Starting phenix.real_space_refine on Tue May 13 02:42:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmy_29300/05_2025/8fmy_29300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmy_29300/05_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_29300/05_2025/8fmy_29300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmy_29300/05_2025/8fmy_29300.map" model { file = "/net/cci-nas-00/data/ceres_data/8fmy_29300/05_2025/8fmy_29300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmy_29300/05_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-5687/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: 5.59, per 1000 atoms: 0.58 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: 2.24 Conformation dependent library (CDL) restraints added in 1.2 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: 1.30 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: 2.89 Time building geometry restraints manager: 2.61 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: 0.06 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: 0.870 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.200 Find NCS groups from input model: 0.180 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- 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 9738 Z= 0.401 Angle : 1.164 7.388 13248 Z= 0.716 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 Details of bonding type rmsd hydrogen bonds : bond 0.19047 ( 424) hydrogen bonds : angle 6.99219 ( 1146) SS BOND : bond 0.00989 ( 12) SS BOND : angle 2.74375 ( 24) covalent geometry : bond 0.00831 ( 9726) covalent geometry : angle 1.15894 (13224) *********************** 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 : 1.085 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.6826 time to fit residues: 101.7811 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 : 1.000 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.070712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.056601 restraints weight = 21949.235| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.52 r_work: 0.2699 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9738 Z= 0.161 Angle : 0.617 5.536 13248 Z= 0.352 Chirality : 0.045 0.139 1614 Planarity : 0.004 0.051 1695 Dihedral : 5.058 18.006 1350 Min Nonbonded Distance : 2.578 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: 0.43 (0.23), residues: 1254 helix: 1.18 (0.25), residues: 405 sheet: 0.48 (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 0.011 0.002 PHE A 234 TYR 0.013 0.002 TYR C 45 ARG 0.004 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.06122 ( 424) hydrogen bonds : angle 5.26779 ( 1146) SS BOND : bond 0.00195 ( 12) SS BOND : angle 1.03456 ( 24) covalent geometry : bond 0.00344 ( 9726) covalent geometry : angle 0.61608 (13224) *********************** 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 : 1.012 Fit side-chains REVERT: A 296 MET cc_start: 0.8668 (mtm) cc_final: 0.8454 (mtp) REVERT: B 426 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8181 (tt) outliers start: 9 outliers final: 2 residues processed: 38 average time/residue: 1.1375 time to fit residues: 47.5823 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 : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 426 ILE 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: 0.7980 chunk 97 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 ASN C 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.058049 restraints weight = 22184.930| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.54 r_work: 0.2734 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9738 Z= 0.119 Angle : 0.515 6.313 13248 Z= 0.289 Chirality : 0.043 0.159 1614 Planarity : 0.003 0.032 1695 Dihedral : 4.552 15.762 1350 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.28 % Allowed : 5.05 % Favored : 94.67 % 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: 2.19 (0.27), residues: 372 sheet: 0.34 (0.30), residues: 285 loop : -0.24 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 307 HIS 0.001 0.001 HIS C 134 PHE 0.008 0.001 PHE A 234 TYR 0.010 0.001 TYR A 274 ARG 0.003 0.000 ARG C 415 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 424) hydrogen bonds : angle 4.72191 ( 1146) SS BOND : bond 0.00195 ( 12) SS BOND : angle 0.78952 ( 24) covalent geometry : bond 0.00243 ( 9726) covalent geometry : angle 0.51452 (13224) *********************** 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 32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 1.108 Fit side-chains REVERT: A 296 MET cc_start: 0.8570 (mtm) cc_final: 0.8354 (mtp) REVERT: B 426 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8148 (tt) outliers start: 3 outliers final: 0 residues processed: 31 average time/residue: 1.4152 time to fit residues: 47.8514 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 : 1.048 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3030 r_free = 0.3030 target = 0.065827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.052009 restraints weight = 22455.212| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.51 r_work: 0.2599 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 9738 Z= 0.269 Angle : 0.652 5.376 13248 Z= 0.368 Chirality : 0.048 0.148 1614 Planarity : 0.004 0.042 1695 Dihedral : 4.965 17.984 1350 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.83 % Allowed : 5.23 % Favored : 93.94 % 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: 0.53 (0.24), residues: 1254 helix: 2.13 (0.27), residues: 369 sheet: 0.08 (0.32), residues: 246 loop : -0.59 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 307 HIS 0.003 0.001 HIS C 134 PHE 0.015 0.003 PHE A 234 TYR 0.017 0.002 TYR A 274 