Starting phenix.real_space_refine on Fri Mar 14 05:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmy_29300/03_2025/8fmy_29300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmy_29300/03_2025/8fmy_29300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fmy_29300/03_2025/8fmy_29300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmy_29300/03_2025/8fmy_29300.map" model { file = "/net/cci-nas-00/data/ceres_data/8fmy_29300/03_2025/8fmy_29300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmy_29300/03_2025/8fmy_29300.cif" } resolution = 2.66 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= 0.015 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 57 5.16 5 C 6036 2.51 5 N 1611 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9597 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3199 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 13, 'TRANS': 406} Restraints were copied for chains: C, B Time building chain proxies: 6.05, per 1000 atoms: 0.63 Number of scatterers: 9597 At special positions: 0 Unit cell: (103, 104, 98, 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 57 16.00 O 1893 8.00 N 1611 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 362 " distance=2.04 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 391 " distance=2.04 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 416 " distance=2.04 Simple disulfide: pdb=" SG CYS C 330 " - pdb=" SG CYS C 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 339 " distance=2.04 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 362 " distance=2.04 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 362 " distance=2.04 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 391 " distance=2.04 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 391 " distance=2.04 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 416 " distance=2.04 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 416 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.3 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 40.0% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.556A pdb=" N LEU A 32 " --> pdb=" O HIS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 71 through 105 removed outlier: 3.500A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.930A pdb=" N MET A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 124 through 136 removed outlier: 3.650A pdb=" N HIS A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.619A pdb=" N ALA A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.628A pdb=" N GLY A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 186 removed outlier: 3.565A pdb=" N ILE A 186 " --> pdb=" O ILE A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 190 through 219 removed outlier: 3.668A pdb=" N ILE A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.521A pdb=" N GLN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 232 through 235 removed outlier: 4.100A pdb=" N ASN A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.763A pdb=" N LEU A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.619A pdb=" N SER A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'B' and resid 28 through 33 removed outlier: 3.557A pdb=" N LEU B 32 " --> pdb=" O HIS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 71 through 105 removed outlier: 3.751A pdb=" N ASN B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Proline residue: B 88 - end of helix removed outlier: 3.930A pdb=" N MET B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 124 through 136 removed outlier: 3.650A pdb=" N HIS B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.619A pdb=" N ALA B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.628A pdb=" N GLY B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 removed outlier: 3.565A pdb=" N ILE B 186 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'B' and resid 190 through 219 removed outlier: 3.667A pdb=" N ILE B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 201 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Proline residue: B 215 - end of helix removed outlier: 3.521A pdb=" N GLN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 235 removed outlier: 4.101A pdb=" N ASN B 235 " --> pdb=" O SER B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 237 through 245 removed outlier: 3.762A pdb=" N LEU B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.620A pdb=" N SER B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 358 through 362 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.557A pdb=" N LEU C 32 " --> pdb=" O HIS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 70 Processing helix chain 'C' and resid 71 through 105 removed outlier: 3.750A pdb=" N ASN C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Proline residue: C 88 - end of helix removed outlier: 3.931A pdb=" N MET C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 92 " --> pdb=" O PRO C 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.651A pdb=" N HIS C 134 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.618A pdb=" N ALA C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.628A pdb=" N GLY C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 186 removed outlier: 3.565A pdb=" N ILE C 186 " --> pdb=" O ILE C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 186' Processing helix chain 'C' and resid 190 through 219 removed outlier: 3.667A pdb=" N ILE C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Proline residue: C 215 - end of helix removed outlier: 3.521A pdb=" N GLN C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 232 through 235 removed outlier: 4.100A pdb=" N ASN C 235 " --> pdb=" O SER C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 237 through 245 removed outlier: 3.762A pdb=" N LEU C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.619A pdb=" N SER C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 330 Processing helix chain 'C' and resid 348 through 356 Processing helix chain 'C' and resid 358 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 332 removed outlier: 3.643A pdb=" N LYS A 48 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU A 294 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR A 42 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 292 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN A 44 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA A 290 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N LYS A 46 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LYS A 48 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU A 286 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE A 314 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE A 325 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 161 removed outlier: 8.404A pdb=" N THR A 167 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A 55 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 267 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU A 278 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE A 265 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU A 280 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY A 263 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411 Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 399 removed outlier: 7.065A pdb=" N LEU A 425 " --> pdb=" O MET B 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 331 through 332 removed outlier: 3.643A pdb=" N LYS B 48 " --> pdb=" O CYS B 339 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU B 294 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR B 42 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 292 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN B 44 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA B 290 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N LYS B 46 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LYS B 48 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU B 286 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE B 314 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 325 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 157 through 161 removed outlier: 8.403A pdb=" N THR B 167 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU B 55 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 267 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU B 278 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE B 265 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU B 280 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY B 263 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 300 through 302 Processing sheet with id=AB2, first strand: chain 'B' and resid 409 through 411 Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 399 removed outlier: 7.080A pdb=" N LEU B 425 " --> pdb=" O MET C 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 332 removed outlier: 3.642A pdb=" N LYS C 48 " --> pdb=" O CYS C 339 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N GLU C 294 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR C 42 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 292 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ASN C 44 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA C 290 " --> pdb=" O ASN C 44 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N LYS C 46 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LYS C 48 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU C 286 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE C 314 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE C 325 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 161 removed outlier: 8.403A pdb=" N THR C 167 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU C 55 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 267 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU C 278 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE C 265 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU C 280 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLY C 263 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 300 through 302 424 hydrogen bonds defined for protein. 