Starting phenix.real_space_refine on Thu Jul 31 07:43:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jp6_36469/07_2025/8jp6_36469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jp6_36469/07_2025/8jp6_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_2025/8jp6_36469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jp6_36469/07_2025/8jp6_36469.map" model { file = "/net/cci-nas-00/data/ceres_data/8jp6_36469/07_2025/8jp6_36469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jp6_36469/07_2025/8jp6_36469.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.79, per 1000 atoms: 0.58 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: 2.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.30 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: 3.74 Time building geometry restraints manager: 3.47 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: 0.06 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.730 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (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 TRP 0.013 0.002 TRP A 104 HIS 0.008 0.001 HIS G 55 PHE 0.015 0.001 PHE F 52 TYR 0.014 0.001 TYR A 127 ARG 0.004 0.001 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.12109 ( 649) hydrogen bonds : angle 5.41474 ( 1857) SS BOND : bond 0.00179 ( 4) SS BOND : angle 2.74086 ( 8) covalent geometry : bond 0.00342 (13794) covalent geometry : angle 0.59258 (18630) *********************** 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 : 1.775 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: symmetry clash REVERT: A 218 ASN cc_start: 0.8281 (t0) cc_final: 0.7938 (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: 0.8574 (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: 0.8009 (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: 0.8484 (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: 0.7928 (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: 0.8428 (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: 0.7416 (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: 0.8537 (t) outliers start: 2 outliers final: 2 residues processed: 314 average time/residue: 0.2608 time to fit residues: 118.2114 Evaluate side-chains 220 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 140 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 96 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 185 GLN A 235 ASN A 243 HIS B 333 GLN B 339 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS C 86 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 185 GLN E 235 ASN E 243 HIS F 333 GLN F 339 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS G 86 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.167968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110881 restraints weight = 17479.165| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.53 r_work: 0.3060 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13798 Z= 0.209 Angle : 0.597 9.355 18638 Z= 0.317 Chirality : 0.046 0.155 1916 Planarity : 0.004 0.038 2510 Dihedral : 5.294 59.798 1792 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 15.91 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1650 helix: 1.88 (0.23), residues: 520 sheet: 0.45 (0.30), residues: 340 loop : -1.32 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 126 HIS 0.007 0.001 HIS B 342 PHE 0.024 0.002 PHE F 307 TYR 0.020 0.002 TYR H 138 ARG 0.004 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 649) hydrogen bonds : angle 4.58812 ( 1857) SS BOND : bond 0.00117 ( 4) SS BOND : angle 2.92809 ( 8) covalent geometry : bond 0.00495 (13794) covalent geometry : angle 0.59373 (18630) *********************** 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 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 1.534 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: symmetry clash REVERT: A 218 ASN cc_start: 0.8209 (t0) cc_final: 0.7864 (t0) REVERT: A 226 ASP cc_start: 0.8957 (t70) cc_final: 0.8687 (t70) REVERT: A 354 MET cc_start: 0.8074 (tpp) cc_final: 0.7765 (ttm) REVERT: B 48 TYR cc_start: 0.8840 (p90) cc_final: 0.8623 (p90) REVERT: B 215 MET cc_start: 0.8503 (mtp) cc_final: 0.8140 (mtp) REVERT: B 225 ASN cc_start: 0.7735 (m110) cc_final: 0.7466 (p0) REVERT: B 286 LYS cc_start: 0.9152 (mttt) cc_final: 0.8930 (mmtp) REVERT: B 354 MET cc_start: 0.8295 (ttm) cc_final: 0.7787 (tmm) REVERT: C 73 GLN cc_start: 0.8529 (tt0) cc_final: 0.8036 (pp30) REVERT: C 126 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8200 (ptp90) REVERT: C 132 ASN cc_start: 0.8813 (t0) cc_final: 0.8528 (t0) REVERT: D 49 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 67 MET cc_start: 0.8275 (mpp) cc_final: 0.7746 (mpp) REVERT: D 75 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7948 (t70) REVERT: D 101 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7868 (t-90) REVERT: D 128 ASP cc_start: 0.8073 (m-30) cc_final: 0.7803 (t0) REVERT: D 144 SER cc_start: 0.9054 (m) cc_final: 0.8840 (t) REVERT: E 218 ASN cc_start: 0.8236 (t0) cc_final: 0.7898 (t0) REVERT: E 226 ASP cc_start: 0.8958 (t70) cc_final: 0.8691 (t70) REVERT: E 295 HIS cc_start: 0.8713 (t-90) cc_final: 0.8285 (t-90) REVERT: E 354 MET cc_start: 0.8078 (tpp) cc_final: 0.7762 (ttm) REVERT: F 215 MET cc_start: 0.8501 (mtp) cc_final: 0.8118 (mtp) REVERT: F 225 ASN cc_start: 0.7708 (m110) cc_final: 0.7453 (p0) REVERT: F 354 MET cc_start: 0.8391 (ttm) cc_final: 0.8061 (tmm) REVERT: G 73 GLN cc_start: 0.8486 (tt0) cc_final: 0.8007 (pp30) REVERT: G 126 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8152 (ptp90) REVERT: H 75 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8258 (t-90) REVERT: H 128 ASP cc_start: 0.8073 (m-30) cc_final: 0.7795 (t0) outliers start: 24 outliers final: 13 residues processed: 255 average time/residue: 0.2318 time to fit residues: 88.3429 Evaluate side-chains 222 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 41 LEU 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 93 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 72 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 117 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 39 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 185 GLN A 297 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS C 49 GLN C 75 HIS ** D 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 185 GLN E 297 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS G 49 GLN G 75 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.168446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109532 restraints weight = 17535.606| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.52 r_work: 0.3062 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13798 Z= 0.172 Angle : 0.570 8.193 18638 Z= 0.302 Chirality : 0.044 0.148 1916 Planarity : 0.004 0.040 2510 Dihedral : 4.875 57.223 1790 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.11 % Allowed : 16.60 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1650 helix: 1.95 (0.23), residues: 520 sheet: 0.36 (0.30), residues: 340 loop : -1.29 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 126 HIS 0.005 0.001 HIS F 342 PHE 0.016 0.002 PHE B 52 TYR 0.021 0.002 TYR G 138 ARG 0.003 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 649) hydrogen bonds : angle 4.40614 ( 1857) SS BOND : bond 0.00190 ( 4) SS BOND : angle 3.05051 ( 8) covalent geometry : bond 0.00405 (13794) covalent geometry : angle 0.56640 (18630) *********************** 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 280 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 1.392 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: 0.8198 (t0) cc_final: 0.7861 (t0) REVERT: A 226 ASP cc_start: 0.8958 (t70) cc_final: 0.8700 (t70) REVERT: A 287 GLU cc_start: 0.9130 (pt0) cc_final: 0.8930 (pp20) REVERT: A 354 MET cc_start: 0.8095 (tpp) cc_final: 0.7765 (ttm) REVERT: B 90 ARG cc_start: 0.8769 (mtt90) cc_final: 0.8562 (mtt-85) REVERT: B 215 MET cc_start: 0.8482 (mtp) cc_final: 0.8125 (mtp) REVERT: B 354 MET cc_start: 0.8284 (ttm) cc_final: 0.7854 (tmm) REVERT: C 73 GLN cc_start: 0.8522 (tt0) cc_final: 0.8008 (pp30) REVERT: C 132 ASN cc_start: 0.8833 (t0) cc_final: 0.8530 (t0) REVERT: C 138 TYR cc_start: 0.7300 (t80) cc_final: 0.7027 (t80) REVERT: D 53 MET cc_start: 0.9007 (mmm) cc_final: 0.8612 (mmm) REVERT: D 75 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.8018 (t70) REVERT: D 144 SER cc_start: 0.9205 (m) cc_final: 0.8906 (t) REVERT: E 218 ASN cc_start: 0.8206 (t0) cc_final: 0.7866 (t0) REVERT: E 226 ASP cc_start: 0.8948 (t70) cc_final: 0.8694 (t70) REVERT: E 295 HIS cc_start: 0.8738 (t-90) cc_final: 0.8478 (t-90) REVERT: E 354 MET cc_start: 0.8113 (tpp) cc_final: 0.7793 (ttm) REVERT: F 90 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8567 (mtt-85) REVERT: F 215 MET cc_start: 0.8498 (mtp) cc_final: 0.8144 (mtp) REVERT: F 354 MET cc_start: 0.8384 (ttm) cc_final: 0.8073 (tmm) REVERT: G 73 GLN cc_start: 0.8482 (tt0) cc_final: 0.7970 (pp30) REVERT: G 