ARG 0.003 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.07452 ( 424) hydrogen bonds : angle 5.38383 ( 1146) SS BOND : bond 0.00381 ( 12) SS BOND : angle 1.20315 ( 24) covalent geometry : bond 0.00676 ( 9726) covalent geometry : angle 0.65068 (13224) *********************** 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 36 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 1.122 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 35 average time/residue: 1.2224 time to fit residues: 47.2651 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 : 1.165 ------------------------------------------------------------------------------- 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: 0.9980 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 0.0270 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.057001 restraints weight = 21853.699| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.48 r_work: 0.2715 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9738 Z= 0.104 Angle : 0.472 4.660 13248 Z= 0.267 Chirality : 0.043 0.137 1614 Planarity : 0.003 0.032 1695 Dihedral : 4.464 16.159 1350 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.83 % Allowed : 6.52 % Favored : 92.65 % 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: 0.68 (0.24), residues: 1254 helix: 2.33 (0.27), residues: 375 sheet: 0.11 (0.31), residues: 258 loop : -0.56 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 307 HIS 0.001 0.001 HIS C 134 PHE 0.006 0.001 PHE B 375 TYR 0.009 0.001 TYR B 300 ARG 0.001 0.000 ARG C 415 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 424) hydrogen bonds : angle 4.61533 ( 1146) SS BOND : bond 0.00138 ( 12) SS BOND : angle 0.69117 ( 24) covalent geometry : bond 0.00210 ( 9726) covalent geometry : angle 0.47165 (13224) *********************** 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 39 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 1.006 Fit side-chains REVERT: A 146 MET cc_start: 0.7513 (mmp) cc_final: 0.7275 (mmm) REVERT: B 146 MET cc_start: 0.7828 (mmm) cc_final: 0.7595 (mtp) REVERT: B 426 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8224 (tt) outliers start: 9 outliers final: 3 residues processed: 39 average time/residue: 1.1184 time to fit residues: 48.0515 Evaluate side-chains 32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 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: 5.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3134 r_free = 0.3134 target = 0.070870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057172 restraints weight = 21973.526| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.49 r_work: 0.2733 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9738 Z= 0.104 Angle : 0.465 5.351 13248 Z= 0.261 Chirality : 0.042 0.129 1614 Planarity : 0.003 0.036 1695 Dihedral : 4.217 16.266 1350 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.73 % Allowed : 6.89 % 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: 2.51 (0.27), residues: 375 sheet: 0.13 (0.31), residues: 258 loop : -0.51 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 307 HIS 0.002 0.001 HIS B 134 PHE 0.007 0.001 PHE B 238 TYR 0.010 0.001 TYR A 274 ARG 0.002 0.000 ARG C 415 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 424) hydrogen bonds : angle 4.48465 ( 1146) SS BOND : bond 0.00170 ( 12) SS BOND : angle 0.65252 ( 24) covalent geometry : bond 0.00221 ( 9726) covalent geometry : angle 0.46444 (13224) *********************** 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 37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 1.122 Fit side-chains REVERT: B 426 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8184 (tt) outliers start: 8 outliers final: 2 residues processed: 34 average time/residue: 1.3220 time to fit residues: 49.3186 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 : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 404 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.069310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.055652 restraints weight = 22192.660| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.48 r_work: 0.2698 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9738 Z= 0.135 Angle : 0.508 11.385 13248 Z= 0.282 Chirality : 0.043 0.135 1614 Planarity : 0.003 0.034 1695 Dihedral : 4.308 16.731 1350 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.83 % Allowed : 7.62 % Favored : 91.55 % 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: 0.80 (0.24), residues: 1254 helix: 2.57 (0.28), residues: 375 sheet: 0.09 (0.31), residues: 258 loop : -0.54 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.010 0.002 PHE B 238 TYR 0.012 0.001 TYR A 274 ARG 0.001 0.000 ARG C 415 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 424) hydrogen bonds : angle 4.64739 ( 1146) SS BOND : bond 0.00218 ( 12) SS BOND : angle 0.71233 ( 24) covalent geometry : bond 0.00315 ( 9726) covalent geometry : angle 0.50713 (13224) *********************** 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 : 1.094 Fit side-chains REVERT: B 426 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8253 (tt) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 1.1539 time to fit residues: 48.3426 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 : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 349 HIS Chi-restraints excluded: chain C residue 404 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.0060 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.054302 restraints weight = 22565.911| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.53 r_work: 0.2668 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9738 Z= 0.172 Angle : 