry : angle 0.59258 / 0.32 (18630) SS BOND : bond 0.00179 / 0.10 ( 4) SS BOND : angle 2.74086 / 1.49 ( 8) hydrogen bonds : bond 0.12109 / 8.71 ( 649) hydrogen bonds : angle 5.41474 / 3.81 ( 1857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 312 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8281 (t0) cc_final: 0.7939 (t0) REVERT: A 226 ASP cc_start: 0.8577 (t70) cc_final: 0.8350 (t70) REVERT: A 354 MET cc_start: 0.8114 (tpp) cc_final: 0.7729 (ttm) REVERT: B 48 TYR cc_start: 0.8787 (p90) cc_final: 0.8575 (p90) REVERT: B 215 MET cc_start: 0.8706 (mtp) cc_final: 0.8317 (mtp) REVERT: B 225 ASN cc_start: 0.7582 (m110) cc_final: 0.7224 (p0) REVERT: B 354 MET cc_start: 0.7829 (ttm) cc_final: 0.7577 (tmm) REVERT: C 73 GLN cc_start: 0.8321 (tt0) cc_final: 0.8010 (pp30) REVERT: D 122 ASP cc_start: 0.8444 (m-30) cc_final: 0.8056 (m-30) REVERT: D 144 SER cc_start: 0.8733 (m) cc_final: 0.8485 (t) REVERT: E 49 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8725 (ttpp) REVERT: E 218 ASN cc_start: 0.8246 (t0) cc_final: 0.7903 (t0) REVERT: E 226 ASP cc_start: 0.8590 (t70) cc_final: 0.8359 (t70) REVERT: E 295 HIS cc_start: 0.8947 (t-90) cc_final: 0.8344 (t-90) REVERT: E 354 MET cc_start: 0.8085 (tpp) cc_final: 0.7700 (ttm) REVERT: F 215 MET cc_start: 0.8647 (mtp) cc_final: 0.8292 (mtp) REVERT: F 225 ASN cc_start: 0.7584 (m110) cc_final: 0.7261 (p0) REVERT: F 354 MET cc_start: 0.7831 (ttm) cc_final: 0.7620 (tmm) REVERT: G 71 GLU cc_start: 0.8631 (tp30) cc_final: 0.8416 (tp30) REVERT: G 73 GLN cc_start: 0.8310 (tt0) cc_final: 0.7965 (pp30) REVERT: H 48 ASP cc_start: 0.7937 (m-30) cc_final: 0.7417 (t0) REVERT: H 122 ASP cc_start: 0.8419 (m-30) cc_final: 0.8133 (m-30) REVERT: H 144 SER cc_start: 0.8782 (m) cc_final: 0.8538 (t) outliers start: 2 outliers final: 2 residues processed: 314 average time/residue: 0.1003 time to fit residues: 46.3840 Evaluate side-chains 219 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain H residue 101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.0570 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN A 162 ASN A 235 ASN A 243 HIS A 311 HIS B 162 ASN B 333 GLN B 339 ASN C 49 GLN C 75 HIS C 86 ASN D 51 HIS D 75 HIS E 79 GLN E 235 ASN E 243 HIS E 351 GLN F 162 ASN F 333 GLN F 339 ASN G 49 GLN G 75 HIS G 86 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.175049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115777 restraints weight = 17441.906| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.38 r_work: 0.3170 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13798 Z= 0.106 Angle : 0.538 9.899 18638 Z= 0.284 Chirality : 0.043 0.149 1916 Planarity : 0.003 0.031 2510 Dihedral : 5.028 59.479 1792 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.66 % Allowed : 15.42 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.35 (0.21), residues: 1650 helix: 2.01 (0.23), residues: 520 sheet: 1.19 (0.31), residues: 320 loop : -1.46 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 350 TYR 0.017 0.001 TYR G 138 PHE 0.022 0.001 PHE F 307 TRP 0.010 0.001 TRP F 126 HIS 0.005 0.001 HIS D 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (13794) covalent geometry : angle 0.53569 / 0.28 (18630) SS BOND : bond 0.00411 / 0.25 ( 4) SS BOND : angle 2.40639 / 1.29 ( 8) hydrogen bonds : bond 0.03229 / 2.21 ( 649) hydrogen bonds : angle 4.38331 / 3.08 ( 1857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8003 (t0) cc_final: 0.7713 (t0) REVERT: A 226 ASP cc_start: 0.8958 (t70) cc_final: 0.8559 (t70) REVERT: A 304 LYS cc_start: 0.9208 (ptpt) cc_final: 0.8920 (tppt) REVERT: A 354 MET cc_start: 0.8055 (tpp) cc_final: 0.7726 (ttm) REVERT: B 48 TYR cc_start: 0.8818 (p90) cc_final: 0.8598 (p90) REVERT: B 173 GLN cc_start: 0.8077 (pm20) cc_final: 0.7839 (pm20) REVERT: B 215 MET cc_start: 0.8726 (mtp) cc_final: 0.8483 (mtp) REVERT: B 223 ASP cc_start: 0.8532 (t0) cc_final: 0.7912 (t0) REVERT: B 225 ASN cc_start: 0.7760 (m110) cc_final: 0.7075 (p0) REVERT: B 226 ASP cc_start: 0.8534 (m-30) cc_final: 0.8008 (m-30) REVERT: B 286 LYS cc_start: 0.9205 (mttt) cc_final: 0.8966 (mmtp) REVERT: B 354 MET cc_start: 