138 TYR cc_start: 0.7308 (t80) cc_final: 0.7087 (t80) REVERT: H 75 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.8345 (t-90) outliers start: 45 outliers final: 20 residues processed: 272 average time/residue: 0.2436 time to fit residues: 96.5206 Evaluate side-chains 234 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 55 HIS 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 185 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 136 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN C 75 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN E 298 GLN F 290 GLN G 75 HIS H 70 GLN H 80 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109678 restraints weight = 16934.546| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.22 r_work: 0.2974 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13798 Z= 0.150 Angle : 0.575 8.703 18638 Z= 0.303 Chirality : 0.044 0.144 1916 Planarity : 0.003 0.041 2510 Dihedral : 4.544 24.041 1788 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.11 % Allowed : 17.29 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1650 helix: 1.86 (0.23), residues: 520 sheet: 0.63 (0.31), residues: 324 loop : -1.36 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.007 0.001 HIS H 80 PHE 0.014 0.001 PHE F 307 TYR 0.017 0.001 TYR D 76 ARG 0.005 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 649) hydrogen bonds : angle 4.30506 ( 1857) SS BOND : bond 0.00179 ( 4) SS BOND : angle 2.79250 ( 8) covalent geometry : bond 0.00350 (13794) covalent geometry : angle 0.57203 (18630) *********************** 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 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 1.491 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: A 218 ASN cc_start: 0.8273 (t0) cc_final: 0.7918 (t0) REVERT: A 226 ASP cc_start: 0.9074 (t70) cc_final: 0.8771 (t70) REVERT: A 287 GLU cc_start: 0.9109 (pt0) cc_final: 0.8890 (pp20) REVERT: A 352 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7766 (tt) REVERT: A 354 MET cc_start: 0.8213 (tpp) cc_final: 0.7808 (ttm) REVERT: B 215 MET cc_start: 0.8809 (mtp) cc_final: 0.8500 (mtp) REVERT: B 226 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: B 354 MET cc_start: 0.8340 (ttm) cc_final: 0.7848 (tmm) REVERT: C 73 GLN cc_start: 0.8564 (tt0) cc_final: 0.8046 (pp30) REVERT: C 132 ASN cc_start: 0.8879 (t0) cc_final: 0.8561 (t0) REVERT: C 138 TYR cc_start: 0.7397 (t80) cc_final: 0.7112 (t80) REVERT: D 53 MET cc_start: 0.9011 (mmm) cc_final: 0.8590 (mmm) REVERT: D 128 ASP cc_start: 0.8229 (m-30) cc_final: 0.7956 (t0) REVERT: D 144 SER cc_start: 0.9275 (m) cc_final: 0.9035 (t) REVERT: E 218 ASN cc_start: 0.8279 (t0) cc_final: 0.7936 (t0) REVERT: E 226 ASP cc_start: 0.9069 (t70) cc_final: 0.8771 (t70) REVERT: E 352 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7806 (tt) REVERT: E 354 MET cc_start: 0.8257 (tpp) cc_final: 0.7868 (ttm) REVERT: F 215 MET cc_start: 0.8791 (mtp) cc_final: 0.8481 (mtp) REVERT: F 354 MET cc_start: 0.8442 (ttm) cc_final: 0.8087 (tmm) REVERT: G 73 GLN cc_start: 0.8531 (tt0) cc_final: 0.7998 (pp30) REVERT: G 138 TYR cc_start: 0.7451 (t80) cc_final: 0.7139 (t80) REVERT: H 75 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8314 (t-90) REVERT: H 128 ASP cc_start: 0.8245 (m-30) cc_final: 0.7996 (t0) outliers start: 45 outliers final: 21 residues processed: 253 average time/residue: 0.2436 time to fit residues: 90.6987 Evaluate side-chains 226 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 228 GLU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU 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 211 THR Chi-restraints excluded: chain E residue 228 GLU 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 E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain G 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 50 optimal weight: 0.9980 chunk 117 optimal weight: 0.0070 chunk 153 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 133 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 298 GLN B 290 GLN C 119 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN E 298 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN H 75 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113981 restraints weight = 16899.161| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.30 r_work: 0.2989 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13798 Z= 0.107 Angle : 0.560 9.503 18638 Z= 0.298 Chirality : 0.043 0.157 1916 Planarity : 0.003 0.033 2510 