Starting phenix.real_space_refine on Fri Jun 5 04:32:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zk0_60162/06_2026/8zk0_60162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zk0_60162/06_2026/8zk0_60162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zk0_60162/06_2026/8zk0_60162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zk0_60162/06_2026/8zk0_60162.map" model { file = "/net/cci-nas-00/data/ceres_data/8zk0_60162/06_2026/8zk0_60162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zk0_60162/06_2026/8zk0_60162.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 86 5.16 5 C 11057 2.51 5 N 3006 2.21 5 O 3269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17420 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Chain: "B" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Chain: "D" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1597 Classifications: {'peptide': 204} Link IDs: {'CIS': 8, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 184} Chain: "G" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1823 Classifications: {'peptide': 229} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 214} Chain: "E" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2256 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 280} Chain: "F" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3837 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 458} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.08, per 1000 atoms: 0.23 Number of scatterers: 17420 At special positions: 0 Unit cell: (141.31, 151.093, 291.316, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 2 15.00 O 3269 8.00 N 3006 7.00 C 11057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS B 265 " distance=2.02 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.04 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 738.8 milliseconds 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4084 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 38 sheets defined 16.9% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 102 through 105 Processing helix chain 'A' and resid 245 through 322 Proline residue: A 252 - end of helix Proline residue: A 261 - end of helix removed outlier: 3.734A pdb=" N GLY A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.762A pdb=" N ASN B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 322 removed outlier: 3.567A pdb=" N ILE B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Proline residue: B 261 - end of helix removed outlier: 3.613A pdb=" N ILE B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.626A pdb=" N ARG E 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.747A pdb=" N SER E 121 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 322 Proline residue: E 257 - end of helix removed outlier: 3.988A pdb=" N TRP E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN E 273 " --> pdb=" O PHE E 269 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 246 through 319 removed outlier: 4.515A pdb=" N LEU F 252 " --> pdb=" O TRP F 248 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA F 253 " --> pdb=" O ILE F 249 " (cutoff:3.500A) Proline residue: F 257 - end of helix removed outlier: 4.575A pdb=" N ARG F 313 " --> pdb=" O LEU F 309 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TRP F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.744A pdb=" N ASN F 330 " --> pdb=" O HIS F 326 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 Processing helix chain 'F' and resid 425 through 428 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.129A pdb=" N ILE A 39 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 143 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 41 " --> pdb=" O ALA A 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.598A pdb=" N PHE A 67 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 157 removed outlier: 5.881A pdb=" N ARG A 162 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS A 156 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLY A 160 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE A 201 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.617A pdb=" N ASN A 465 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N HIS A 471 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 376 removed outlier: 3.702A pdb=" N TRP A 398 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 31 through 33 removed outlier: 3.962A pdb=" N ALA B 109 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 42 removed outlier: 6.056A pdb=" N ILE B 39 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ALA B 143 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA B 41 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 82 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 150 through 156 removed outlier: 6.372A pdb=" N ARG B 162 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE B 201 