Starting phenix.real_space_refine on Tue Jun 17 07:57:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sxh_40852/06_2025/8sxh_40852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sxh_40852/06_2025/8sxh_40852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sxh_40852/06_2025/8sxh_40852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sxh_40852/06_2025/8sxh_40852.map" model { file = "/net/cci-nas-00/data/ceres_data/8sxh_40852/06_2025/8sxh_40852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sxh_40852/06_2025/8sxh_40852.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 12327 2.51 5 N 3468 2.21 5 O 3894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19719 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2706 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "B" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2988 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 22, 'TRANS': 376} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 844 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2706 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "F" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2988 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 22, 'TRANS': 376} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 844 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2706 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2988 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 22, 'TRANS': 376} Chain: "K" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 844 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 12.96, per 1000 atoms: 0.66 Number of scatterers: 19719 At special positions: 0 Unit cell: (197.478, 192.51, 89.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 3894 8.00 N 3468 7.00 C 12327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 2.5 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4752 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 30 sheets defined 41.4% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 42 through 60 removed outlier: 3.670A pdb=" N LEU A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.736A pdb=" N ASP A 339 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 340 " --> pdb=" O ASN A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 340' Processing helix chain 'A' and resid 417 through 434 removed outlier: 3.806A pdb=" N ARG A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.653A pdb=" N LEU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.794A pdb=" N GLU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 214 through 230 removed outlier: 5.309A pdb=" N VAL B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.697A pdb=" N ALA B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.591A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 417 removed outlier: 3.944A pdb=" N SER B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 417' Processing helix chain 'B' and resid 417 through 435 Processing helix chain 'C' and resid 49 through 65 Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.559A pdb=" N ALA C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 99 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 118 through 133 Processing helix chain 'C' and resid 135 through 148 Processing helix chain 'E' and resid 42 through 60 removed outlier: 3.646A pdb=" N ALA E 58 " --> pdb=" O ASP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 80 Processing helix chain 'E' and resid 91 through 101 Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 152 through 161 Processing helix chain 'E' and resid 214 through 230 Processing helix chain 'E' and resid 248 through 260 Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'E' and resid 336 through 340 removed outlier: 3.727A pdb=" N ASP E 339 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG E 340 " --> pdb=" O ASN E 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 336 through 340' Processing helix chain 'E' and resid 417 through 434 removed outlier: 3.833A pdb=" N ARG E 434 " --> pdb=" O LEU E 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 60 removed outlier: 3.807A pdb=" N LEU F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 82 Processing helix chain 'F' and resid 89 through 98 removed outlier: 3.826A pdb=" N GLU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 152 through 161 Processing helix chain 'F' and resid 214 through 230 removed outlier: 5.228A pdb=" N VAL F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 260 removed outlier: 3.718A pdb=" N ALA F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.732A pdb=" N ILE F 306 " --> pdb=" O ALA F 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 417 removed outlier: 3.886A pdb=" N SER F 416 " --> pdb=" O ARG F 412 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP F 417 " --> pdb=" O PRO F 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 412 through 417' Processing helix chain 'F' and resid 417 through 435 Processing helix chain 'G' and resid 49 through 65 Processing helix chain 'G' and resid 67 through 83 removed outlier: 3.615A pdb=" N ALA G 71 " --> pdb=" O ARG G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 118 through 133 Processing helix chain 'G' and resid 135 through 148 Processing helix chain 'I' and resid 42 through 60 removed outlier: 3.544A pdb=" N LEU I 46 " --> pdb=" O PRO I 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA I 58 " --> pdb=" O ASP I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 