Dihedral : 4.371 22.431 1788 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.63 % Allowed : 18.26 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1650 helix: 1.89 (0.23), residues: 516 sheet: 0.86 (0.31), residues: 324 loop : -1.28 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 126 HIS 0.005 0.001 HIS H 80 PHE 0.014 0.001 PHE H 141 TYR 0.017 0.001 TYR D 76 ARG 0.004 0.000 ARG E 350 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 649) hydrogen bonds : angle 4.22337 ( 1857) SS BOND : bond 0.00240 ( 4) SS BOND : angle 2.47096 ( 8) covalent geometry : bond 0.00237 (13794) covalent geometry : angle 0.55798 (18630) *********************** 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 264 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 1.548 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: 0.8163 (t0) cc_final: 0.7809 (t0) REVERT: A 226 ASP cc_start: 0.9011 (t70) cc_final: 0.8694 (t70) REVERT: A 354 MET cc_start: 0.8252 (tpp) cc_final: 0.7813 (ttm) REVERT: B 215 MET cc_start: 0.8795 (mtp) cc_final: 0.8484 (mtp) REVERT: B 226 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: B 354 MET cc_start: 0.8337 (ttm) cc_final: 0.8001 (tmm) REVERT: C 48 ASP cc_start: 0.7811 (t0) cc_final: 0.7583 (m-30) REVERT: C 49 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8015 (tp40) REVERT: C 73 GLN cc_start: 0.8531 (tt0) cc_final: 0.8043 (pp30) REVERT: C 117 LEU cc_start: 0.8544 (tt) cc_final: 0.8303 (tp) REVERT: C 132 ASN cc_start: 0.8824 (t0) cc_final: 0.8469 (t0) REVERT: C 138 TYR cc_start: 0.7386 (t80) cc_final: 0.7064 (t80) REVERT: D 53 MET cc_start: 0.9016 (mmm) cc_final: 0.8646 (mmm) REVERT: D 67 MET cc_start: 0.7858 (mpp) cc_final: 0.7454 (mpp) REVERT: D 128 ASP cc_start: 0.8289 (m-30) cc_final: 0.7996 (t0) REVERT: E 49 LYS cc_start: 0.9203 (ttpt) cc_final: 0.8930 (ttpp) REVERT: E 218 ASN cc_start: 0.8160 (t0) cc_final: 0.7828 (t0) REVERT: E 226 ASP cc_start: 0.9024 (t70) cc_final: 0.8705 (t70) REVERT: E 294 GLU cc_start: 0.8955 (tp30) cc_final: 0.8714 (tp30) REVERT: E 354 MET cc_start: 0.8300 (tpp) cc_final: 0.7788 (ttm) REVERT: F 215 MET cc_start: 0.8782 (mtp) cc_final: 0.8473 (mtp) REVERT: F 226 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8142 (m-30) REVERT: F 354 MET cc_start: 0.8408 (ttm) cc_final: 0.8055 (tmm) REVERT: G 73 GLN cc_start: 0.8494 (tt0) cc_final: 0.7970 (pp30) REVERT: G 117 LEU cc_start: 0.8506 (tt) cc_final: 0.8289 (tp) REVERT: G 138 TYR cc_start: 0.7419 (t80) cc_final: 0.7093 (t80) REVERT: H 56 LEU cc_start: 0.9534 (tp) cc_final: 0.9141 (pp) REVERT: H 128 ASP cc_start: 0.8268 (m-30) cc_final: 0.8018 (t0) outliers start: 38 outliers final: 20 residues processed: 249 average time/residue: 0.2359 time to fit residues: 87.6335 Evaluate side-chains 236 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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 290 GLN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 72 LEU 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 D residue 75 HIS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 290 GLN Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 226 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 163 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 298 GLN B 290 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 GLN ** 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 = 0.4004 r_free = 0.4004 target = 0.168402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113505 restraints weight = 17124.957| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.20 r_work: 0.3073 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13798 Z= 0.124 Angle : 0.570 9.160 18638 Z= 0.303 Chirality : 0.043 0.153 1916 Planarity : 0.003 0.032 2510 Dihedral : 4.339 22.682 1788 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.97 % Allowed : 18.81 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1650 helix: 1.80 (0.23), residues: 520 sheet: 0.89 (0.30), residues: 324 loop : -1.22 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 126 HIS 0.006 0.001 HIS D 55 PHE 0.014 0.001 PHE H 141 TYR 0.019 0.001 TYR D 76 ARG 0.004 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 649) hydrogen bonds : angle 4.16255 ( 1857) SS BOND : bond 0.00212 ( 4) SS BOND : angle 2.46423 ( 8) covalent geometry : bond 0.00283 (13794) covalent geometry : angle 0.56811 (18630) *********************** 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 272 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 