Starting phenix.real_space_refine on Fri Feb 14 01:40:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmy_29300/02_2025/8fmy_29300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmy_29300/02_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_29300/02_2025/8fmy_29300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmy_29300/02_2025/8fmy_29300.map" model { file = "/net/cci-nas-00/data/ceres_data/8fmy_29300/02_2025/8fmy_29300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmy_29300/02_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-5592/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: 5.65, per 1000 atoms: 0.59 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=4, 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 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 1.2 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: 1.29 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: 3.14 Time building geometry restraints manager: 2.92 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: 5494 15.33 - 30.65: 342 30.65 - 45.98: 62 45.98 - 61.31: 27 61.31 - 76.64: 18 Dihedral angle restraints: 5943 sinusoidal: 2274 harmonic: 3669 Sorted by residual: 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 dihedral pdb=" CA ASP A 440 " pdb=" C ASP A 440 " pdb=" N ASN A 441 " pdb=" CA ASN A 441 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA ASP B 440 " pdb=" C ASP B 440 " pdb=" N ASN B 441 " pdb=" CA ASN B 441 " ideal model delta harmonic sigma weight residual 180.00 163.24 16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5940 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: 2.03 - 2.61: 20 2.61 - 3.18: 7854 3.18 - 3.75: 12638 3.75 - 4.33: 18293 4.33 - 4.90: 31002 Nonbonded interactions: 69807 Sorted by model distance: nonbonded pdb=" SG CYS C 330 " pdb=" SG CYS C 339 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS B 330 " pdb=" SG CYS B 339 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS B 393 " pdb=" SG CYS B 416 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS C 393 " pdb=" SG CYS C 416 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS B 354 " pdb=" SG CYS B 362 " model vdw 2.041 3.760 ... (remaining 69802 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.390 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.110 ------------------------------------------------------------------------------- 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= 0.545 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 : 2.034 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 : 1.141 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.7932 time to fit residues: 108.3172 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 : 1.146 ------------------------------------------------------------------------------- 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: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.068943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.054938 restraints weight = 22294.559| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.54 r_work: 0.2674 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9726 Z= 0.267 Angle : 0.639 5.625 13224 Z= 0.365 Chirality : 0.046 0.140 1614 Planarity : 0.004 0.051 1695 Dihedral : 5.080 18.435 1350 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.83 % Allowed : 4.13 % Favored : 95.04 % 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: 0.27 (0.23), residues: 1254 helix: 1.03 (0.25), residues: 405 sheet: 0.54 (0.32), residues: 252 loop : -0.52 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 307 HIS 0.003 0.001 HIS B 257 PHE 0.012 0.002 PHE A 234 TYR 0.014 0.002 TYR A 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 43 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 1.146 Fit side-chains REVERT: A 296 MET cc_start: 0.8677 (mtm) cc_final: 0.8476 (mtp) REVERT: B 426 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8217 (tt) outliers start: 9 outliers final: 2 residues processed: 39 average time/residue: 1.2199 time to fit residues: 52.5658 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 : 1.157 ------------------------------------------------------------------------------- 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: 9.9990 chunk 97 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.068829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054912 restraints weight = 22578.015| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.55 r_work: 0.2667 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9726 Z= 0.223 Angle : 0.555 6.488 13224 Z= 0.314 Chirality : 0.044 0.160 1614 Planarity : 0.003 0.034 1695 Dihedral : 4.720 16.310 1350 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.73 % Allowed : 5.33 % 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: 0.76 (0.24), residues: 1254 helix: 2.07 (0.27), residues: 369 sheet: 0.31 (0.32), residues: 249 loop : -0.32 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 307 HIS 0.002 0.001 HIS C 257 PHE 0.010 0.002 PHE A 234 TYR 0.012 0.001 TYR A 274 ARG 0.002 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 36 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 1.070 Fit side-chains REVERT: A 296 MET cc_start: 0.8594 (mtm) cc_final: 0.8387 (mtp) REVERT: B 426 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8273 (tt) REVERT: C 146 MET cc_start: 0.7671 (mmp) cc_final: 0.7464 (mmm) outliers start: 8 outliers final: 1 residues processed: 34 average time/residue: 1.3262 time to fit residues: 49.3769 Evaluate side-chains 29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 HIS 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: 10.0000 chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 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 = 0.2991 r_free = 0.2991 target = 0.063562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.050100 restraints weight = 22890.766| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.48 r_work: 0.2558 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 9726 Z= 0.608 Angle : 0.736 6.242 13224 Z= 0.413 Chirality : 0.051 0.143 1614 