80 Processing helix chain 'I' and resid 91 through 101 Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 152 through 161 Processing helix chain 'I' and resid 214 through 230 Processing helix chain 'I' and resid 248 through 260 Processing helix chain 'I' and resid 272 through 276 Processing helix chain 'I' and resid 302 through 314 removed outlier: 3.507A pdb=" N GLN I 314 " --> pdb=" O ALA I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 340 removed outlier: 3.744A pdb=" N ASP I 339 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG I 340 " --> pdb=" O ASN I 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 336 through 340' Processing helix chain 'I' and resid 417 through 434 removed outlier: 3.797A pdb=" N ARG I 434 " --> pdb=" O LEU I 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 60 removed outlier: 3.682A pdb=" N LEU J 46 " --> pdb=" O PRO J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 82 Processing helix chain 'J' and resid 89 through 98 Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 152 through 161 Processing helix chain 'J' and resid 214 through 230 removed outlier: 5.350A pdb=" N VAL J 220 " --> pdb=" O GLY J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 260 removed outlier: 3.665A pdb=" N ALA J 252 " --> pdb=" O VAL J 248 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE J 259 " --> pdb=" O VAL J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 314 removed outlier: 3.628A pdb=" N ILE J 306 " --> pdb=" O ALA J 302 " (cutoff:3.500A) Processing helix chain 'J' and resid 412 through 417 removed outlier: 3.960A pdb=" N SER J 416 " --> pdb=" O ARG J 412 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP J 417 " --> pdb=" O PRO J 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 412 through 417' Processing helix chain 'J' and resid 417 through 435 Processing helix chain 'K' and resid 49 through 65 Processing helix chain 'K' and resid 67 through 83 removed outlier: 3.549A pdb=" N ALA K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 99 Processing helix chain 'K' and resid 101 through 115 Processing helix chain 'K' and resid 118 through 133 Processing helix chain 'K' and resid 135 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 106 removed outlier: 3.684A pdb=" N PHE A 104 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 187 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 114 removed outlier: 7.991A pdb=" N GLU A 110 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 147 removed outlier: 5.361A pdb=" N ILE A 140 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 173 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 196 removed outlier: 6.973A pdb=" N LEU A 292 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET A 320 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 294 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280 removed outlier: 3.572A pdb=" N LEU A 277 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS A 343 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU A 334 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N THR A 345 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 332 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 374 Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 88 removed outlier: 5.645A pdb=" N LYS B 343 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU B 334 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N THR B 345 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR B 332 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 6.599A pdb=" N THR B 171 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE B 143 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 169 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 200 removed outlier: 5.429A pdb=" N SER B 196 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ARG B 207 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL B 198 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR B 205 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 204 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASP B 240 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B 206 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 237 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU B 295 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU B 239 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 372 through 375 Processing sheet with id=AB3, first strand: chain 'E' and resid 104 through 106 removed outlier: 3.742A pdb=" N PHE E 104 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA E 187 " --> pdb=" O GLY E 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 109 through 114 removed outlier: 8.032A pdb=" N GLU E 110 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL E 121 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 147 removed outlier: 5.311A pdb=" N ILE E 140 " --> pdb=" O VAL E 173 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 173 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 194 through 196 removed outlier: 6.930A pdb=" N LEU E 292 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N MET E 320 " --> pdb=" O LEU E 292 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL E 294 " --> pdb=" O MET E 320 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 277 through 280 removed outlier: 3.509A pdb=" N LEU E 277 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 266 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR E 