0.552 11.610 13248 Z= 0.302 Chirality : 0.044 0.136 1614 Planarity : 0.003 0.036 1695 Dihedral : 4.410 16.605 1350 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.73 % Allowed : 8.08 % Favored : 91.18 % 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: 0.70 (0.24), residues: 1254 helix: 2.54 (0.28), residues: 375 sheet: 0.08 (0.31), residues: 255 loop : -0.67 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 307 HIS 0.004 0.001 HIS C 349 PHE 0.013 0.002 PHE B 238 TYR 0.014 0.001 TYR A 274 ARG 0.001 0.000 ARG C 108 Details of bonding type rmsd hydrogen bonds : bond 0.05653 ( 424) hydrogen bonds : angle 4.82380 ( 1146) SS BOND : bond 0.00252 ( 12) SS BOND : angle 0.81818 ( 24) covalent geometry : bond 0.00419 ( 9726) covalent geometry : angle 0.55157 (13224) *********************** 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 37 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 1.038 Fit side-chains REVERT: B 426 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8287 (tt) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 1.2302 time to fit residues: 48.5683 Evaluate side-chains 35 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 B residue 426 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 404 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 118 optimal weight: 0.0370 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.069035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.055331 restraints weight = 22104.310| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.50 r_work: 0.2690 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9738 Z= 0.131 Angle : 0.509 11.267 13248 Z= 0.280 Chirality : 0.043 0.131 1614 Planarity : 0.003 0.034 1695 Dihedral : 4.335 16.501 1350 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.46 % Allowed : 8.45 % 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: 0.75 (0.24), residues: 1254 helix: 2.62 (0.28), residues: 372 sheet: 0.07 (0.32), residues: 258 loop : -0.63 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 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 A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 424) hydrogen bonds : angle 4.68300 ( 1146) SS BOND : bond 0.00196 ( 12) SS BOND : angle 0.70121 ( 24) covalent geometry : bond 0.00302 ( 9726) covalent geometry : angle 0.50858 (13224) *********************** 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 35 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 1.030 Fit side-chains REVERT: A 146 MET cc_start: 0.8027 (mmm) cc_final: 0.7533 (mtp) REVERT: B 426 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8245 (tt) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 1.3183 time to fit residues: 50.5367 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 : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 404 LEU 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: 0.6980 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.070866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.057192 restraints weight = 22194.780| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.51 r_work: 0.2733 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9738 Z= 0.101 Angle : 0.472 11.621 13248 Z= 0.258 Chirality : 0.042 0.124 1614 Planarity : 0.003 0.033 1695 Dihedral : 4.150 16.489 1350 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.46 % Allowed : 8.63 % Favored : 90.91 % 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: 2.68 (0.28), residues: 372 sheet: 0.30 (0.30), residues: 288 loop : -0.54 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 307 HIS 0.001 0.000 HIS C 134 PHE 0.006 0.001 PHE B 281 TYR 0.010 0.001 TYR C 274 ARG 0.001 0.000 ARG C 415 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 424) hydrogen bonds : angle 4.44099 ( 1146) SS BOND : bond 0.00159 ( 12) SS BOND : angle 0.57742 ( 24) covalent geometry : bond 0.00215 ( 9726) covalent geometry : angle 0.47227 (13224) ********************** 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 35 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 1.146 Fit side-chains REVERT: A 146 MET cc_start: 0.7951 (mmm) cc_final: 0.7435 (mtp) REVERT: B 426 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8178 (tt) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 1.2394 time to fit residues: 48.0049 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 : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 225 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3044 r_free = 0.3044 target = 0.066279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.052642 restraints weight = 22505.384| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.49 r_work: 0.2631 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9738 Z= 0.228 Angle : 0.608 11.809 13248 Z= 0.331 Chirality : 0.045 0.140 1614 Planarity : 0.004 0.037 1695 Dihedral : 4.545 17.023 1350 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.73 % Allowed : 8.36 % Favored : 90.91 % 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: 0.62 (0.24), residues: 1254 helix: 2.58 (0.28), residues: 369 sheet: -0.00 (0.32), residues: 255 loop : -0.74 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 307 HIS 0.003 0.001 HIS C 134 PHE 0.013 0.002 PHE C 281 TYR 0.017 0.002 TYR A 274 ARG 0.002 0.000 ARG C 318 Details of bonding type rmsd hydrogen bonds : bond 0.06507 ( 424) hydrogen bonds : angle 5.05908 ( 1146) SS BOND : bond 0.00307 ( 12) SS BOND : angle 0.96456 ( 24) covalent geometry : bond 0.00570 ( 9726) covalent geometry : angle 0.60739 (13224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4553.47 seconds wall clock time: 79 minutes 40.96 seconds (4780.96 seconds total)