1146 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: 3.20 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2997 1.34 - 1.46: 1888 1.46 - 1.59: 4757 1.59 - 1.72: 0 1.72 - 1.84: 84 Bond restraints: 9726 Sorted by residual: bond pdb=" N ASP C 172 " pdb=" CA ASP C 172 " ideal model delta sigma weight residual 1.460 1.496 -0.037 2.20e-02 2.07e+03 2.76e+00 bond pdb=" N ASP A 172 " pdb=" CA ASP A 172 " ideal model delta sigma weight residual 1.460 1.496 -0.036 2.20e-02 2.07e+03 2.75e+00 bond pdb=" N ASP B 172 " pdb=" CA ASP B 172 " ideal model delta sigma weight residual 1.460 1.496 -0.036 2.20e-02 2.07e+03 2.67e+00 bond pdb=" CA THR B 173 " pdb=" C THR B 173 " ideal model delta sigma weight residual 1.524 1.542 -0.019 1.27e-02 6.20e+03 2.12e+00 bond pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.27e-02 6.20e+03 2.02e+00 ... (remaining 9721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11284 1.48 - 2.96: 1502 2.96 - 4.43: 339 4.43 - 5.91: 76 5.91 - 7.39: 23 Bond angle restraints: 13224 Sorted by residual: angle pdb=" N THR B 173 " pdb=" CA THR B 173 " pdb=" C THR B 173 " ideal model delta sigma weight residual 111.07 115.94 -4.87 1.07e+00 8.73e-01 2.07e+01 angle pdb=" N THR C 173 " pdb=" CA THR C 173 " pdb=" C THR C 173 " ideal model delta sigma weight residual 111.07 115.93 -4.86 1.07e+00 8.73e-01 2.06e+01 angle pdb=" N THR A 173 " pdb=" CA THR A 173 " pdb=" C THR A 173 " ideal model delta sigma weight residual 111.07 115.89 -4.82 1.07e+00 8.73e-01 2.03e+01 angle pdb=" N LYS B 68 " pdb=" CA LYS B 68 " pdb=" C LYS B 68 " ideal model delta sigma weight residual 111.33 116.31 -4.98 1.21e+00 6.83e-01 1.70e+01 angle pdb=" N LYS C 68 " pdb=" CA LYS C 68 " pdb=" C LYS C 68 " ideal model delta sigma weight residual 111.33 116.29 -4.96 1.21e+00 6.83e-01 1.68e+01 ... (remaining 13219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 5514 15.33 - 30.65: 342 30.65 - 45.98: 62 45.98 - 61.31: 31 61.31 - 76.64: 18 Dihedral angle restraints: 5967 sinusoidal: 2298 harmonic: 3669 Sorted by residual: dihedral pdb=" CB CYS B 393 " pdb=" SG CYS B 393 " pdb=" SG CYS B 416 " pdb=" CB CYS B 416 " ideal model delta sinusoidal sigma weight residual 93.00 153.09 -60.09 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS C 393 " pdb=" SG CYS C 393 " pdb=" SG CYS C 416 " pdb=" CB CYS C 416 " ideal model delta sinusoidal sigma weight residual 93.00 153.09 -60.09 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CB CYS A 393 " pdb=" SG CYS A 393 " pdb=" SG CYS A 416 " pdb=" CB CYS A 416 " ideal model delta sinusoidal sigma weight residual 93.00 153.08 -60.08 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 5964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 782 0.039 - 0.077: 496 0.077 - 0.116: 233 0.116 - 0.155: 85 0.155 - 0.193: 18 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CA ILE C 183 " pdb=" N ILE C 183 " pdb=" C ILE C 183 " pdb=" CB ILE C 183 " both_signs ideal model delta sigma weight residual False 2.43 2.24 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.24 0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA ILE B 183 " pdb=" N ILE B 183 " pdb=" C ILE B 183 " pdb=" CB ILE B 183 " both_signs ideal model delta sigma weight residual False 2.43 2.24 0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 1611 not shown) Planarity restraints: 1695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ILE A 210 " 0.060 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.022 2.00e-02 2.50e+03 pdb=" N THR A 211 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 210 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C ILE B 210 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE B 210 " -0.022 2.00e-02 2.50e+03 pdb=" N THR B 211 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 210 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ILE C 210 " -0.059 2.00e-02 2.50e+03 pdb=" O ILE C 210 " 0.022 2.00e-02 2.50e+03 pdb=" N THR C 211 " 0.020 2.00e-02 2.50e+03 ... (remaining 1692 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 3594 2.91 - 3.41: 8340 3.41 - 3.91: 14234 3.91 - 4.40: 15737 4.40 - 4.90: 27878 Nonbonded interactions: 69783 Sorted by model distance: nonbonded pdb=" O THR A 319 " pdb=" OG1 THR A 320 " model vdw 2.417 3.040 nonbonded pdb=" O THR B 319 " pdb=" OG1 THR B 320 " model vdw 2.417 3.040 nonbonded pdb=" O THR C 319 " pdb=" OG1 THR C 320 " model vdw 2.417 3.040 nonbonded pdb=" OD1 ASN A 44 " pdb=" OG SER A 336 " model vdw 2.505 3.040 nonbonded pdb=" OD1 ASN B 44 " pdb=" OG SER B 336 " model vdw 2.505 3.040 ... (remaining 69778 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.008 0.050 9726 Z= 0.542 Angle : 1.159 7.388 13224 Z= 0.715 Chirality : 0.062 0.193 1614 Planarity : 0.007 0.049 1695 Dihedral : 12.096 76.635 3573 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -1.16 (0.21), residues: 1254 helix: -1.03 (0.21), residues: 402 sheet: 0.31 (0.31), residues: 258 loop : -0.98 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.007 TRP B 307 HIS 0.006 0.002 HIS B 257 PHE 0.023 0.005 PHE C 281 TYR 0.042 0.006 TYR A 45 ARG 0.013 0.002 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.7653 time to fit residues: 106.8734 Evaluate side-chains 32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.070803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.056672 restraints weight = 21945.197| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.52 r_work: 0.2710 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9726 Z= 0.223 Angle : 0.618 5.462 13224 Z= 0.353 Chirality : 0.045 0.140 1614 Planarity : 0.004 0.050 1695 