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 190 " --> pdb=" O ALA B 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 179 Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AB5, first strand: chain 'B' and resid 325 through 327 removed outlier: 7.126A pdb=" N VAL B 461 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR B 474 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE B 463 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 374 through 376 removed outlier: 3.674A pdb=" N TRP B 398 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.591A pdb=" N THR D 116 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE D 35 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.591A pdb=" N THR D 116 " --> pdb=" O VAL D 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=AC1, first strand: chain 'D' and resid 128 through 134 removed outlier: 6.009A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU D 180 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU D 162 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS D 182 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 128 through 134 removed outlier: 6.009A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 151 through 155 removed outlier: 3.684A pdb=" N THR D 190 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.063A pdb=" N SER G 11 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL G 35 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER G 51 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.063A pdb=" N SER G 11 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 133 through 137 removed outlier: 3.864A pdb=" N LEU G 153 " --> pdb=" O PHE G 137 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR G 191 " --> pdb=" O LYS G 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 133 through 137 removed outlier: 3.864A pdb=" N LEU G 153 " --> pdb=" O PHE G 137 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR G 191 " --> pdb=" O LYS G 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AD1, first strand: chain 'G' and resid 165 through 170 removed outlier: 3.723A pdb=" N HIS G 208 " --> pdb=" O PHE G 227 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 225 " --> pdb=" O CYS G 210 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 32 through 34 Processing sheet with id=AD3, first strand: chain 'E' and resid 40 through 43 removed outlier: 6.218A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 190 through 191 removed outlier: 3.746A pdb=" N VAL E 195 " --> pdb=" O GLU E 203 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 190 through 191 removed outlier: 6.966A pdb=" N VAL E 204 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR E 169 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA E 206 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG E 167 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL E 208 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU E 165 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET E 210 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N HIS E 163 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR E 157 " --> pdb=" O GLY E 161 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N HIS E 163 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 176 through 180 removed outlier: 8.728A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS F 163 " --> pdb=" O MET F 210 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET F 210 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLU F 165 " --> pdb=" O VAL F 208 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL F 208 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ARG F 167 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA F 206 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR F 169 " --> pdb=" O VAL F 204 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL F 204 " --> pdb=" O THR F 169 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL F 195 " --> pdb=" O ALA F 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 32 through 34 Processing sheet with id=AD8, first strand: chain 'F' and resid 40 through 43 removed outlier: 6.259A pdb=" N ILE F 40 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA F 144 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA F 42 " --> pdb=" O ALA F 144 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU F 65 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL F 78 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP F 67 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 338 through 339 Processing sheet with id=AE1, first strand: chain 'F' and resid 338 through 339 removed outlier: 5.689A pdb=" N ASN F 475 " --> pdb=" O HIS F 481 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS F 481 " --> pdb=" O ASN F 475 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 383 through 385 removed outlier: 3.535A pdb=" N THR F 449 " --> pdb=" O THR F 443 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.12 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: 5738 1.34 - 1.46: 3987 1.46 - 1.58: 7958 1.58 - 1.70: 3 1.70 - 1.82: 126 Bond restraints: 17812 Sorted by residual: bond pdb=" O16 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sigma weight residual 1.697 1.642 0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" O16 H6P F 601 " pdb=" P13 H6P F 601 " ideal model delta sigma weight residual 1.594 1.647 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" C28 H6P F 601 " pdb=" O29 H6P F 601 " ideal model delta sigma weight residual 1.442 1.400 0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C31 H6P F 601 " pdb=" O33 H6P F 601 " ideal model delta sigma weight residual 1.440 1.400 0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" CB CYS A 265 " pdb=" SG CYS A 265 " ideal model delta sigma weight residual 1.808 1.752 0.056 3.30e-02 9.18e+02 2.89e+00 ... (remaining 17807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 23823 2.22 - 4.43: 267 4.43 - 6.65: 25 6.65 - 8.87: 4 8.87 - 11.08: 10 Bond angle restraints: 24129 Sorted by residual: angle pdb=" N VAL D 155 " pdb=" CA VAL D 155 " pdb=" CB VAL D 155 " ideal model delta sigma weight residual 112.65 102.38 10.27 1.00e+00 1.00e+00 1.05e+02 angle pdb=" N VAL D 155 " pdb=" CA VAL D 155 " pdb=" C VAL D 155 " ideal model delta sigma weight residual 106.42 117.50 -11.08 1.51e+00 4.39e-01 5.39e+01 angle pdb=" N ILE F 352 " pdb=" CA ILE F 352 " pdb=" C ILE F 352 " ideal model delta sigma weight residual 113.20 107.52 5.68 9.60e-01 1.09e+00 3.51e+01 angle pdb=" N TYR D 34 " pdb=" CA TYR D 34 " pdb=" C TYR D 34 " ideal model delta sigma weight residual 109.76 100.45 9.31 1.64e+00 3.72e-01 3.22e+01 angle pdb=" C GLY D 43 " pdb=" N ASN D 44 " pdb=" CA ASN D 44 " ideal model delta sigma weight residual 121.70 131.15 -9.45 1.80e+00 3.09e-01 2.76e+01 ... (remaining 24124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.53: 10157 26.53 - 53.05: 590 53.05 - 79.58: 56 79.58 - 106.11: 14 106.11 - 132.64: 1 Dihedral angle restraints: 10818 sinusoidal: 4471 harmonic: 6347 Sorted by residual: dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual -86.00 -153.19 67.19 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual 93.00 51.78 41.22 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" O15 H6P F 601 " pdb=" O16 H6P F 601 " pdb=" P13 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sinusoidal sigma weight residual 161.66 -65.70 -132.64 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 10815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2174 0.052 - 0.104: 351 0.104 - 0.156: 123 0.156 - 0.209: 3 0.209 - 0.261: 3 Chirality restraints: 2654 Sorted by residual: chirality pdb=" CA MET D 25 " pdb=" N MET D 25 " pdb=" C MET D 25 " pdb=" CB MET D 25 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA TYR D 34 " pdb=" N TYR D 34 " pdb=" C TYR D 34 " pdb=" CB TYR D 34 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASP D 54 " pdb=" N ASP D 54 " pdb=" C ASP D 54 " pdb=" CB ASP D 54 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2651 not shown) Planarity restraints: 3115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 260 " 0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO B 261 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 33 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C TYR D 33 " -0.037 2.00e-02 2.50e+03 pdb=" O TYR D 33 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR D 34 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 260 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 261 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " 0.029 5.00e-02 4.00e+02 ... (remaining 3112 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 221 2.64 - 3.21: 15468 3.21 - 3.77: 25156 3.77 - 4.34: 35166 4.34 - 4.90: 60018 Nonbonded interactions: 136029 Sorted by model distance: nonbonded pdb=" OE2 GLU G 202 " pdb=" OG SER G 203 " model vdw 2.081 3.040 nonbonded pdb=" OE1 GLN G 169 " pdb=" NH2 ARG G 209 " model vdw 2.089 3.120 nonbonded pdb=" O LEU B 415 " pdb=" OG SER B 435 " model vdw 2.103 3.040 nonbonded pdb=" O PHE A 480 " pdb=" OG SER A 481 " model vdw 2.107 3.040 nonbonded pdb=" O GLU G 143 " pdb=" OG1 THR G 144 " model vdw 2.114 3.040 ... (remaining 136024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.110 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 0.056 17826 Z= 0.137 Angle : 0.624 11.082 24157 Z= 0.345 Chirality : 0.046 0.261 2654 Planarity : 0.004 0.060 3115 Dihedral : 15.857 132.636 6692 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 0.57 % Allowed : 14.47 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2185 helix: 2.64 (0.28), residues: 326 sheet: 0.38 (0.19), residues: 769 loop : -1.15 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 286 TYR 0.010 0.001 TYR B 126 PHE 0.019 0.001 