267 " --> pdb=" O TYR E 350 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYS E 343 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU E 334 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR E 345 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR E 332 " --> pdb=" O THR E 345 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 86 through 88 removed outlier: 5.647A pdb=" N LYS F 343 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU F 334 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N THR F 345 " --> pdb=" O THR F 332 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR F 332 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 109 through 111 Processing sheet with id=AC1, first strand: chain 'F' and resid 146 through 147 removed outlier: 6.597A pdb=" N THR F 171 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE F 143 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR F 169 " --> pdb=" O ILE F 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 194 through 200 removed outlier: 5.481A pdb=" N SER F 196 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG F 207 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL F 198 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR F 205 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA F 204 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP F 240 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU F 206 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU F 237 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU F 295 " --> pdb=" O LEU F 237 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU F 239 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 372 through 375 Processing sheet with id=AC4, first strand: chain 'I' and resid 104 through 106 removed outlier: 3.713A pdb=" N PHE I 104 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA I 187 " --> pdb=" O GLY I 106 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 109 through 114 removed outlier: 7.893A pdb=" N GLU I 110 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 146 through 147 removed outlier: 5.342A pdb=" N ILE I 140 " --> pdb=" O VAL I 173 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL I 173 " --> pdb=" O ILE I 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 194 through 196 Processing sheet with id=AC8, first strand: chain 'I' and resid 277 through 280 removed outlier: 3.502A pdb=" N LEU I 277 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL I 266 " --> pdb=" O PHE I 279 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR I 267 " --> pdb=" O TYR I 350 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N THR I 345 " --> pdb=" O THR I 332 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR I 332 " --> pdb=" O THR I 345 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 86 through 88 removed outlier: 5.588A pdb=" N LYS J 343 " --> pdb=" O LEU J 334 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU J 334 " --> pdb=" O LYS J 343 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N THR J 345 " --> pdb=" O THR J 332 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR J 332 " --> pdb=" O THR J 345 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 109 through 111 Processing sheet with id=AD2, first strand: chain 'J' and resid 146 through 147 removed outlier: 6.618A pdb=" N THR J 171 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE J 143 " --> pdb=" O THR J 169 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR J 169 " --> pdb=" O ILE J 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 194 through 200 removed outlier: 5.517A pdb=" N SER J 196 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG J 207 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL J 198 " --> pdb=" O TYR J 205 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR J 205 " --> pdb=" O VAL J 198 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA J 204 " --> pdb=" O VAL J 238 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP J 240 " --> pdb=" O ALA J 204 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU J 206 " --> pdb=" O ASP J 240 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU J 237 " --> pdb=" O VAL J 293 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU J 295 " --> pdb=" O LEU J 237 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU J 239 " --> pdb=" O LEU J 295 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2583 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: 6.40 Time building geometry restraints manager: 5.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6821 1.34 - 1.46: 3011 1.46 - 1.57: 10091 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 19983 Sorted by residual: bond pdb=" C GLU E 200 " pdb=" N PRO E 201 " ideal model delta sigma weight residual 1.330 1.340 -0.010 1.19e-02 7.06e+03 7.26e-01 bond pdb=" C VAL J 61 " pdb=" N GLU J 62 " ideal model delta sigma weight residual 1.339 1.293 0.046 5.57e-02 3.22e+02 6.97e-01 bond pdb=" N VAL I 333 " pdb=" CA VAL I 333 " ideal model delta sigma weight residual 1.474 1.463 0.011 1.57e-02 4.06e+03 5.11e-01 bond pdb=" N VAL A 333 " pdb=" CA VAL A 333 " ideal model delta sigma weight residual 1.474 1.463 0.011 1.57e-02 4.06e+03 5.04e-01 bond pdb=" CA THR A 345 " pdb=" C THR A 345 " ideal model delta sigma weight residual 1.526 1.519 0.008 1.15e-02 7.56e+03 4.63e-01 ... (remaining 19978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 25477 0.81 - 1.62: 1253 1.62 - 2.43: 142 2.43 - 3.24: 79 3.24 - 4.05: 85 Bond angle restraints: 27036 Sorted by residual: angle pdb=" N LEU E 292 " pdb=" CA LEU E 292 " pdb=" C LEU E 292 " ideal model delta sigma weight residual 108.26 110.87 -2.61 1.66e+00 3.63e-01 2.48e+00 angle pdb=" N VAL F 219 " pdb=" CA VAL F 219 " pdb=" C VAL F 219 " ideal model delta sigma weight residual 110.36 108.80 1.56 1.05e+00 9.07e-01 2.22e+00 angle pdb=" N VAL F 293 " pdb=" CA VAL F 293 " pdb=" C VAL F 293 " ideal model delta sigma weight residual 109.34 106.26 3.08 2.08e+00 2.31e-01 2.20e+00 angle pdb=" N ALA J 301 " pdb=" CA ALA J 301 " pdb=" C ALA J 301 " ideal model delta sigma weight residual 111.96 114.03 -2.07 1.41e+00 5.03e-01 2.16e+00 angle pdb=" C MET I 77 " pdb=" N LEU I 78 " pdb=" CA LEU I 78 " ideal model delta sigma weight residual 121.81 119.20 2.61 1.83e+00 2.99e-01 2.03e+00 ... (remaining 27031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 11146 17.37 - 34.74: 890 34.74 - 52.10: 203 52.10 - 69.47: 28 69.47 - 86.84: 24 Dihedral angle restraints: 12291 sinusoidal: 4863 harmonic: 7428 Sorted by residual: dihedral pdb=" CA ASP J 323 " pdb=" CB ASP J 323 " pdb=" CG ASP J 323 " pdb=" OD1 ASP J 323 " ideal model delta sinusoidal sigma weight residual -30.00 -89.40 59.40 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP F 323 " pdb=" CB ASP F 323 " pdb=" CG ASP F 323 " pdb=" OD1 ASP F 323 " ideal model delta sinusoidal sigma weight residual -30.00 -88.95 58.95 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP B 323 " pdb=" CB ASP B 323 " pdb=" CG ASP B 323 " pdb=" OD1 ASP B 323 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 12288 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1917 0.027 - 0.053: 789 0.053 - 0.080: 167 0.080 - 0.106: 153 0.106 - 0.133: 94 Chirality restraints: 3120 Sorted by residual: chirality pdb=" CA VAL F 173 " pdb=" N VAL F 173 " pdb=" C VAL F 173 " pdb=" CB VAL F 173 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE J 366 " pdb=" N ILE J 366 " pdb=" C ILE J 366 " pdb=" CB ILE J 366 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL J 173 " pdb=" N VAL J 173 " pdb=" C VAL J 173 " pdb=" CB VAL J 173 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 3117 not shown) Planarity restraints: 3597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 285 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO E 286 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 286 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 286 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 285 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO I 286 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 286 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 286 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 285 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 286 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.017 5.00e-02 4.00e+02 ... (remaining 3594 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 252 2.58 - 3.16: 18038 3.16 - 3.74: 30550 3.74 - 4.32: 39952 4.32 - 4.90: 66953 Nonbonded interactions: 155745 Sorted by model distance: nonbonded pdb=" OD2 ASP A 285 " pdb=" OG SER A 287 " model vdw 1.996 3.040 nonbonded pdb=" OG1 THR B 332 " pdb=" OG1 THR B 346 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR J 332 " pdb=" OG1 THR J 346 " model vdw 2.055 3.040 nonbonded pdb=" OG1 THR F 332 " pdb=" OG1 THR F 346 " model vdw 2.093 3.040 nonbonded pdb=" OG1 THR A 332 " pdb=" OG1 THR A 346 " model vdw 2.111 3.040 ... (remaining 155740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 38 through 375 or resid 414 through 436)) selection = chain 'E' selection = (chain 'F' and (resid 38 through 375 or resid 414 through 436)) selection = chain 'I' selection = (chain 'J' and (resid 38 through 375 or resid 414 through 436)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.910 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 45.690 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 0.046 19983 Z= 0.117 Angle : 0.457 4.047 27036 Z= 0.235 Chirality : 0.039 0.133 3120 Planarity : 0.003 0.033 3597 Dihedral : 13.702 86.839 7539 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2580 helix: 2.19 (0.17), residues: 978 sheet: -0.18 (0.25), residues: 438 loop : -0.09 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 111 HIS 0.001 0.001 HIS B 84 PHE 0.006 0.001 PHE B 211 TYR 0.010 0.001 TYR A 87 ARG 0.002 0.000 ARG E 55 Details of bonding type rmsd hydrogen bonds : bond 0.16381 ( 903) hydrogen bonds : angle 5.52998 ( 2583) covalent geometry : bond 0.00257 (19983) covalent geometry : angle 0.45747 (27036) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 2.153 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 292 LEU cc_start: 0.8984 (tt) cc_final: 0.8584 (tt) REVERT: B 175 ASP cc_start: 0.6566 (t0) cc_final: 0.6299 (t0) REVERT: C 139 MET cc_start: 0.7643 (mtm) cc_final: 0.7361 (mtp) REVERT: F 175 ASP cc_start: 0.6899 (t0) cc_final: 0.6522 (t0) REVERT: F 391 HIS cc_start: 0.8563 (p-80) cc_final: 0.8272 (p-80) REVERT: G 66 ASN cc_start: 0.8090 (t0) cc_final: 0.7744 (t0) REVERT: G 93 ARG cc_start: 0.8561 (mmt90) cc_final: 0.8153 (mmt90) REVERT: J 153 MET cc_start: 0.7590 (tmm) cc_final: 0.7190 (tmm) REVERT: K 137 GLU cc_start: 0.8161 (pm20) cc_final: 0.7954 (pm20) REVERT: K 145 VAL cc_start: 0.8003 (t) cc_final: 0.7784 (t) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3461 time to fit residues: 141.9023 Evaluate side-chains 183 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 199 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 121 optimal weight: 0.0270 chunk 148 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 394 ASN E 225 GLN E 360 GLN F 151 GLN F 394 ASN I 360 GLN J 394 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.154471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.124841 restraints weight = 35151.