1.578 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: 0.8171 (t0) cc_final: 0.7825 (t0) REVERT: A 226 ASP cc_start: 0.8950 (t70) cc_final: 0.8658 (t70) REVERT: A 354 MET cc_start: 0.8264 (tpp) cc_final: 0.7728 (ttm) REVERT: B 215 MET cc_start: 0.8738 (mtp) cc_final: 0.8421 (mtp) REVERT: B 223 ASP cc_start: 0.8470 (t0) cc_final: 0.7894 (t0) REVERT: B 226 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: B 354 MET cc_start: 0.8315 (ttm) cc_final: 0.8003 (tmm) REVERT: C 48 ASP cc_start: 0.7649 (t0) cc_final: 0.7375 (m-30) REVERT: C 73 GLN cc_start: 0.8474 (tt0) cc_final: 0.8033 (pp30) REVERT: C 132 ASN cc_start: 0.8822 (t0) cc_final: 0.8482 (t0) REVERT: C 138 TYR cc_start: 0.7433 (t80) cc_final: 0.7109 (t80) REVERT: D 53 MET cc_start: 0.9050 (mmm) cc_final: 0.8666 (mmm) REVERT: D 67 MET cc_start: 0.8003 (mpp) cc_final: 0.7648 (mpp) REVERT: D 128 ASP cc_start: 0.8185 (m-30) cc_final: 0.7955 (t0) REVERT: E 49 LYS cc_start: 0.9200 (ttpt) cc_final: 0.8891 (ttpp) REVERT: E 218 ASN cc_start: 0.8224 (t0) cc_final: 0.7886 (t0) REVERT: E 226 ASP cc_start: 0.8954 (t70) cc_final: 0.8662 (t70) REVERT: E 352 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7723 (tt) REVERT: E 354 MET cc_start: 0.8230 (tpp) cc_final: 0.7669 (ttm) REVERT: F 215 MET cc_start: 0.8731 (mtp) cc_final: 0.8413 (mtp) REVERT: F 223 ASP cc_start: 0.8439 (t0) cc_final: 0.7868 (t0) REVERT: F 226 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: F 354 MET cc_start: 0.8373 (ttm) cc_final: 0.8096 (tmm) REVERT: G 73 GLN cc_start: 0.8449 (tt0) cc_final: 0.7923 (pp30) REVERT: G 138 TYR cc_start: 0.7384 (t80) cc_final: 0.7047 (t80) REVERT: H 128 ASP cc_start: 0.8190 (m-30) cc_final: 0.7977 (t0) outliers start: 43 outliers final: 28 residues processed: 260 average time/residue: 0.2894 time to fit residues: 110.9732 Evaluate side-chains 239 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG 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 326 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 72 LEU 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 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 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 34 optimal weight: 0.0170 chunk 21 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 297 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN C 75 HIS C 86 ASN D 70 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS F 79 GLN F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.166878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109770 restraints weight = 16979.609| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.40 r_work: 0.2972 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13798 Z= 0.179 Angle : 0.613 11.521 18638 Z= 0.326 Chirality : 0.045 0.218 1916 Planarity : 0.004 0.034 2510 Dihedral : 4.484 24.122 1788 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.04 % Allowed : 19.02 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1650 helix: 1.74 (0.23), residues: 518 sheet: 0.69 (0.30), residues: 326 loop : -1.22 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 126 HIS 0.010 0.001 HIS D 80 PHE 0.017 0.002 PHE F 52 TYR 0.019 0.002 TYR D 76 ARG 0.005 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 649) hydrogen bonds : angle 4.31726 ( 1857) SS BOND : bond 0.00157 ( 4) SS BOND : angle 2.71610 ( 8) covalent geometry : bond 0.00419 (13794) covalent geometry : angle 0.61031 (18630) *********************** 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 259 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 3.781 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: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8287 (t0) cc_final: 0.7931 (t0) REVERT: A 226 ASP cc_start: 0.9073 (t70) cc_final: 0.8770 (t70) REVERT: A 354 MET cc_start: 0.8291 (tpp) cc_final: 0.7746 (ttm) REVERT: B 215 MET cc_start: 0.8808 (mtp) cc_final: 0.8478 (mtp) REVERT: B 223 ASP cc_start: 0.8558 (t0) cc_final: 0.7952 (t0) REVERT: B 226 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: B 286 LYS cc_start: 0.8841 (mmtp) cc_final: 0.8555 (mmtm) REVERT: B 289 TYR cc_start: 0.8024 (m-80) cc_final: 0.7665 (m-10) REVERT: B 354 MET cc_start: 0.8348 (ttm) cc_final: 0.8023 (tmm) REVERT: C 73 GLN cc_start: 0.8483 (tt0) cc_final: 0.8023 (pp30) REVERT: C 132 ASN cc_start: 0.8829 (t0) cc_final: 0.8391 (t0) REVERT: C 138 TYR cc_start: 0.7576 (t80) cc_final: 0.7237 (t80) REVERT: D 53 MET cc_start: 0.9041 (mmm) cc_final: 0.8664 (mmm) REVERT: D 79 MET cc_start: 