PHE E 242 TRP 0.013 0.001 TRP F 332 HIS 0.004 0.001 HIS E 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (17812) covalent geometry : angle 0.62190 / 0.34 (24129) SS BOND : bond 0.00452 / 0.30 ( 14) SS BOND : angle 1.62794 / 1.01 ( 28) hydrogen bonds : bond 0.11880 / 7.91 ( 766) hydrogen bonds : angle 5.89867 / 3.99 ( 2124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.855 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: G 123 ASP cc_start: 0.8282 (p0) cc_final: 0.8056 (p0) outliers start: 11 outliers final: 2 residues processed: 96 average time/residue: 0.1648 time to fit residues: 23.7986 Evaluate side-chains 65 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain D residue 67 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN B 357 HIS D 8 HIS G 147 GLN E 151 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.051904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.037066 restraints weight = 143932.268| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 5.29 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17826 Z= 0.219 Angle : 0.660 9.116 24157 Z= 0.342 Chirality : 0.045 0.271 2654 Planarity : 0.004 0.052 3115 Dihedral : 5.466 90.301 2416 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 1.52 % Allowed : 14.58 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2185 helix: 2.66 (0.28), residues: 327 sheet: 0.39 (0.19), residues: 784 loop : -1.00 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 88 TYR 0.017 0.002 TYR F 172 PHE 0.014 0.002 PHE E 242 TRP 0.015 0.001 TRP F 295 HIS 0.005 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (17812) covalent geometry : angle 0.65891 / 0.34 (24129) SS BOND : bond 0.00475 / 0.30 ( 14) SS BOND : angle 1.23449 / 0.76 ( 28) hydrogen bonds : bond 0.05461 / 3.74 ( 766) hydrogen bonds : angle 5.21540 / 3.55 ( 2124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.783 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: B 355 PHE cc_start: 0.8199 (t80) cc_final: 0.7817 (t80) REVERT: D 62 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8636 (p0) outliers start: 29 outliers final: 12 residues processed: 89 average time/residue: 0.1311 time to fit residues: 19.0496 Evaluate side-chains 69 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain D residue 3 GLU Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 203 optimal weight: 0.0040 chunk 160 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN E 186 ASN F 318 GLN ** F 374 ASN ** 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 = 0.3700 r_free = 0.3700 target = 0.050943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.035858 restraints weight = 144676.474| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 5.37 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17826 Z= 0.214 Angle : 0.615 9.473 24157 Z= 0.319 Chirality : 0.043 0.168 2654 Planarity : 0.004 0.049 3115 Dihedral : 5.131 75.779 2414 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 1.46 % Allowed : 15.67 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2185 helix: 2.87 (0.28), residues: 327 sheet: 0.41 (0.19), residues: 769 loop : -0.95 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG F 291 TYR 0.016 0.001 TYR A 78 PHE 0.027 0.001 PHE A 127 TRP 0.017 0.001 TRP A 178 HIS 0.031 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (17812) covalent geometry : angle 0.61448 / 0.32 (24129) SS BOND : bond 0.00525 / 0.32 ( 14) SS BOND : angle 1.11081 / 0.68 ( 28) hydrogen bonds : bond 0.05225 / 3.57 ( 766) hydrogen bonds : angle 5.11814 / 3.48 ( 2124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.9073 (mmm) cc_final: 0.8719 (mmm) REVERT: B 355 PHE cc_start: 0.8404 (t80) cc_final: 0.7970 (t80) REVERT: D 9 GLN cc_start: 0.8783 (mp10) cc_final: 0.8394 (tm-30) REVERT: D 62 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8699 (p0) REVERT: F 43 MET cc_start: 0.6729 (tmm) cc_final: 0.5717 (tmm) outliers start: 28 outliers final: 9 residues processed: 83 average time/residue: 0.1334 time to fit residues: 17.9557 Evaluate side-chains 65 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 221 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 100 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 216 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 0.0010 chunk 192 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 186 ASN F 330 ASN ** F 374 ASN ** 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 = 0.3722 r_free = 0.3722 target = 0.051494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.036646 restraints weight = 145353.900| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 5.33 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17826 Z= 0.124 Angle : 0.563 9.353 24157 Z= 0.290 Chirality : 0.043 0.149 2654 Planarity : 0.004 0.048 3115 Dihedral : 4.829 66.289 2414 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 1.72 % Allowed : 16.56 