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122985 restraints weight = 42179.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124497 restraints weight = 40621.725| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19983 Z= 0.125 Angle : 0.546 7.089 27036 Z= 0.282 Chirality : 0.041 0.138 3120 Planarity : 0.004 0.037 3597 Dihedral : 3.853 16.989 2823 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.76 % Allowed : 8.45 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2580 helix: 1.95 (0.16), residues: 1011 sheet: -0.03 (0.26), residues: 414 loop : 0.16 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP G 111 HIS 0.006 0.001 HIS J 391 PHE 0.028 0.001 PHE B 180 TYR 0.018 0.001 TYR K 141 ARG 0.004 0.000 ARG J 401 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 903) hydrogen bonds : angle 4.22094 ( 2583) covalent geometry : bond 0.00285 (19983) covalent geometry : angle 0.54622 (27036) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 2.159 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: B 160 MET cc_start: 0.8834 (tpp) cc_final: 0.8610 (tpp) REVERT: B 175 ASP cc_start: 0.6617 (t0) cc_final: 0.6340 (t0) REVERT: B 274 ASN cc_start: 0.7015 (p0) cc_final: 0.6814 (p0) REVERT: B 391 HIS cc_start: 0.8644 (p-80) cc_final: 0.8056 (p-80) REVERT: C 83 ARG cc_start: 0.7340 (ptt180) cc_final: 0.6804 (tmm-80) REVERT: F 175 ASP cc_start: 0.7018 (t0) cc_final: 0.6698 (t0) REVERT: F 391 HIS cc_start: 0.8728 (p-80) cc_final: 0.8320 (p-80) REVERT: F 432 VAL cc_start: 0.9014 (t) cc_final: 0.8809 (t) REVERT: G 93 ARG cc_start: 0.8335 (mmt90) cc_final: 0.8130 (mmt90) REVERT: I 226 LEU cc_start: 0.8449 (tp) cc_final: 0.8165 (tt) REVERT: I 292 LEU cc_start: 0.8989 (tt) cc_final: 0.8581 (tt) REVERT: J 153 MET cc_start: 0.7505 (tmm) cc_final: 0.7062 (tmm) outliers start: 16 outliers final: 11 residues processed: 218 average time/residue: 0.3459 time to fit residues: 113.4139 Evaluate side-chains 186 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 134 optimal weight: 0.0770 chunk 234 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 360 GLN B 297 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN ** I 419 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 = 0.3994 r_free = 0.3994 target = 0.148034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.112829 restraints weight = 37023.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111846 restraints weight = 32068.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113782 restraints weight = 31740.725| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19983 Z= 0.116 Angle : 0.528 8.161 27036 Z= 0.271 Chirality : 0.041 0.186 3120 Planarity : 0.004 0.036 3597 Dihedral : 3.836 17.991 2823 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.10 % Allowed : 11.60 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.17), residues: 2580 helix: 1.84 (0.16), residues: 1011 sheet: 0.06 (0.26), residues: 384 loop : 0.06 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 111 HIS 0.006 0.001 HIS J 391 PHE 0.018 0.001 PHE B 180 TYR 0.030 0.001 TYR K 141 ARG 0.006 0.000 ARG G 134 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 903) hydrogen bonds : angle 4.00756 ( 2583) covalent geometry : bond 0.00263 (19983) covalent geometry : angle 0.52824 (27036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8464 (tt) REVERT: B 160 MET cc_start: 0.8927 (tpp) cc_final: 0.8560 (tpp) REVERT: B 175 ASP cc_start: 0.7083 (t0) cc_final: 0.6789 (t0) REVERT: B 184 LEU cc_start: 0.8939 (mm) cc_final: 0.8728 (mt) REVERT: B 391 HIS cc_start: 0.8740 (p-80) cc_final: 0.8121 (p-80) REVERT: C 83 ARG cc_start: 0.8086 (ptt180) cc_final: 0.7167 (tmm-80) REVERT: F 175 ASP cc_start: 0.7441 (t0) cc_final: 0.7088 (t0) REVERT: F 184 LEU cc_start: 0.8589 (mm) cc_final: 0.8376 (mt) REVERT: F 391 HIS cc_start: 0.8722 (p-80) cc_final: 0.8340 (p-80) REVERT: G 92 PHE cc_start: 0.7918 (t80) cc_final: 0.7431 (t80) REVERT: G 93 ARG cc_start: 0.8725 (mmt90) cc_final: 0.8370 (mmt90) REVERT: G 96 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8778 (mt-10) REVERT: J 153 MET cc_start: 0.7522 (tmm) cc_final: 0.6984 (tmm) REVERT: J 375 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7581 (tm-30) REVERT: K 137 GLU cc_start: 0.7963 (pm20) cc_final: 0.7682 (pm20) outliers start: 23 outliers final: 15 residues processed: 206 average time/residue: 0.3424 time to fit residues: 106.3053 Evaluate side-chains 193 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 213 optimal weight: 0.0470 chunk 29 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 230 optimal weight: 0.9980 chunk 187 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN F 297 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.148101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113249 restraints weight = 37264.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112818 restraints weight = 30944.