0.8746 (ppp) cc_final: 0.8399 (ppp) REVERT: D 128 ASP cc_start: 0.8248 (m-30) cc_final: 0.8022 (t0) REVERT: E 218 ASN cc_start: 0.8309 (t0) cc_final: 0.7974 (t0) REVERT: E 226 ASP cc_start: 0.9067 (t70) cc_final: 0.8764 (t70) REVERT: E 352 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7767 (tt) REVERT: E 354 MET cc_start: 0.8258 (tpp) cc_final: 0.7694 (ttm) REVERT: F 215 MET cc_start: 0.8788 (mtp) cc_final: 0.8463 (mtp) REVERT: F 223 ASP cc_start: 0.8544 (t0) cc_final: 0.7905 (t0) REVERT: F 226 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: F 289 TYR cc_start: 0.8090 (m-80) cc_final: 0.7768 (m-10) REVERT: F 354 MET cc_start: 0.8389 (ttm) cc_final: 0.8049 (tmm) REVERT: G 41 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7031 (tt) REVERT: G 73 GLN cc_start: 0.8515 (tt0) cc_final: 0.8005 (pp30) REVERT: H 56 LEU cc_start: 0.9361 (tt) cc_final: 0.9152 (pp) REVERT: H 128 ASP cc_start: 0.8263 (m-30) cc_final: 0.8030 (t0) outliers start: 44 outliers final: 27 residues processed: 248 average time/residue: 0.3222 time to fit residues: 118.8154 Evaluate side-chains 239 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 185 GLN 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 326 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU 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 90 ARG Chi-restraints excluded: chain E residue 93 VAL 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 E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 59 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 33 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 73 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS F 79 GLN F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.167916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113629 restraints weight = 16916.685| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.19 r_work: 0.3043 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13798 Z= 0.132 Angle : 0.592 12.666 18638 Z= 0.315 Chirality : 0.044 0.222 1916 Planarity : 0.003 0.033 2510 Dihedral : 4.376 23.522 1788 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.11 % Allowed : 18.88 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1650 helix: 1.75 (0.23), residues: 514 sheet: 0.80 (0.30), residues: 324 loop : -1.22 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.006 0.001 HIS D 55 PHE 0.013 0.001 PHE E 52 TYR 0.018 0.001 TYR D 76 ARG 0.006 0.000 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 649) hydrogen bonds : angle 4.23209 ( 1857) SS BOND : bond 0.00211 ( 4) SS BOND : angle 2.54949 ( 8) covalent geometry : bond 0.00304 (13794) covalent geometry : angle 0.58998 (18630) *********************** 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 262 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 1.518 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: 0.8241 (t0) cc_final: 0.7886 (t0) REVERT: A 226 ASP cc_start: 0.9005 (t70) cc_final: 0.8718 (t70) REVERT: A 354 MET cc_start: 0.8310 (tpp) cc_final: 0.7731 (ttm) REVERT: B 215 MET cc_start: 0.8722 (mtp) cc_final: 0.8411 (mtp) REVERT: B 223 ASP cc_start: 0.8467 (t0) cc_final: 0.7857 (t0) REVERT: B 226 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: B 354 MET cc_start: 0.8330 (ttm) cc_final: 0.8017 (tmm) REVERT: C 48 ASP cc_start: 0.7906 (t0) cc_final: 0.7325 (m-30) REVERT: C 73 GLN cc_start: 0.8479 (tt0) cc_final: 0.8015 (pp30) REVERT: C 132 ASN cc_start: 0.8800 (t0) cc_final: 0.8403 (t0) REVERT: C 138 TYR cc_start: 0.7545 (t80) cc_final: 0.7220 (t80) REVERT: D 53 MET cc_start: 0.8986 (mmm) cc_final: 0.8589 (mmm) REVERT: D 79 MET cc_start: 0.8803 (ppp) cc_final: 0.8567 (ppp) REVERT: D 128 ASP cc_start: 0.8204 (m-30) cc_final: 0.7999 (t0) REVERT: E 218 ASN cc_start: 0.8251 (t0) cc_final: 0.7914 (t0) REVERT: E 226 ASP cc_start: 0.8990 (t70) cc_final: 0.8701 (t70) REVERT: E 352 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7719 (tt) REVERT: E 354 MET cc_start: 0.8266 (tpp) cc_final: 0.7674 (ttm) REVERT: F 215 MET cc_start: 0.8713 (mtp) cc_final: 0.8401 (mtp) REVERT: F 223 ASP cc_start: 0.8464 (t0) cc_final: 0.7851 (t0) REVERT: F 226 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: F 354 MET cc_start: 0.8374 (ttm) cc_final: 0.8107 (tmm) REVERT: G 41 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7006 (tt) REVERT: G 71 GLU cc_start: 0.8788 (tp30) cc_final: 0.8239 (tm-30) REVERT: G 73 GLN cc_start: 0.8424 (tt0) cc_final: 0.7947 (pp30) REVERT: G 132 ASN cc_start: 0.8847 (t0) cc_final: 0.8341 (t0) REVERT: G 138 TYR cc_start: 0.7527 (t80) cc_final: 0.7199 (t80) REVERT: H 128 ASP cc_start: 0.8203 (m-30) cc_final: 0.7984 (t0) outliers start: 45 outliers final: 26 residues processed: 249 average time/residue: 0.2940 time to fit residues: 109.7513 Evaluate side-chains 235 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG 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 326 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain C residue 41 LEU 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 D residue 80 HIS Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 93 VAL 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 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 130 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 98 optimal weight: 0.0980 chunk 137 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS F 79 GLN F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.166742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112686 restraints weight = 16887.021| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.19 r_work: 0.3043 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13798 Z= 0.170 Angle : 0.645 13.890 18638 Z= 0.344 Chirality : 0.045 0.218 1916 Planarity : 0.004 0.034 2510 Dihedral : 4.454 24.027 1788 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.84 % Allowed : 19.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1650 helix: 1.63 (0.23), residues: 518 sheet: 0.71 (0.30), residues: 324 loop : -1.23 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 126 HIS 0.006 0.001 HIS D 55 PHE 0.016 0.001 PHE F 52 TYR 0.020 0.002 TYR F 289 ARG 0.006 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 649) hydrogen bonds : angle 4.30556 ( 1857) SS BOND : bond 0.00168 ( 4) SS BOND : angle 2.66331 ( 8) covalent geometry : bond 0.00397 (13794) covalent geometry : angle 0.64238 (18630) *********************** 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 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 1.428 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: 0.8279 (t0) cc_final: 0.7941 (t0) REVERT: A 226 ASP cc_start: 0.9030 (t70) cc_final: 0.8766 (t70) REVERT: A 354 MET cc_start: 0.8315 (tpp) cc_final: 0.7736 (ttm) REVERT: B 215 MET cc_start: 0.8721 (mtp) cc_final: 0.8411 (mtp) REVERT: B 223 ASP cc_start: 0.8489 (t0) cc_final: 0.7937 (t0) REVERT: B 226 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: B 354 MET cc_start: 0.8346 (ttm) cc_final: 0.8041 (tmm) REVERT: C 48 ASP cc_start: 0.7803 (t0) cc_final: 0.7197 (m-30) REVERT: C 73 GLN cc_start: 0.8473 (tt0) cc_final: 0.8027 (pp30) REVERT: C 132 ASN cc_start: 0.8800 (t0) cc_final: 0.8381 (t0) REVERT: D 53 MET cc_start: 0.8934 (mmm) cc_final: 0.8547 (mmm) REVERT: D 128 ASP cc_start: 0.8192 (m-30) cc_final: 0.7990 (t0) REVERT: E 218 ASN cc_start: 0.8312 (t0) cc_final: 0.7976 (t0) REVERT: E 226 ASP cc_start: 0.9011 (t70) cc_final: 0.8748 (t70) REVERT: E 352 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7761 (tt) REVERT: E 354 MET cc_start: 0.8317 (tpp) cc_final: 0.7741 (ttm) REVERT: F 215 MET cc_start: 0.8689 (mtp) cc_final: 0.8375 (mtp) REVERT: F 223 ASP cc_start: 0.8486 (t0) cc_final: 0.7938 (t0) REVERT: F 226 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: F 343 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8124 (mp) REVERT: F 354 MET cc_start: 0.8360 (ttm) cc_final: 0.8068 (tmm) REVERT: G 41 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7034 (tt) REVERT: G 71 GLU cc_start: 0.8847 (tp30) cc_final: 0.8413 (tp30) REVERT: G 73 GLN cc_start: 0.8460 (tt0) cc_final: 0.7987 (pp30) REVERT: G 132 ASN cc_start: 0.8899 (t0) cc_final: 0.8380 (t0) outliers start: 41 outliers final: 29 residues processed: 248 average time/residue: 0.2792 time to fit residues: 103.7657 Evaluate side-chains 237 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 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 326 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain G 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 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 147 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS F 79 GLN F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.168400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113499 restraints weight = 16914.050| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.18 r_work: 0.3061 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13798 Z= 0.125 Angle : 0.641 13.968 18638 Z= 0.345 