0.8354 (ttm) cc_final: 0.8048 (tmm) REVERT: C 73 GLN cc_start: 0.8461 (tt0) cc_final: 0.8030 (pp30) REVERT: C 89 ASP cc_start: 0.8446 (p0) cc_final: 0.8215 (p0) REVERT: C 126 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8150 (ptp90) REVERT: C 132 ASN cc_start: 0.8712 (t0) cc_final: 0.8486 (t0) REVERT: C 138 TYR cc_start: 0.7335 (t80) cc_final: 0.6650 (t80) REVERT: D 49 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7959 (tm-30) REVERT: D 67 MET cc_start: 0.8320 (mpp) cc_final: 0.7743 (mpp) REVERT: D 75 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7750 (t-90) REVERT: D 101 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7752 (t-90) REVERT: D 127 ASP cc_start: 0.8627 (m-30) cc_final: 0.8406 (m-30) REVERT: D 128 ASP cc_start: 0.8115 (m-30) cc_final: 0.7894 (t0) REVERT: D 131 ASN cc_start: 0.7974 (p0) cc_final: 0.6690 (t0) REVERT: E 49 LYS cc_start: 0.9126 (ttpt) cc_final: 0.8924 (ttpp) REVERT: E 218 ASN cc_start: 0.8028 (t0) cc_final: 0.7737 (t0) REVERT: E 226 ASP cc_start: 0.8956 (t70) cc_final: 0.8564 (t70) REVERT: E 354 MET cc_start: 0.8087 (tpp) cc_final: 0.7793 (ttm) REVERT: F 173 GLN cc_start: 0.8096 (pm20) cc_final: 0.7868 (pm20) REVERT: F 215 MET cc_start: 0.8703 (mtp) cc_final: 0.8465 (mtp) REVERT: F 225 ASN cc_start: 0.7761 (m110) cc_final: 0.7150 (p0) REVERT: F 354 MET cc_start: 0.8415 (ttm) cc_final: 0.8093 (tmm) REVERT: G 73 GLN cc_start: 0.8513 (tt0) cc_final: 0.8047 (pp30) REVERT: G 89 ASP cc_start: 0.8472 (p0) cc_final: 0.8233 (p0) REVERT: G 116 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: G 126 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8149 (ptp90) REVERT: G 132 ASN cc_start: 0.8706 (t0) cc_final: 0.8488 (t0) REVERT: G 138 TYR cc_start: 0.7338 (t80) cc_final: 0.6614 (t80) REVERT: H 75 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8239 (t-90) REVERT: H 127 ASP cc_start: 0.8632 (m-30) cc_final: 0.8420 (m-30) REVERT: H 128 ASP cc_start: 0.8139 (m-30) cc_final: 0.7918 (t0) REVERT: H 131 ASN cc_start: 0.7963 (p0) cc_final: 0.6627 (t0) outliers start: 24 outliers final: 10 residues processed: 259 average time/residue: 0.0878 time to fit residues: 34.3416 Evaluate side-chains 227 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS A 297 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS B 43 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS C 86 ASN D 75 HIS D 80 HIS E 69 HIS E 162 ASN E 297 GLN F 43 HIS ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 GLN G 75 HIS G 86 ASN H 75 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.172430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114239 restraints weight = 17583.814| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.67 r_work: 0.3107 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13798 Z= 0.117 Angle : 0.530 7.638 18638 Z= 0.281 Chirality : 0.043 0.139 1916 Planarity : 0.003 0.032 2510 Dihedral : 4.609 53.992 1790 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.07 % Allowed : 17.15 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.34 (0.21), residues: 1650 helix: 1.92 (0.23), residues: 520 sheet: 0.95 (0.31), residues: 326 loop : -1.30 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 350 TYR 0.017 0.001 TYR H 76 PHE 0.012 0.001 PHE B 307 TRP 0.009 0.001 TRP F 126 HIS 0.010 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13794) covalent geometry : angle 0.52729 / 0.28 (18630) SS BOND : bond 0.00199 / 0.12 ( 4) SS BOND : angle 2.58228 / 1.40 ( 8) hydrogen bonds : bond 0.03192 / 2.17 ( 649) hydrogen bonds : angle 4.28859 / 3.01 ( 1857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.7962 (t0) cc_final: 0.7622 (t0) REVERT: A 226 ASP cc_start: 0.8846 (t70) cc_final: 0.8519 (t70) REVERT: A 354 MET cc_start: 0.8031 (tpp) cc_final: 0.7701 (ttm) REVERT: B 215 MET cc_start: 0.8545 (mtp) cc_final: 0.8205 (mtp) REVERT: B 225 ASN cc_start: 0.7686 (m110) cc_final: 0.7277 (p0) REVERT: B 255 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8099 (t0) REVERT: B 354 MET cc_start: 0.8310 (ttm) cc_final: 0.7998 (tmm) REVERT: C 73 GLN cc_start: 0.8386 (tt0) cc_final: 0.7982 (pp30) REVERT: C 132 ASN cc_start: 0.8704 (t0) cc_final: 0.8437 (t0) REVERT: C 138 TYR cc_start: 0.7027 (t80) cc_final: 0.6773 (t80) REVERT: D 53 MET cc_start: 0.8779 (mmm) cc_final: 0.8477 (mmm) REVERT: D 127 ASP cc_start: 0.8544 (m-30) cc_final: 0.8316 (m-30) REVERT: D 128 ASP cc_start: 0.8110 (m-30) cc_final: 0.7841 (t0) REVERT: E 218 ASN cc_start: 0.7987 (t0) cc_final: 0.7663 (t0) REVERT: E 226 ASP cc_start: 0.8861 (t70) cc_final: 0.8526 (t70) REVERT: E 354 MET cc_start: 0.8058 (tpp) cc_final: 0.7733 (ttm) REVERT: F 215 MET cc_start: 0.8517 (mtp) cc_final: 0.8200 (mtp) REVERT: F 255 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8102 (t0) REVERT: F 354 MET cc_start: 0.8371 (ttm) cc_final: 0.8049 (tmm) REVERT: G 48 ASP cc_start: 0.7417 (t0) cc_final: 0.7131 (m-30) REVERT: G 112 MET cc_start: 0.8022 (mtm) cc_final: 0.7713 (mtp) REVERT: G 132 ASN cc_start: 0.8691 (t0) cc_final: 0.8427 (t0) REVERT: H 49 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7428 (tm-30) REVERT: H 53 MET cc_start: 0.9174 (mmm) cc_final: 0.8767 (mmm) REVERT: H 127 ASP cc_start: 0.8547 (m-30) cc_final: 0.8318 (m-30) REVERT: H 128 ASP cc_start: 0.8138 (m-30) cc_final: 0.7857 (t0) outliers start: 30 outliers final: 14 residues processed: 255 average time/residue: 0.0857 time to fit residues: 33.5883 Evaluate side-chains 229 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 71 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 162 optimal weight: 40.0000 chunk 69 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 297 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 290 GLN B 295 HIS C 86 ASN D 75 HIS D 80 HIS E 185 GLN F 173 GLN F 290 GLN F 295 HIS F 349 ASN G 86 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.165826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108346 restraints weight = 17012.307| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.30 r_work: 0.2950 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13798 Z= 0.216 Angle : 0.596 7.796 18638 Z= 0.317 Chirality : 0.046 0.153 1916 Planarity : 0.004 0.040 2510 Dihedral : 4.714 24.792 1788 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.35 % Allowed : 17.91 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.18 (0.21), residues: 1650 helix: 1.96 (0.23), residues: 516 sheet: 0.52 (0.30), residues: 328 loop : -1.35 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.018 0.002 TYR D 76 PHE 0.021 0.002 PHE B 52 TRP 0.009 0.002 TRP F 126 HIS 0.021 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (13794) covalent geometry : angle 0.59220 / 0.32 (18630) SS BOND : bond 0.00191 / 0.11 ( 4) SS BOND : angle 3.16251 / 1.72 ( 8) hydrogen bonds : bond 0.03533 / 2.38 ( 649) hydrogen bonds : angle 4.42198 / 3.10 ( 1857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8280 (t0) cc_final: 0.7932 (t0) REVERT: A 226 ASP cc_start: 0.9126 (t70) cc_final: 0.8811 (t70) REVERT: A 352 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7926 (tt) REVERT: A 354 MET cc_start: 0.8195 (tpp) cc_final: 0.7800 (ttm) REVERT: B 215 MET cc_start: 0.8825 (mtp) cc_final: 0.8501 (mtp) REVERT: B 225 ASN cc_start: 0.7836 (m110) cc_final: 0.7428 (p0) REVERT: B 354 MET cc_start: 0.8384 (ttm) cc_final: 0.8014 (tmm) REVERT: C 67 MET cc_start: 0.7016 (ptp) cc_final: 0.6675 (ptp) REVERT: C 73 GLN cc_start: 0.8526 (tt0) cc_final: 0.8084 (pp30) REVERT: C 132 ASN cc_start: 0.8778 (t0) cc_final: 0.8541 (t0) REVERT: C 138 TYR cc_start: 0.7471 (t80) cc_final: 0.7193 (t80) REVERT: D 53 MET cc_start: 0.8863 (mmm) cc_final: 0.8498 (mmm) REVERT: D 127 ASP cc_start: 0.8552 (m-30) cc_final: 0.8292 (m-30) REVERT: E 185 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: E 218 ASN cc_start: 0.8317 (t0) cc_final: 0.7960 (t0) REVERT: E 226 ASP cc_start: 0.9117 (t70) cc_final: 0.8809 (t70) REVERT: E 352 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7941 (tt) REVERT: E 354 MET cc_start: 0.8252 (tpp) cc_final: 0.7865 (ttm) REVERT: F 215 MET cc_start: 0.8799 (mtp) cc_final: 0.8476 (mtp) REVERT: F 354 MET cc_start: 0.8447 (ttm) cc_final: 0.8072 (tmm) REVERT: G 73 GLN cc_start: 0.8549 (tt0) cc_final: 0.8114 (pp30) REVERT: G 132 ASN cc_start: 0.8781 (t0) cc_final: 0.8540 (t0) REVERT: H 49 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7526 (tm-30) REVERT: H 53 MET cc_start: 0.9140 (mmm) cc_final: 0.8738 (mmm) REVERT: H 127 ASP cc_start: 0.8567 (m-30) cc_final: 0.8292 (m-30) outliers start: 34 outliers final: 15 residues processed: 252 average time/residue: 0.0940 time to fit residues: 35.3323 Evaluate side-chains 225 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 40 optimal weight: 2.9990 chunk 141 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 297 GLN A 298 GLN A 342 HIS B 173 GLN B 290 GLN C 75 HIS D 80 HIS E 185 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 HIS F 290 GLN G 86 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111021 restraints weight = 16977.909| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.30 r_work: 0.3051 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13798 Z= 0.151 Angle : 0.573 8.889 18638 Z= 0.303 Chirality : 0.044 0.144 1916 Planarity : 0.004 0.042 2510 Dihedral : 4.559 24.067 1788 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.90 % Allowed : 19.02 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.18 (0.21), residues: 1650 helix: 1.89 (0.23), residues: 516 sheet: 0.65 (0.31), residues: 324 loop : -1.35 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 350 TYR 0.023 0.002 TYR G 138 PHE 0.014 0.001 PHE B 52 TRP 0.011 0.001 TRP F 126 HIS 0.005 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (13794) covalent geometry : angle 0.57020 / 0.30 (18630) SS BOND : bond 0.00194 / 0.11 ( 4) SS BOND : angle 2.84397 / 1.54 ( 8) hydrogen bonds : bond 0.03270 / 2.18 ( 649) hydrogen bonds : angle 4.28890 / 3.00 ( 1857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8152 (t0) cc_final: 0.7800 (t0) REVERT: A 226 ASP cc_start: 0.9042 (t70) cc_final: 0.8740 (t70) REVERT: A 352 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7890 (tt) REVERT: A 354 MET cc_start: 0.8235 (tpp) cc_final: 0.7831 (ttm) REVERT: B 215 MET cc_start: 0.8784 (mtp) cc_final: 0.8456 (mtp) REVERT: B 226 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: B 354 MET cc_start: 0.8352 (ttm) cc_final: 0.7998 (tmm) REVERT: C 132 ASN cc_start: 0.8738 (t0) cc_final: 0.8484 (t0) REVERT: D 53 MET cc_start: 0.8914 (mmm) cc_final: 0.8541 (mmm) REVERT: D 127 ASP cc_start: 0.8549 (m-30) cc_final: 0.8283 (m-30) REVERT: E 218 ASN cc_start: 0.8262 (t0) cc_final: 0.7910 (t0) REVERT: E 226 ASP cc_start: 0.9038 (t70) cc_final: 0.8745 (t70) REVERT: E 352 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7927 (tt) REVERT: E 354 MET cc_start: 0.8258 (tpp) cc_final: 0.7836 (ttm) REVERT: F 215 MET cc_start: 0.8783 (mtp) cc_final: 0.8452 (mtp) REVERT: F 354 MET cc_start: 0.8406 (ttm) cc_final: 0.8035 (tmm) REVERT: G 73 GLN cc_start: 0.8538 (tt0) cc_final: 0.8128 (pp30) REVERT: G 132 ASN cc_start: 0.8759 (t0) cc_final: 0.8500 (t0) REVERT: H 41 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7232 (mm) REVERT: H 49 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7601 (tm-30) REVERT: H 53 MET cc_start: 0.9160 (mmm) cc_final: 0.8759 (mmm) REVERT: H 75 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.7873 (t70) REVERT: H 127 ASP cc_start: 0.8530 (m-30) cc_final: 0.8254 (m-30) outliers start: 42 outliers final: 19 residues processed: 247 average time/residue: 0.0912 time to fit residues: 33.9873 Evaluate side-chains 222 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 298 GLN B 173 GLN B 290 GLN C 73 GLN C 75 HIS D 75 HIS D 80 HIS E 185 GLN E 298 GLN F 290 GLN G 49 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114611 restraints weight = 17008.409| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.25 r_work: 0.3087 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13798 Z= 0.106 Angle : 0.552 8.508 18638 Z= 0.290 Chirality : 0.043 0.140 1916 Planarity : 0.003 0.034 2510 Dihedral : 4.363 22.732 1788 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.18 % Allowed : 18.40 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.29 (0.21), residues: 1650 helix: 1.89 (0.23), residues: 516 sheet: 0.78 (0.30), residues: 