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.113951 restraints weight = 30176.627| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19983 Z= 0.114 Angle : 0.529 9.963 27036 Z= 0.269 Chirality : 0.041 0.239 3120 Planarity : 0.004 0.114 3597 Dihedral : 3.818 17.862 2823 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.43 % Allowed : 13.85 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2580 helix: 1.84 (0.16), residues: 1005 sheet: 0.04 (0.26), residues: 384 loop : 0.03 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 111 HIS 0.002 0.000 HIS J 391 PHE 0.020 0.001 PHE J 180 TYR 0.032 0.001 TYR K 141 ARG 0.011 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 903) hydrogen bonds : angle 3.90805 ( 2583) covalent geometry : bond 0.00262 (19983) covalent geometry : angle 0.52925 (27036) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.6854 (tp30) cc_final: 0.6587 (tp30) REVERT: B 43 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8533 (tt) REVERT: B 69 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8278 (mm) REVERT: B 160 MET cc_start: 0.8939 (tpp) cc_final: 0.8533 (tpp) REVERT: B 175 ASP cc_start: 0.7221 (t0) cc_final: 0.6938 (t0) REVERT: B 184 LEU cc_start: 0.8967 (mm) cc_final: 0.8707 (mt) REVERT: B 391 HIS cc_start: 0.8732 (p-80) cc_final: 0.8026 (p-80) REVERT: C 83 ARG cc_start: 0.8020 (ptt180) cc_final: 0.7132 (tmm-80) REVERT: F 175 ASP cc_start: 0.7453 (t0) cc_final: 0.7194 (t0) REVERT: F 184 LEU cc_start: 0.8629 (mm) cc_final: 0.8355 (mt) REVERT: F 391 HIS cc_start: 0.8737 (p-80) cc_final: 0.8373 (p-80) REVERT: G 92 PHE cc_start: 0.7744 (t80) cc_final: 0.7259 (t80) REVERT: J 153 MET cc_start: 0.7529 (tmm) cc_final: 0.6979 (tmm) REVERT: J 375 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7530 (tm-30) outliers start: 30 outliers final: 15 residues processed: 212 average time/residue: 0.3373 time to fit residues: 109.1027 Evaluate side-chains 192 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 246 optimal weight: 0.7980 chunk 63 optimal weight: 0.0870 chunk 200 optimal weight: 0.9990 chunk 230 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 213 optimal weight: 0.0870 chunk 252 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.149077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114721 restraints weight = 37117.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114286 restraints weight = 30551.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115471 restraints weight = 29257.665| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19983 Z= 0.103 Angle : 0.518 9.396 27036 Z= 0.264 Chirality : 0.041 0.237 3120 Planarity : 0.004 0.037 3597 Dihedral : 3.729 17.603 2823 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.29 % Allowed : 15.71 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.17), residues: 2580 helix: 1.89 (0.16), residues: 1002 sheet: 0.07 (0.26), residues: 384 loop : -0.02 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP K 111 HIS 0.004 0.001 HIS A 84 PHE 0.016 0.001 PHE G 92 TYR 0.032 0.001 TYR K 141 ARG 0.006 0.000 ARG C 123 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 903) hydrogen bonds : angle 3.83604 ( 2583) covalent geometry : bond 0.00230 (19983) covalent geometry : angle 0.51762 (27036) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.8943 (tpp) cc_final: 0.8523 (tpp) REVERT: B 175 ASP cc_start: 0.7242 (t0) cc_final: 0.6964 (t0) REVERT: B 184 LEU cc_start: 0.8954 (mm) cc_final: 0.8677 (mt) REVERT: B 391 HIS cc_start: 0.8631 (p-80) cc_final: 0.7956 (p-80) REVERT: C 83 ARG cc_start: 0.8028 (ptt180) cc_final: 0.7162 (tmm-80) REVERT: C 123 ARG cc_start: 0.7396 (mmp-170) cc_final: 0.7030 (mmp-170) REVERT: F 69 LEU cc_start: 0.8449 (mm) cc_final: 0.8203 (tp) REVERT: F 175 ASP cc_start: 0.7409 (t0) cc_final: 0.7151 (t0) REVERT: F 184 LEU cc_start: 0.8631 (mm) cc_final: 0.8342 (mt) REVERT: F 391 HIS cc_start: 0.8688 (p-80) cc_final: 0.8401 (p-80) REVERT: G 92 PHE cc_start: 0.7721 (t80) cc_final: 0.7506 (t80) REVERT: I 92 ASP cc_start: 0.7687 (m-30) cc_final: 0.7304 (t0) REVERT: J 153 MET cc_start: 0.7545 (tmm) cc_final: 0.6821 (tmm) REVERT: J 375 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7480 (tm-30) REVERT: K 94 ILE cc_start: 0.9255 (tt) cc_final: 0.8735 (mm) outliers start: 27 outliers final: 19 residues processed: 216 average time/residue: 0.3273 time to fit residues: 107.5156 Evaluate side-chains 195 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 39 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 128 optimal weight: 0.0030 chunk 136 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.146800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111802 restraints weight = 37212.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110501 restraints weight = 32260.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112220 restraints weight = 33687.326| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19983 Z= 0.142 Angle : 0.562 10.212 27036 Z= 0.283 Chirality : 0.042 0.269 3120 Planarity : 0.004 0.039 3597 Dihedral : 3.877 17.761 2823 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.67 % Allowed : 16.76 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.16), residues: 2580 helix: 1.76 (0.16), residues: 1005 sheet: 0.01 (0.26), residues: 384 loop : -0.02 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP K 111 HIS 0.002 0.001 HIS J 391 PHE 0.017 0.001 PHE J 180 TYR 0.037 0.002 TYR K 141 ARG 0.010 0.000 ARG C 134 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 903) hydrogen bonds : angle 3.95904 ( 2583) covalent geometry : bond 0.00335 (19983) covalent geometry : angle 0.56218 (27036) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8583 (tt) REVERT: B 175 ASP cc_start: 0.7317 (t0) cc_final: 