Dihedral : 5.010 17.608 1350 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.83 % Allowed : 4.04 % Favored : 95.13 % 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: 0.39 (0.23), residues: 1254 helix: 1.08 (0.25), residues: 405 sheet: 0.50 (0.32), residues: 249 loop : -0.34 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 307 HIS 0.003 0.001 HIS B 257 PHE 0.010 0.002 PHE A 234 TYR 0.013 0.002 TYR C 45 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 1.061 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 38 average time/residue: 1.1427 time to fit residues: 47.8347 Evaluate side-chains 33 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN B 301 ASN C 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.073284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.059230 restraints weight = 22165.651| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.54 r_work: 0.2758 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9726 Z= 0.143 Angle : 0.508 7.246 13224 Z= 0.284 Chirality : 0.043 0.163 1614 Planarity : 0.003 0.032 1695 Dihedral : 4.522 15.811 1350 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.28 % Allowed : 4.87 % Favored : 94.86 % 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: 0.94 (0.24), residues: 1254 helix: 2.16 (0.27), residues: 372 sheet: 0.39 (0.30), residues: 285 loop : -0.19 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 307 HIS 0.001 0.000 HIS B 257 PHE 0.007 0.001 PHE A 234 TYR 0.009 0.001 TYR B 274 ARG 0.003 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 1.157 Fit side-chains REVERT: B 426 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8140 (tt) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 1.3506 time to fit residues: 52.9900 Evaluate side-chains 28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.051074 restraints weight = 22637.184| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.51 r_work: 0.2582 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 9726 Z= 0.560 Angle : 0.720 8.827 13224 Z= 0.403 Chirality : 0.050 0.143 1614 Planarity : 0.004 0.044 1695 Dihedral : 5.133 18.514 1350 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.92 % Allowed : 5.42 % Favored : 93.66 % 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: 0.30 (0.24), residues: 1254 helix: 1.80 (0.27), residues: 387 sheet: 0.09 (0.32), residues: 249 loop : -0.78 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 307 HIS 0.003 0.001 HIS C 134 PHE 0.017 0.003 PHE C 281 TYR 0.019 0.002 TYR B 274 ARG 0.004 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 1.178 Fit side-chains REVERT: C 146 MET cc_start: 0.7926 (mmp) cc_final: 0.7713 (mmm) outliers start: 10 outliers final: 3 residues processed: 35 average time/residue: 1.3652 time to fit residues: 52.4139 Evaluate side-chains 31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.067935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.054244 restraints weight = 22188.631| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.51 r_work: 0.2655 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9726 Z= 0.224 Angle : 0.536 8.286 13224 Z= 0.302 Chirality : 0.044 0.136 1614 Planarity : 0.003 0.033 1695 Dihedral : 4.722 16.915 1350 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.83 % Allowed : 6.43 % Favored : 92.75 % 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: 0.48 (0.24), residues: 1254 helix: 2.19 (0.28), residues: 375 sheet: 0.03 (0.32), residues: 246 loop : -0.72 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.009 0.002 PHE A 281 TYR 0.012 0.001 TYR A 274 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 1.045 Fit side-chains REVERT: B 146 MET cc_start: 0.7921 (mmm) cc_final: 0.7704 (mtp) outliers start: 9 outliers final: 6 residues processed: 37 average time/residue: 1.1874 time to fit residues: 48.3086 Evaluate side-chains 34 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 0.0040 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.071718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.058087 restraints weight = 22077.021| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.49 r_work: 0.2754 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9726 Z= 0.122 Angle : 0.457 9.368 13224 Z= 0.254 Chirality : 0.042 0.133 1614 Planarity : 0.003 0.034 1695 Dihedral : 4.257 16.412 1350 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.28 % Allowed : 7.35 % Favored : 92.38 % 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 (0.24), residues: 1254 helix: 2.40 (0.27), residues: 375 sheet: 0.27 (0.30), residues: 288 loop : -0.53 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 307 HIS 0.001 0.000 HIS B 349 PHE 0.006 0.001 PHE B 375 TYR 0.008 0.001 TYR B 300 ARG 0.001 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 1.068 Fit side-chains REVERT: A 146 MET cc_start: 0.7527 (mmp) cc_final: 0.7285 (mmm) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 1.3229 time to fit residues: 46.3808 Evaluate side-chains 29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.071027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057470 restraints weight = 22172.311| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.49 r_work: 0.2740 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9726 