324 loop : -1.25 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 350 TYR 0.024 0.001 TYR G 138 PHE 0.011 0.001 PHE A 293 TRP 0.013 0.001 TRP F 126 HIS 0.013 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (13794) covalent geometry : angle 0.54929 / 0.29 (18630) SS BOND : bond 0.00224 / 0.13 ( 4) SS BOND : angle 2.53386 / 1.37 ( 8) hydrogen bonds : bond 0.03010 / 2.01 ( 649) hydrogen bonds : angle 4.17347 / 2.92 ( 1857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8123 (t0) cc_final: 0.7790 (t0) REVERT: A 226 ASP cc_start: 0.8994 (t70) cc_final: 0.8676 (t70) REVERT: A 354 MET cc_start: 0.8308 (tpp) cc_final: 0.7788 (ttm) REVERT: B 215 MET cc_start: 0.8761 (mtp) cc_final: 0.8444 (mtp) REVERT: B 226 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: B 255 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8170 (t0) REVERT: B 354 MET cc_start: 0.8320 (ttm) cc_final: 0.7992 (tmm) REVERT: C 73 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8252 (pp30) REVERT: C 132 ASN cc_start: 0.8697 (t0) cc_final: 0.8416 (t0) REVERT: D 53 MET cc_start: 0.8837 (mmm) cc_final: 0.8540 (mmm) REVERT: D 67 MET cc_start: 0.7896 (mpp) cc_final: 0.7650 (mpp) REVERT: D 79 MET cc_start: 0.9041 (ppp) cc_final: 0.8651 (ppp) REVERT: D 127 ASP cc_start: 0.8524 (m-30) cc_final: 0.8246 (m-30) REVERT: E 218 ASN cc_start: 0.8167 (t0) cc_final: 0.7839 (t0) REVERT: E 226 ASP cc_start: 0.8981 (t70) cc_final: 0.8668 (t70) REVERT: E 354 MET cc_start: 0.8334 (tpp) cc_final: 0.7776 (ttm) REVERT: F 215 MET cc_start: 0.8763 (mtp) cc_final: 0.8446 (mtp) REVERT: F 226 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: F 255 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8223 (t0) REVERT: F 354 MET cc_start: 0.8380 (ttm) cc_final: 0.8060 (tmm) REVERT: G 132 ASN cc_start: 0.8693 (t0) cc_final: 0.8408 (t0) REVERT: H 49 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7668 (tm-30) REVERT: H 53 MET cc_start: 0.9103 (mmm) cc_final: 0.8716 (mmm) REVERT: H 75 HIS cc_start: 0.8670 (OUTLIER) cc_final: 0.7898 (t70) REVERT: H 127 ASP cc_start: 0.8514 (m-30) cc_final: 0.8226 (m-30) outliers start: 46 outliers final: 21 residues processed: 242 average time/residue: 0.1016 time to fit residues: 36.7792 Evaluate side-chains 220 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 150 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 135 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 298 GLN B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 75 HIS E 185 GLN E 298 GLN F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN H 70 GLN ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.168516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112640 restraints weight = 16979.069| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.34 r_work: 0.3031 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13798 Z= 0.148 Angle : 0.580 9.230 18638 Z= 0.308 Chirality : 0.045 0.305 1916 Planarity : 0.003 0.033 2510 Dihedral : 4.498 26.231 1788 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.32 % Allowed : 18.88 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.22 (0.21), residues: 1650 helix: 1.75 (0.23), residues: 514 sheet: 0.76 (0.30), residues: 324 loop : -1.22 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 115 TYR 0.023 0.002 TYR G 138 PHE 0.014 0.001 PHE E 52 TRP 0.010 0.001 TRP F 126 HIS 0.007 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (13794) covalent geometry : angle 0.57722 / 0.31 (18630) SS BOND : bond 0.00176 / 0.10 ( 4) SS BOND : angle 2.65302 / 1.44 ( 8) hydrogen bonds : bond 0.03272 / 2.19 ( 649) hydrogen bonds : angle 4.30412 / 3.00 ( 1857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8216 (t0) cc_final: 0.7866 (t0) REVERT: A 226 ASP cc_start: 0.9054 (t70) cc_final: 0.8732 (t70) REVERT: A 354 MET cc_start: 0.8235 (tpp) cc_final: 0.7700 (ttm) REVERT: B 215 MET cc_start: 0.8821 (mtp) cc_final: 0.8493 (mtp) REVERT: B 226 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: B 255 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8287 (t0) REVERT: B 354 MET cc_start: 0.8353 (ttm) cc_final: 0.8018 (tmm) REVERT: C 73 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8176 (pp30) REVERT: C 132 ASN cc_start: 0.8730 (t0) cc_final: 0.8449 (t0) REVERT: D 53 MET cc_start: 0.8863 (mmm) cc_final: 0.8528 (mmm) REVERT: D 67 MET cc_start: 0.7928 (mpp) cc_final: 0.7706 (mpp) REVERT: D 127 ASP cc_start: 0.8617 (m-30) cc_final: 0.8315 (m-30) REVERT: E 218 ASN cc_start: 0.8272 (t0) cc_final: 0.7898 (t0) REVERT: E 226 ASP cc_start: 0.9031 (t70) cc_final: 0.8720 (t70) REVERT: E 354 MET cc_start: 0.8295 (tpp) cc_final: 0.7717 (ttm) REVERT: F 215 MET cc_start: 0.8818 (mtp) cc_final: 0.8494 (mtp) REVERT: F 226 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: F 255 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8289 (t0) REVERT: F 286 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8432 (mmtt) REVERT: F 354 MET cc_start: 0.8408 (ttm) cc_final: 0.8102 (tmm) REVERT: G 71 GLU cc_start: 0.9064 (tp30) cc_final: 0.8641 (tp30) REVERT: G 132 ASN cc_start: 0.8744 (t0) cc_final: 0.8460 (t0) REVERT: H 49 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7780 (tm-30) REVERT: H 53 MET cc_start: 0.9124 (mmm) cc_final: 0.8794 (mmm) REVERT: H 75 HIS cc_start: 0.8691 (OUTLIER) cc_final: 0.7854 (t70) REVERT: H 127 ASP cc_start: 0.8584 (m-30) cc_final: 0.8272 (m-30) outliers start: 48 outliers final: 29 residues processed: 233 average time/residue: 0.1133 time to fit residues: 39.1911 Evaluate side-chains 239 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 298 GLN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 0.0270 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 75 HIS E 185 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114364 restraints weight = 16817.881| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.22 r_work: 0.3048 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13798 Z= 0.117 Angle : 0.582 12.798 18638 Z= 0.312 Chirality : 0.044 0.243 1916 Planarity : 0.003 0.032 2510 Dihedral : 4.375 22.829 1788 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.70 % Allowed : 18.74 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.27 (0.21), residues: 1650 helix: 1.70 (0.23), residues: 518 sheet: 0.82 (0.30), residues: 324 loop : -1.15 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 115 TYR 0.028 0.001 TYR G 138 PHE 0.012 0.001 PHE E 293 TRP 0.012 0.001 TRP F 126 HIS 0.008 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (13794) covalent geometry : angle 0.57945 / 0.31 (18630) SS BOND : bond 0.00210 / 0.13 ( 4) SS BOND : angle 2.50918 / 1.36 ( 8) hydrogen bonds : bond 0.03181 / 2.14 ( 649) hydrogen bonds : angle 4.28320 / 2.96 ( 1857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8132 (t0) cc_final: 0.7796 (t0) REVERT: A 226 ASP cc_start: 0.8993 (t70) cc_final: 0.8703 (t70) REVERT: A 354 MET cc_start: 0.8277 (tpp) cc_final: 0.7710 (ttm) REVERT: B 215 MET cc_start: 0.8741 (mtp) cc_final: 0.8426 (mtp) REVERT: B 226 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: B 255 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8200 (t0) REVERT: B 354 MET cc_start: 0.8313 (ttm) cc_final: 0.8017 (tmm) REVERT: C 73 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8298 (pp30) REVERT: C 132 ASN cc_start: 0.8685 (t0) cc_final: 0.8405 (t0) REVERT: D 53 MET cc_start: 0.8814 (mmm) cc_final: 0.8490 (mmm) REVERT: D 79 MET cc_start: 0.8772 (ppp) cc_final: 0.8499 (ppp) REVERT: D 127 ASP cc_start: 0.8566 (m-30) cc_final: 0.8271 (m-30) REVERT: E 218 ASN cc_start: 0.8195 (t0) cc_final: 0.7851 (t0) REVERT: E 226 ASP cc_start: 0.8972 (t70) cc_final: 0.8688 (t70) REVERT: E 354 MET cc_start: 0.8292 (tpp) cc_final: 0.7712 (ttm) REVERT: F 215 MET cc_start: 0.8743 (mtp) cc_final: 0.8428 (mtp) REVERT: F 226 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: F 255 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8189 (t0) REVERT: F 289 TYR cc_start: 0.8052 (m-80) cc_final: 0.7773 (m-10) REVERT: F 354 MET cc_start: 0.8329 (ttm) cc_final: 0.8090 (tmm) REVERT: G 71 GLU cc_start: 0.9001 (tp30) cc_final: 0.8566 (tp30) REVERT: G 132 ASN cc_start: 0.8711 (t0) cc_final: 0.8415 (t0) REVERT: H 49 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7856 (tm-30) REVERT: H 53 MET cc_start: 0.9039 (mmm) cc_final: 0.8817 (mmm) REVERT: H 75 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.7867 (t70) REVERT: H 127 ASP cc_start: 0.8538 (m-30) cc_final: 0.8231 (m-30) outliers start: 39 outliers final: 26 residues processed: 242 average time/residue: 0.1029 time to fit residues: 37.5181 Evaluate side-chains 226 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 75 HIS Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 52 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN E 185 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.165785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110455 restraints weight = 17044.478| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.36 r_work: 0.3014 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13798 Z= 0.232 Angle : 0.663 16.907 18638 Z= 0.355 Chirality : 0.047 0.239 1916 Planarity : 0.004 0.041 2510 Dihedral : 4.696 24.799 1788 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.70 % Allowed : 19.78 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.08 (0.21), residues: 1650 helix: 1.66 (0.23), residues: 518 sheet: 0.48 (0.30), residues: 328 loop : -1.25 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 115 TYR 0.030 0.002 TYR G 138 PHE 0.023 0.002 PHE B 52 TRP 0.007 0.002 TRP A 104 HIS 0.012 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (13794) covalent geometry : angle 0.65993 / 0.35 (18630) SS BOND : bond 0.00118 / 0.07 ( 4) SS BOND : angle 3.01406 / 1.65 ( 8) hydrogen bonds : bond 0.03711 / 2.47 ( 649) hydrogen bonds : angle 4.52908 / 3.14 ( 1857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8332 (t0) cc_final: 0.7978 (t0) REVERT: A 226 ASP cc_start: 0.9084 (t70) cc_final: 0.8800 (t70) REVERT: A 354 MET cc_start: 0.8193 (tpp) cc_final: 0.7649 (ttm) REVERT: B 215 MET cc_start: 0.8801 (mtp) cc_final: 0.8452 (mtp) REVERT: B 226 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: B 255 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8423 (t0) REVERT: B 354 MET cc_start: 0.8325 (ttm) cc_final: 0.7987 (tmm) REVERT: C 73 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8055 (pp30) REVERT: C 132 ASN cc_start: 0.8772 (t0) cc_final: 0.8512 (t0) REVERT: D 53 MET cc_start: 0.8838 (mmm) cc_final: 0.8444 (mmm) REVERT: D 79 MET cc_start: 0.8758 (ppp) cc_final: 0.8478 (ppp) REVERT: D 127 ASP cc_start: 0.8618 (m-30) cc_final: 0.8314 (m-30) REVERT: E 218 ASN cc_start: 0.8398 (t0) cc_final: 0.8024 (t0) REVERT: E 226 ASP cc_start: 0.9052 (t70) cc_final: 0.8776 (t70) REVERT: E 304 LYS cc_start: 0.9307 (ptpt) cc_final: 0.9084 (tppt) REVERT: E 354 MET cc_start: 0.8255 (tpp) cc_final: 0.7706 (ttm) REVERT: F 215 MET cc_start: 0.8783 (mtp) cc_final: 0.8428 (mtp) REVERT: F 223 ASP cc_start: 0.8567 (t0) cc_final: 0.8165 (t0) REVERT: F 226 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: F 255 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8423 (t0) REVERT: F 354 MET cc_start: 0.8400 (ttm) cc_final: 0.8088 (tmm) REVERT: G 48 ASP cc_start: 0.7458 (t0) cc_final: 0.7094 (m-30) REVERT: G 71 GLU cc_start: 0.9049 (tp30) cc_final: 0.8570 (tp30) REVERT: G 132 ASN cc_start: 0.8763 (t0) cc_final: 0.8489 (t0) REVERT: H 49 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8047 (tm-30) REVERT: H 53 MET cc_start: 0.9126 (mmm) cc_final: 0.8760 (mmm) REVERT: H 67 MET cc_start: 0.8248 (mpp) cc_final: 0.7925 (mpp) REVERT: H 127 ASP cc_start: 0.8623 (m-30) cc_final: 0.8311 (m-30) outliers start: 39 outliers final: 27 residues processed: 238 average time/residue: 0.1000 time to fit residues: 36.2197 Evaluate side-chains 230 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN E 185 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** 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 = 0.4005 r_free = 0.4005 target = 0.168729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111582 restraints weight = 17055.790| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.22 r_work: 0.3072 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13798 Z= 0.132 Angle : 0.645 15.589 18638 Z= 0.344 Chirality : 0.045 