0.7047 (t0) REVERT: B 184 LEU cc_start: 0.8973 (mm) cc_final: 0.8698 (mt) REVERT: B 391 HIS cc_start: 0.8756 (p-80) cc_final: 0.8102 (p-80) REVERT: C 83 ARG cc_start: 0.8131 (ptt180) cc_final: 0.7249 (tmm-80) REVERT: C 134 ARG cc_start: 0.8868 (mpp-170) cc_final: 0.8400 (mpp-170) REVERT: E 95 GLU cc_start: 0.8564 (pp20) cc_final: 0.8311 (pp20) REVERT: F 175 ASP cc_start: 0.7435 (t0) cc_final: 0.7171 (t0) REVERT: F 184 LEU cc_start: 0.8675 (mm) cc_final: 0.8383 (mt) REVERT: F 391 HIS cc_start: 0.8780 (p-80) cc_final: 0.8452 (p-80) REVERT: J 153 MET cc_start: 0.7543 (tmm) cc_final: 0.6762 (tmm) REVERT: J 375 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7461 (tm-30) outliers start: 35 outliers final: 27 residues processed: 215 average time/residue: 0.3301 time to fit residues: 108.6007 Evaluate side-chains 199 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 62 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 173 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 192 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN E 360 GLN ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 360 GLN ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.147093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111955 restraints weight = 37478.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110756 restraints weight = 31927.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112013 restraints weight = 32690.469| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19983 Z= 0.126 Angle : 0.563 10.592 27036 Z= 0.285 Chirality : 0.042 0.274 3120 Planarity : 0.004 0.039 3597 Dihedral : 3.884 16.831 2823 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.81 % Allowed : 17.53 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.16), residues: 2580 helix: 1.70 (0.16), residues: 1005 sheet: 0.00 (0.26), residues: 384 loop : -0.04 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP K 111 HIS 0.002 0.000 HIS J 391 PHE 0.049 0.001 PHE G 92 TYR 0.037 0.001 TYR K 141 ARG 0.007 0.000 ARG J 401 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 903) hydrogen bonds : angle 3.96736 ( 2583) covalent geometry : bond 0.00295 (19983) covalent geometry : angle 0.56319 (27036) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8569 (tt) REVERT: B 175 ASP cc_start: 0.7359 (t0) cc_final: 0.7090 (t0) REVERT: B 184 LEU cc_start: 0.8968 (mm) cc_final: 0.8684 (mt) REVERT: B 391 HIS cc_start: 0.8762 (p-80) cc_final: 0.8104 (p-80) REVERT: C 83 ARG cc_start: 0.8116 (ptt180) cc_final: 0.7243 (tmm-80) REVERT: C 134 ARG cc_start: 0.8905 (mpp-170) cc_final: 0.8281 (mpp-170) REVERT: F 175 ASP cc_start: 0.7413 (t0) cc_final: 0.7134 (t0) REVERT: F 184 LEU cc_start: 0.8697 (mm) cc_final: 0.8406 (mt) REVERT: F 391 HIS cc_start: 0.8753 (p-80) cc_final: 0.8373 (p-80) REVERT: I 95 GLU cc_start: 0.8564 (pp20) cc_final: 0.7752 (pt0) REVERT: I 98 GLU cc_start: 0.6831 (tp30) cc_final: 0.6494 (tp30) REVERT: J 153 MET cc_start: 0.7540 (tmm) cc_final: 0.6979 (tmm) REVERT: J 375 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7439 (tm-30) outliers start: 38 outliers final: 31 residues processed: 214 average time/residue: 0.3440 time to fit residues: 111.5609 Evaluate side-chains 201 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 224 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 156 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN I 360 GLN ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.147861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112761 restraints weight = 37233.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.111718 restraints weight = 30851.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113070 restraints weight = 31376.580| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19983 Z= 0.113 Angle : 0.562 11.156 27036 Z= 0.285 Chirality : 0.042 0.283 3120 Planarity : 0.004 0.039 3597 Dihedral : 3.842 15.685 2823 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.58 % Allowed : 17.72 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.16), residues: 2580 helix: 1.70 (0.16), residues: 1005 sheet: 0.03 (0.26), residues: 384 loop : -0.07 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 111 HIS 0.002 0.000 HIS J 391 PHE 0.031 0.001 PHE G 92 TYR 0.039 0.001 TYR K 141 ARG 0.007 0.000 ARG F 401 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 903) hydrogen bonds : angle 3.95506 ( 2583) covalent geometry : bond 0.00260 (19983) covalent geometry : angle 0.56180 (27036) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8539 (tt) REVERT: B 175 ASP cc_start: 0.7294 (t0) cc_final: 0.7049 (t0) REVERT: B 184 LEU cc_start: 0.8960 (mm) cc_final: 0.8716 (mt) REVERT: B 391 HIS cc_start: 0.8723 (p-80) cc_final: 0.8015 (p-80) REVERT: C 83 ARG cc_start: 0.8044 (ptt180) cc_final: 0.7163 (tmm-80) REVERT: C 134 ARG cc_start: 0.8964 (mpp-170) cc_final: 0.8311 (mpp-170) REVERT: F 175 ASP cc_start: 0.7446 (t0) cc_final: 0.7205 (t0) REVERT: F 184 LEU cc_start: 0.8701 (mm) cc_final: 0.8387 (mt) REVERT: F 391 HIS cc_start: 0.8633 (p-80) cc_final: 0.8332 (p-80) REVERT: J 153 MET cc_start: 0.7530 (tmm) cc_final: 0.6806 (tmm) REVERT: J 375 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7424 (tm-30) outliers start: 33 outliers final: 27 residues processed: 209 average time/residue: 0.3268 time to fit residues: 103.6159 Evaluate side-chains 194 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 368 VAL Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 184 optimal weight: 10.0000 chunk 151 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 360 GLN ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.145415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110044 restraints weight = 37228.