Chirality : 0.045 0.251 1916 Planarity : 0.003 0.033 2510 Dihedral : 4.334 23.060 1788 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.56 % Allowed : 19.71 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1650 helix: 1.63 (0.23), residues: 518 sheet: 0.83 (0.30), residues: 324 loop : -1.18 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 126 HIS 0.006 0.001 HIS D 55 PHE 0.013 0.001 PHE H 141 TYR 0.021 0.001 TYR B 48 ARG 0.003 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 649) hydrogen bonds : angle 4.26976 ( 1857) SS BOND : bond 0.00213 ( 4) SS BOND : angle 2.46111 ( 8) covalent geometry : bond 0.00278 (13794) covalent geometry : angle 0.63861 (18630) ********************** 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 256 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 219 time to evaluate : 1.410 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: A 218 ASN cc_start: 0.8195 (t0) cc_final: 0.7844 (t0) REVERT: A 226 ASP cc_start: 0.8975 (t70) cc_final: 0.8701 (t70) REVERT: A 354 MET cc_start: 0.8304 (tpp) cc_final: 0.7691 (ttm) REVERT: B 215 MET cc_start: 0.8712 (mtp) cc_final: 0.8402 (mtp) REVERT: B 223 ASP cc_start: 0.8479 (t0) cc_final: 0.7896 (t0) REVERT: B 226 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: B 354 MET cc_start: 0.8334 (ttm) cc_final: 0.8031 (tmm) REVERT: C 48 ASP cc_start: 0.7753 (t0) cc_final: 0.7252 (m-30) REVERT: C 73 GLN cc_start: 0.8405 (tt0) cc_final: 0.7969 (pp30) REVERT: C 132 ASN cc_start: 0.8782 (t0) cc_final: 0.8392 (t0) REVERT: D 53 MET cc_start: 0.8889 (mmm) cc_final: 0.8594 (mmm) REVERT: D 128 ASP cc_start: 0.8187 (m-30) cc_final: 0.7965 (t0) REVERT: E 218 ASN cc_start: 0.8203 (t0) cc_final: 0.7869 (t0) REVERT: E 226 ASP cc_start: 0.8945 (t70) cc_final: 0.8674 (t70) REVERT: E 352 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7710 (tt) REVERT: E 354 MET cc_start: 0.8277 (tpp) cc_final: 0.7655 (ttm) REVERT: F 215 MET cc_start: 0.8676 (mtp) cc_final: 0.8367 (mtp) REVERT: F 223 ASP cc_start: 0.8451 (t0) cc_final: 0.7839 (t0) REVERT: F 226 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: F 289 TYR cc_start: 0.8042 (m-80) cc_final: 0.7810 (m-10) REVERT: F 354 MET cc_start: 0.8343 (ttm) cc_final: 0.8118 (tmm) REVERT: G 41 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7108 (tt) REVERT: G 71 GLU cc_start: 0.8860 (tp30) cc_final: 0.8251 (tm-30) REVERT: G 73 GLN cc_start: 0.8436 (tt0) cc_final: 0.7956 (pp30) REVERT: G 132 ASN cc_start: 0.8863 (t0) cc_final: 0.8329 (t0) REVERT: H 48 ASP cc_start: 0.8064 (m-30) cc_final: 0.7431 (t70) REVERT: H 56 LEU cc_start: 0.9465 (tp) cc_final: 0.9193 (pp) REVERT: H 122 ASP cc_start: 0.8392 (m-30) cc_final: 0.7992 (m-30) REVERT: H 128 ASP cc_start: 0.8322 (t0) cc_final: 0.8003 (t0) outliers start: 37 outliers final: 26 residues processed: 247 average time/residue: 0.2337 time to fit residues: 86.4376 Evaluate side-chains 241 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ARG 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 326 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 55 HIS Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 226 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 80 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 173 GLN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS F 173 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.168534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111492 restraints weight = 16989.881| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.36 r_work: 0.3060 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13798 Z= 0.138 Angle : 0.671 17.365 18638 Z= 0.358 Chirality : 0.045 0.255 1916 Planarity : 0.003 0.033 2510 Dihedral : 4.350 22.894 1788 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.77 % Allowed : 20.19 % Favored : 77.04 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1650 helix: 1.65 (0.23), residues: 518 sheet: 0.84 (0.30), residues: 324 loop : -1.15 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 126 HIS 0.005 0.001 HIS D 55 PHE 0.013 0.001 PHE H 141 TYR 0.028 0.002 TYR B 48 ARG 0.006 0.000 ARG F 350 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 649) hydrogen bonds : angle 4.30300 ( 1857) SS BOND : bond 0.00218 ( 4) SS BOND : angle 2.45820 ( 8) covalent geometry : bond 0.00314 (13794) covalent geometry : angle 0.66876 (18630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8345.45 seconds wall clock time: 148 minutes 15.80 seconds (8895.80 seconds total)