0.242 1916 Planarity : 0.003 0.034 2510 Dihedral : 4.442 23.113 1788 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.21 % Allowed : 20.33 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 (0.21), residues: 1650 helix: 1.92 (0.23), residues: 494 sheet: 0.72 (0.30), residues: 324 loop : -1.09 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 115 TYR 0.024 0.002 TYR C 138 PHE 0.012 0.001 PHE E 52 TRP 0.013 0.001 TRP B 126 HIS 0.007 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13794) covalent geometry : angle 0.64292 / 0.34 (18630) SS BOND : bond 0.00200 / 0.12 ( 4) SS BOND : angle 2.60178 / 1.41 ( 8) hydrogen bonds : bond 0.03276 / 2.18 ( 649) hydrogen bonds : angle 4.36936 / 3.01 ( 1857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8208 (t0) cc_final: 0.7873 (t0) REVERT: A 226 ASP cc_start: 0.9024 (t70) cc_final: 0.8759 (t70) REVERT: A 354 MET cc_start: 0.8273 (tpp) cc_final: 0.7677 (ttm) REVERT: B 48 TYR cc_start: 0.8693 (p90) cc_final: 0.8491 (p90) REVERT: B 215 MET cc_start: 0.8732 (mtp) cc_final: 0.8419 (mtp) REVERT: B 226 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: B 255 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8303 (t0) REVERT: B 354 MET cc_start: 0.8309 (ttm) cc_final: 0.8040 (tmm) REVERT: C 71 GLU cc_start: 0.8748 (tp30) cc_final: 0.8326 (tm-30) REVERT: C 73 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8361 (pp30) REVERT: C 132 ASN cc_start: 0.8743 (t0) cc_final: 0.8489 (t0) REVERT: D 53 MET cc_start: 0.8779 (mmm) cc_final: 0.8420 (mmm) REVERT: D 79 MET cc_start: 0.8764 (ppp) cc_final: 0.8499 (ppp) REVERT: D 127 ASP cc_start: 0.8607 (m-30) cc_final: 0.8296 (m-30) REVERT: E 218 ASN cc_start: 0.8235 (t0) cc_final: 0.7893 (t0) REVERT: E 226 ASP cc_start: 0.8985 (t70) cc_final: 0.8725 (t70) REVERT: E 354 MET cc_start: 0.8321 (tpp) cc_final: 0.7719 (ttm) REVERT: F 215 MET cc_start: 0.8747 (mtp) cc_final: 0.8434 (mtp) REVERT: F 223 ASP cc_start: 0.8496 (t0) cc_final: 0.7829 (t0) REVERT: F 226 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: F 255 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8254 (t0) REVERT: F 354 MET cc_start: 0.8365 (ttm) cc_final: 0.8129 (tmm) REVERT: G 48 ASP cc_start: 0.7279 (t0) cc_final: 0.6937 (m-30) REVERT: G 71 GLU cc_start: 0.8998 (tp30) cc_final: 0.8142 (tm-30) REVERT: G 132 ASN cc_start: 0.8758 (t0) cc_final: 0.8495 (t0) REVERT: H 49 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8006 (tm-30) REVERT: H 53 MET cc_start: 0.9041 (mmm) cc_final: 0.8735 (mmm) REVERT: H 67 MET cc_start: 0.8159 (mpp) cc_final: 0.7915 (mpp) REVERT: H 127 ASP cc_start: 0.8500 (m-30) cc_final: 0.8191 (m-30) outliers start: 32 outliers final: 23 residues processed: 238 average time/residue: 0.1048 time to fit residues: 37.7436 Evaluate side-chains 227 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain G residue 75 HIS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 20 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 75 HIS E 185 GLN F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112254 restraints weight = 17048.633| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.36 r_work: 0.3092 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13798 Z= 0.132 Angle : 0.649 14.973 18638 Z= 0.346 Chirality : 0.045 0.275 1916 Planarity : 0.003 0.033 2510 Dihedral : 4.372 22.793 1788 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.28 % Allowed : 20.54 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: 0.26 (0.21), residues: 1650 helix: 1.71 (0.23), residues: 518 sheet: 0.76 (0.30), residues: 324 loop : -1.15 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 115 TYR 0.022 0.002 TYR C 138 PHE 0.011 0.001 PHE E 52 TRP 0.012 0.001 TRP B 126 HIS 0.007 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13794) covalent geometry : angle 0.64732 / 0.35 (18630) SS BOND : bond 0.00206 / 0.12 ( 4) SS BOND : angle 2.51640 / 1.37 ( 8) hydrogen bonds : bond 0.03272 / 2.19 ( 649) hydrogen bonds : angle 4.35436 / 3.00 ( 1857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.88 seconds wall clock time: 61 minutes 46.25 seconds (3706.25 seconds total)