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109168 restraints weight = 31269.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110363 restraints weight = 32325.484| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19983 Z= 0.169 Angle : 0.616 11.415 27036 Z= 0.312 Chirality : 0.043 0.291 3120 Planarity : 0.004 0.040 3597 Dihedral : 4.062 17.988 2823 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.38 % Allowed : 18.62 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2580 helix: 1.60 (0.16), residues: 1002 sheet: -0.01 (0.26), residues: 384 loop : -0.10 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 111 HIS 0.002 0.001 HIS J 391 PHE 0.018 0.001 PHE J 93 TYR 0.040 0.002 TYR K 141 ARG 0.007 0.000 ARG J 401 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 903) hydrogen bonds : angle 4.09472 ( 2583) covalent geometry : bond 0.00403 (19983) covalent geometry : angle 0.61618 (27036) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8624 (tt) REVERT: B 175 ASP cc_start: 0.7354 (t0) cc_final: 0.7126 (t0) REVERT: B 391 HIS cc_start: 0.8796 (p-80) cc_final: 0.8151 (p-80) REVERT: C 83 ARG cc_start: 0.8058 (ptt180) cc_final: 0.7112 (tmm-80) REVERT: C 134 ARG cc_start: 0.8994 (mpp-170) cc_final: 0.8343 (mpp-170) REVERT: F 175 ASP cc_start: 0.7487 (t0) cc_final: 0.7275 (t0) REVERT: F 391 HIS cc_start: 0.8685 (p-80) cc_final: 0.8357 (p-80) REVERT: I 98 GLU cc_start: 0.6882 (tp30) cc_final: 0.6593 (tp30) REVERT: J 153 MET cc_start: 0.7544 (tmm) cc_final: 0.6990 (tmm) REVERT: J 375 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7425 (tm-30) outliers start: 29 outliers final: 28 residues processed: 189 average time/residue: 0.3871 time to fit residues: 111.3149 Evaluate side-chains 190 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 111 VAL Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 chunk 130 optimal weight: 0.0470 chunk 152 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.146305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110842 restraints weight = 37706.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109612 restraints weight = 32400.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110864 restraints weight = 32450.720| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19983 Z= 0.137 Angle : 0.598 11.765 27036 Z= 0.303 Chirality : 0.043 0.296 3120 Planarity : 0.004 0.040 3597 Dihedral : 4.009 16.467 2823 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.38 % Allowed : 18.77 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2580 helix: 1.61 (0.16), residues: 1002 sheet: -0.03 (0.26), residues: 384 loop : -0.14 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP K 111 HIS 0.002 0.001 HIS J 391 PHE 0.018 0.001 PHE J 93 TYR 0.040 0.001 TYR K 141 ARG 0.008 0.000 ARG F 401 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 903) hydrogen bonds : angle 4.03128 ( 2583) covalent geometry : bond 0.00323 (19983) covalent geometry : angle 0.59751 (27036) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 ASP cc_start: 0.7422 (t0) cc_final: 0.7181 (t0) REVERT: B 391 HIS cc_start: 0.8750 (p-80) cc_final: 0.8091 (p-80) REVERT: C 83 ARG cc_start: 0.8088 (ptt180) cc_final: 0.7154 (tmm-80) REVERT: C 134 ARG cc_start: 0.9063 (mpp-170) cc_final: 0.8420 (mpp-170) REVERT: F 175 ASP cc_start: 0.7557 (t0) cc_final: 0.7333 (t0) REVERT: I 98 GLU cc_start: 0.6901 (tp30) cc_final: 0.6600 (tp30) REVERT: J 153 MET cc_start: 0.7517 (tmm) cc_final: 0.7024 (tmm) REVERT: J 375 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7393 (tm-30) REVERT: K 89 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7517 (mm-30) outliers start: 29 outliers final: 27 residues processed: 191 average time/residue: 0.3537 time to fit residues: 102.4046 Evaluate side-chains 189 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 374 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain J residue 43 LEU Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 136 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 175 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** E 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.148169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113172 restraints weight = 37515.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112331 restraints weight = 30504.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113718 restraints weight = 30667.449| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19983 Z= 0.115 Angle : 0.586 11.757 27036 Z= 0.297 Chirality : 0.042 0.309 3120 Planarity : 0.004 0.041 3597 Dihedral : 3.926 17.839 2823 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.38 % Allowed : 19.01 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2580 helix: 1.66 (0.17), residues: 1002 sheet: -0.00 (0.26), residues: 384 loop : -0.15 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP K 111 HIS 0.006 0.001 HIS F 391 PHE 0.044 0.001 PHE G 92 TYR 0.040 0.001 TYR K 141 ARG 0.008 0.000 ARG F 401 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 903) hydrogen bonds : angle 3.97706 ( 2583) covalent geometry : bond 0.00265 (19983) covalent geometry : angle 0.58628 (27036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5553.98 seconds wall clock time: 97 minutes 33.64 seconds (5853.64 seconds total)