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2185 helix: 3.00 (0.28), residues: 326 sheet: 0.54 (0.19), residues: 772 loop : -0.90 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 348 TYR 0.015 0.001 TYR A 78 PHE 0.015 0.001 PHE A 127 TRP 0.015 0.001 TRP F 332 HIS 0.002 0.000 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (17812) covalent geometry : angle 0.56262 / 0.29 (24129) SS BOND : bond 0.00463 / 0.28 ( 14) SS BOND : angle 0.94470 / 0.57 ( 28) hydrogen bonds : bond 0.04826 / 3.32 ( 766) hydrogen bonds : angle 4.84718 / 3.30 ( 2124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.9000 (mmm) cc_final: 0.8645 (mmm) REVERT: B 355 PHE cc_start: 0.8417 (t80) cc_final: 0.7990 (t80) REVERT: D 9 GLN cc_start: 0.8721 (mp10) cc_final: 0.7974 (tm-30) REVERT: D 62 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8655 (p0) REVERT: G 185 MET cc_start: 0.8719 (mpp) cc_final: 0.8443 (mpp) REVERT: E 58 MET cc_start: 0.8999 (ptp) cc_final: 0.8692 (ptp) REVERT: E 290 MET cc_start: 0.9190 (ptm) cc_final: 0.8880 (ptm) REVERT: E 293 MET cc_start: 0.9004 (ppp) cc_final: 0.8521 (ppp) REVERT: F 43 MET cc_start: 0.6844 (tmm) cc_final: 0.5916 (tmm) outliers start: 33 outliers final: 15 residues processed: 86 average time/residue: 0.1182 time to fit residues: 17.3880 Evaluate side-chains 71 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 202 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 0.0050 chunk 85 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 203 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 186 ASN ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.051832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.037054 restraints weight = 143589.327| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 5.30 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17826 Z= 0.105 Angle : 0.545 9.464 24157 Z= 0.277 Chirality : 0.043 0.180 2654 Planarity : 0.003 0.046 3115 Dihedral : 4.549 63.814 2414 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.52 % Allowed : 17.40 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2185 helix: 3.25 (0.28), residues: 326 sheet: 0.60 (0.18), residues: 791 loop : -0.85 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 151 TYR 0.012 0.001 TYR A 78 PHE 0.011 0.001 PHE B 453 TRP 0.015 0.001 TRP F 332 HIS 0.003 0.000 HIS E 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (17812) covalent geometry : angle 0.54461 / 0.28 (24129) SS BOND : bond 0.00370 / 0.23 ( 14) SS BOND : angle 0.88305 / 0.53 ( 28) hydrogen bonds : bond 0.04511 / 3.10 ( 766) hydrogen bonds : angle 4.64378 / 3.16 ( 2124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8985 (mmm) cc_final: 0.8598 (mmm) REVERT: B 355 PHE cc_start: 0.8541 (t80) cc_final: 0.8068 (t80) REVERT: B 387 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7790 (p90) REVERT: G 185 MET cc_start: 0.8813 (mpp) cc_final: 0.8489 (mpp) REVERT: E 293 MET cc_start: 0.9160 (ppp) cc_final: 0.8782 (ppp) REVERT: F 43 MET cc_start: 0.6875 (tmm) cc_final: 0.6371 (tmm) outliers start: 29 outliers final: 11 residues processed: 82 average time/residue: 0.1113 time to fit residues: 15.6464 Evaluate side-chains 66 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 480 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 158 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN F 273 GLN ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 481 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.071274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055718 restraints weight = 141780.703| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.73 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17826 Z= 0.281 Angle : 0.694 15.109 24157 Z= 0.351 Chirality : 0.044 0.159 2654 Planarity : 0.004 0.043 3115 Dihedral : 5.004 54.973 2413 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 1.99 % Allowed : 17.40 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2185 helix: 2.94 (0.28), residues: 327 sheet: 0.33 (0.18), residues: 810 loop : -0.94 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 485 TYR 0.019 0.002 TYR B 126 PHE 0.014 0.002 PHE G 160 TRP 0.015 0.002 TRP A 178 HIS 0.006 0.001 HIS F 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 (17812) covalent geometry : angle 0.69347 / 0.35 (24129) SS BOND : bond 0.00564 / 0.36 ( 14) SS BOND : angle 1.19869 / 0.74 ( 28) hydrogen bonds : bond 0.04988 / 3.40 ( 766) hydrogen bonds : angle 5.10918 / 3.46 ( 2124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 50 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8718 (mtp) cc_final: 0.8364 (mmm) REVERT: B 355 PHE cc_start: 0.8516 (t80) cc_final: 0.8025 (t80) REVERT: D 9 GLN cc_start: 0.8850 (mp10) cc_final: 0.7945 (tm-30) REVERT: D 62 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8657 (p0) REVERT: D 99 MET cc_start: 0.8777 (mmm) cc_final: 0.8551 (mmm) REVERT: G 125 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8199 (tm-30) REVERT: E 210 MET cc_start: 0.8662 (ttt) cc_final: 0.7974 (ppp) REVERT: F 43 MET cc_start: 0.7044 (tmm) cc_final: 0.6397 (tmm) outliers start: 38 outliers final: 18 residues processed: 84 average time/residue: 0.1186 time to fit residues: 16.8169 Evaluate side-chains 67 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 108 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.073442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058084 restraints weight = 141288.521| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.74 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17826 Z= 0.128 Angle : 0.585 10.363 24157 Z= 0.296 Chirality : 0.043 0.260 2654 Planarity : 0.004 0.044 3115 Dihedral : 4.699 55.878 2413 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Rotamer: Outliers : 1.62 % Allowed : 17.97 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 2185 helix: 3.18 (0.28), residues: 326 sheet: 0.44 (0.19), residues: 796 loop : -0.89 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 291 TYR 0.014 0.001 TYR B 126 PHE 0.011 0.001 PHE B 453 TRP 0.012 0.001 TRP F 332 HIS 0.002 0.000 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (17812) covalent geometry : angle 0.58457 / 0.30 (24129) SS BOND : bond 0.00391 / 0.27 ( 14) SS BOND : angle 1.02598 / 0.63 ( 28) hydrogen bonds : bond 0.04589 / 3.17 ( 766) hydrogen bonds : angle 4.85103 / 3.29 ( 2124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 355 PHE cc_start: 0.8538 (t80) cc_final: 0.8067 (t80) REVERT: D 9 GLN cc_start: 0.8799 (mp10) cc_final: 0.7815 (tm-30) REVERT: D 62 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8623 (p0) REVERT: D 99 MET cc_start: 0.8770 (mmm) cc_final: 0.8526 (mmm) REVERT: G 125 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8116 (tm-30) REVERT: G 185 MET cc_start: 0.8796 (mpp) cc_final: 0.8467 (mpp) REVERT: E 210 MET cc_start: 0.8861 (ttt) cc_final: 0.8200 (ppp) REVERT: F 43 MET cc_start: 0.7005 (tmm) cc_final: 0.6507 (tmm) REVERT: F 298 MET cc_start: 0.8397 (tpp) cc_final: 0.8175 (tpp) outliers start: 31 outliers final: 20 residues processed: 78 average time/residue: 0.1317 time to fit residues: 16.9385 Evaluate side-chains 69 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 128 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 189 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 216 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 chunk 170 optimal weight: 0.0030 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN ** F 374 ASN ** 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 = 0.3693 r_free = 0.3693 target = 0.050589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.035701 restraints weight = 144557.213| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 5.32 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17826 Z= 0.134 Angle : 0.576 10.430 24157 Z= 0.292 Chirality : 0.043 0.208 2654 Planarity : 0.004 0.046 3115 Dihedral : 4.617 55.996 2413 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 1.57 % Allowed : 18.18 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2185 helix: 3.43 (0.28), residues: 320 sheet: 0.43 (0.18), residues: 809 loop : -0.89 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.013 0.001 TYR B 126 PHE 0.010 0.001 PHE A 127 TRP 0.012 0.001 TRP F 332 HIS 0.002 0.000 HIS F 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17812) covalent geometry : angle 0.57489 / 0.29 (24129) SS BOND : bond 0.00357 / 0.25 ( 14) SS BOND : angle 1.04369 / 0.64 ( 28) hydrogen bonds : bond 0.04478 / 3.08 ( 766) hydrogen bonds : angle 4.76445 / 3.23 ( 2124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8218 (mpp) cc_final: 0.7902 (mpp) REVERT: B 62 MET cc_start: 0.8627 (mtp) cc_final: 0.8182 (mmt) REVERT: B 355 PHE cc_start: 0.8553 (t80) cc_final: 0.8080 (t80) REVERT: B 387 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7817 (p90) REVERT: D 62 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8667 (p0) REVERT: D 151 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6452 (ttp80) REVERT: G 125 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8357 (tm-30) REVERT: G 185 MET cc_start: 0.8873 (mpp) cc_final: 0.8544 (mpp) REVERT: E 210 MET cc_start: 0.8904 (ttt) cc_final: 0.8202 (ppp) REVERT: F 43 MET cc_start: 0.6998 (tmm) cc_final: 0.6536 (tmm) REVERT: F 298 MET cc_start: 0.8527 (tpp) cc_final: 0.8184 (tpp) outliers start: 30 outliers final: 20 residues processed: 76 average time/residue: 0.1289 time to fit residues: 16.1864 Evaluate side-chains 71 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 187 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** F 374 ASN ** 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 = 0.3676 r_free = 0.3676 target = 0.050103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.035010 restraints weight = 144603.952| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 5.12 