Z= 0.140 Angle : 0.460 8.850 13224 Z= 0.256 Chirality : 0.042 0.126 1614 Planarity : 0.003 0.033 1695 Dihedral : 4.149 16.481 1350 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.83 % Allowed : 7.53 % Favored : 91.64 % 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 (0.24), residues: 1254 helix: 2.51 (0.28), residues: 375 sheet: 0.19 (0.32), residues: 258 loop : -0.53 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 307 HIS 0.001 0.000 HIS C 134 PHE 0.007 0.001 PHE B 238 TYR 0.011 0.001 TYR C 274 ARG 0.001 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 1.055 Fit side-chains REVERT: A 146 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7349 (mmm) outliers start: 9 outliers final: 2 residues processed: 34 average time/residue: 1.2992 time to fit residues: 48.4327 Evaluate side-chains 31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.0370 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.0170 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN C 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.056200 restraints weight = 22373.775| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.51 r_work: 0.2709 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9726 Z= 0.177 Angle : 0.486 10.714 13224 Z= 0.270 Chirality : 0.043 0.131 1614 Planarity : 0.003 0.034 1695 Dihedral : 4.198 16.956 1350 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.46 % Allowed : 8.17 % Favored : 91.37 % 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 (0.24), residues: 1254 helix: 2.56 (0.28), residues: 375 sheet: 0.15 (0.32), residues: 258 loop : -0.55 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 307 HIS 0.002 0.001 HIS C 134 PHE 0.009 0.001 PHE B 238 TYR 0.011 0.001 TYR A 274 ARG 0.001 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 1.143 Fit side-chains REVERT: A 146 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7412 (mmm) outliers start: 5 outliers final: 2 residues processed: 32 average time/residue: 1.7643 time to fit residues: 61.3548 Evaluate side-chains 32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 349 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 0.0170 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 0.0170 chunk 39 optimal weight: 0.3980 chunk 73 optimal weight: 6.9990 chunk 64 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.072610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.059039 restraints weight = 21934.449| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.48 r_work: 0.2779 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9726 Z= 0.102 Angle : 0.442 10.108 13224 Z= 0.243 Chirality : 0.042 0.124 1614 Planarity : 0.003 0.032 1695 Dihedral : 4.033 16.397 1350 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % 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: 0.90 (0.24), residues: 1254 helix: 2.59 (0.27), residues: 375 sheet: 0.29 (0.35), residues: 228 loop : -0.48 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 307 HIS 0.010 0.001 HIS C 349 PHE 0.005 0.001 PHE B 375 TYR 0.007 0.001 TYR C 206 ARG 0.001 0.000 ARG C 415 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 1.4399 time to fit residues: 48.7660 Evaluate side-chains 30 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 123 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.070214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056606 restraints weight = 22345.381| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.50 r_work: 0.2720 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9726 Z= 0.186 Angle : 0.498 12.040 13224 Z= 0.270 Chirality : 0.043 0.129 1614 Planarity : 0.003 0.035 1695 Dihedral : 4.091 16.663 1350 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.28 % Allowed : 8.72 % Favored : 91.00 % 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: 0.88 (0.24), residues: 1254 helix: 2.64 (0.28), residues: 375 sheet: 0.17 (0.32), residues: 258 loop : -0.51 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 307 HIS 0.002 0.001 HIS C 134 PHE 0.009 0.002 PHE B 238 TYR 0.012 0.001 TYR A 274 ARG 0.001 0.000 ARG C 415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 1.025 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 1.3468 time to fit residues: 47.1618 Evaluate side-chains 30 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain C residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.053041 restraints weight = 22507.927| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.48 r_work: 0.2640 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9726 Z= 0.322 Angle : 0.579 11.345 13224 Z= 0.318 Chirality : 0.045 0.139 1614 Planarity : 0.003 0.036 1695 Dihedral : 4.504 17.229 1350 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.64 % Allowed : 8.26 % Favored : 91.09 % 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: 0.67 (0.24), residues: 1254 helix: 2.66 (0.28), residues: 369 sheet: 0.07 (0.32), residues: 255 loop : -0.77 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 307 HIS 0.003 0.001 HIS C 134 PHE 0.013 0.002 PHE C 238 TYR 0.016 0.002 TYR A 274 ARG 0.002 0.000 ARG C 318 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4671.57 seconds wall clock time: 82 minutes 11.62 seconds (4931.62 seconds total)