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17826 Z= 0.183 Angle : 0.606 9.525 24157 Z= 0.306 Chirality : 0.043 0.188 2654 Planarity : 0.004 0.046 3115 Dihedral : 4.694 59.927 2413 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 1.31 % Allowed : 18.50 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2185 helix: 3.42 (0.27), residues: 317 sheet: 0.35 (0.18), residues: 815 loop : -0.91 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 105 TYR 0.014 0.001 TYR B 126 PHE 0.010 0.001 PHE A 127 TRP 0.016 0.001 TRP F 295 HIS 0.004 0.001 HIS F 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (17812) covalent geometry : angle 0.60560 / 0.31 (24129) SS BOND : bond 0.00467 / 0.31 ( 14) SS BOND : angle 1.07848 / 0.68 ( 28) hydrogen bonds : bond 0.04553 / 3.11 ( 766) hydrogen bonds : angle 4.87400 / 3.30 ( 2124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8952 (tm-30) REVERT: B 62 MET cc_start: 0.8716 (mtp) cc_final: 0.8302 (mmm) REVERT: B 355 PHE cc_start: 0.8444 (t80) cc_final: 0.7955 (t80) REVERT: D 62 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8733 (p0) REVERT: G 125 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8454 (tm-30) REVERT: G 185 MET cc_start: 0.8875 (mpp) cc_final: 0.8526 (mpp) REVERT: F 43 MET cc_start: 0.7142 (tmm) cc_final: 0.6633 (tmm) outliers start: 25 outliers final: 18 residues processed: 72 average time/residue: 0.1275 time to fit residues: 15.2149 Evaluate side-chains 69 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 170 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.049915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.034836 restraints weight = 144229.312| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 5.22 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17826 Z= 0.194 Angle : 0.614 9.151 24157 Z= 0.310 Chirality : 0.043 0.191 2654 Planarity : 0.004 0.060 3115 Dihedral : 4.726 52.934 2413 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 1.36 % Allowed : 18.50 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 2185 helix: 3.35 (0.27), residues: 317 sheet: 0.25 (0.18), residues: 818 loop : -0.89 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.015 0.001 TYR B 126 PHE 0.011 0.001 PHE G 160 TRP 0.019 0.001 TRP F 295 HIS 0.003 0.001 HIS F 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (17812) covalent geometry : angle 0.61244 / 0.31 (24129) SS BOND : bond 0.00480 / 0.32 ( 14) SS BOND : angle 1.22538 / 0.88 ( 28) hydrogen bonds : bond 0.04550 / 3.11 ( 766) hydrogen bonds : angle 4.90731 / 3.32 ( 2124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4370 Ramachandran restraints generated. 2185 Oldfield, 0 Emsley, 2185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 GLN cc_start: 0.9287 (mm-40) cc_final: 0.8984 (tm-30) REVERT: B 62 MET cc_start: 0.8691 (mtp) cc_final: 0.8300 (mmm) REVERT: B 355 PHE cc_start: 0.8533 (t80) cc_final: 0.8036 (t80) REVERT: B 387 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7896 (p90) REVERT: D 62 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8757 (p0) REVERT: G 185 MET cc_start: 0.8881 (mpp) cc_final: 0.8555 (mpp) REVERT: F 43 MET cc_start: 0.7321 (tmm) cc_final: 0.6861 (tmm) outliers start: 26 outliers final: 21 residues processed: 75 average time/residue: 0.1229 time to fit residues: 15.1582 Evaluate side-chains 73 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain D residue 8 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 480 SER Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain F residue 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 69 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 97 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.049955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034874 restraints weight = 143786.499| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 5.25 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17826 Z= 0.175 Angle : 0.603 8.836 24157 Z= 0.305 Chirality : 0.043 0.187 2654 Planarity : 0.004 0.052 3115 Dihedral : 4.646 57.081 2413 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.76 % Favored : 95.19 % Rotamer: Outliers : 1.31 % Allowed : 18.70 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.83 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2185 helix: 3.37 (0.27), residues: 317 sheet: 0.32 (0.19), residues: 801 loop : -0.90 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 151 TYR 0.015 0.001 TYR B 126 PHE 0.010 0.001 PHE B 98 TRP 0.012 0.001 TRP F 332 HIS 0.003 0.001 HIS F 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (17812) covalent geometry : angle 0.60249 / 0.30 (24129) SS BOND : bond 0.00427 / 0.28 ( 14) SS BOND : angle 1.06176 / 0.68 ( 28) hydrogen bonds : bond 0.04481 / 3.07 ( 766) hydrogen bonds : angle 4.87086 / 3.30 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.08 seconds wall clock time: 75 minutes 47.58 seconds (4547.58 seconds total)