Planarity : 0.004 0.042 1695 Dihedral : 5.228 18.332 1350 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.01 % Allowed : 6.52 % Favored : 92.47 % 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: 0.13 (0.24), residues: 1254 helix: 1.59 (0.27), residues: 387 sheet: 0.03 (0.33), residues: 249 loop : -0.86 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 307 HIS 0.003 0.001 HIS C 257 PHE 0.019 0.003 PHE C 281 TYR 0.018 0.002 TYR B 274 ARG 0.003 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 38 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 1.217 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 36 average time/residue: 1.3255 time to fit residues: 52.3794 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 : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A 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: 2.9990 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3093 r_free = 0.3093 target = 0.069046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.055444 restraints weight = 22229.143| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.51 r_work: 0.2684 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9726 Z= 0.149 Angle : 0.489 5.043 13224 Z= 0.277 Chirality : 0.043 0.140 1614 Planarity : 0.003 0.032 1695 Dihedral : 4.589 16.181 1350 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.92 % Allowed : 7.71 % 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: 0.44 (0.24), residues: 1254 helix: 2.12 (0.27), residues: 372 sheet: 0.04 (0.31), residues: 258 loop : -0.73 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 307 HIS 0.001 0.001 HIS C 134 PHE 0.006 0.001 PHE A 281 TYR 0.009 0.001 TYR B 300 ARG 0.002 0.000 ARG C 415 *********************** 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 40 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 1.162 Fit side-chains REVERT: B 426 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8282 (tt) outliers start: 10 outliers final: 3 residues processed: 39 average time/residue: 1.2066 time to fit residues: 51.7613 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 : 1.295 ------------------------------------------------------------------------------- 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 210 ILE 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: 1.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.067125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053588 restraints weight = 22561.208| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.51 r_work: 0.2650 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9726 Z= 0.255 Angle : 0.528 5.422 13224 Z= 0.298 Chirality : 0.044 0.138 1614 Planarity : 0.003 0.037 1695 Dihedral : 4.531 16.650 1350 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.47 % Allowed : 7.71 % Favored : 90.82 % 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: 0.49 (0.24), residues: 1254 helix: 2.22 (0.28), residues: 375 sheet: 0.07 (0.32), residues: 255 loop : -0.76 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.011 0.002 PHE C 238 TYR 0.013 0.001 TYR A 274 ARG 0.002 0.000 ARG C 415 *********************** 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 45 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 1.031 Fit side-chains REVERT: B 426 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8307 (tt) REVERT: C 390 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8195 (tp) outliers start: 16 outliers final: 6 residues processed: 42 average time/residue: 1.1953 time to fit residues: 55.0691 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 : 1.085 ------------------------------------------------------------------------------- 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 393 CYS Chi-restraints excluded: chain B residue 426 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 Chi-restraints excluded: chain C residue 390 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 5.9990 chunk 4 optimal weight: 0.0270 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.066357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052955 restraints weight = 22700.357| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.48 r_work: 0.2638 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9726 Z= 0.273 Angle : 0.536 6.988 13224 Z= 0.302 Chirality : 0.044 0.136 1614 Planarity : 0.003 0.034 1695 Dihedral : 4.576 16.831 1350 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.29 % Allowed : 7.62 % 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: 0.42 (0.24), residues: 1254 helix: 2.18 (0.28), residues: 375 sheet: 0.02 (0.32), residues: 255 loop : -0.81 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.011 0.002 PHE A 238 TYR 0.014 0.001 TYR A 274 ARG 0.001 0.000 ARG C 108 *********************** 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 43 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 1.035 Fit side-chains REVERT: A 146 MET cc_start: 0.7766 (mmp) cc_final: 0.7519 (mmm) REVERT: B 390 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8199 (tp) REVERT: B 426 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8313 (tt) REVERT: C 390 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8264 (tp) outliers start: 14 outliers final: 6 residues processed: 43 average time/residue: 1.3362 time to fit residues: 62.5269 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 : 1.142 ------------------------------------------------------------------------------- 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 390 ILE Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 390 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3053 r_free = 0.3053 target = 0.066697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.053243 restraints weight = 22841.984| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.51 r_work: 0.2644 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9726 Z= 0.244 Angle : 0.521 7.770 13224 Z= 0.293 Chirality : 0.044 0.134 1614 Planarity : 0.003 0.035 1695 Dihedral : 4.515 16.890 1350 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.38 % Allowed : 7.81 % Favored : 90.82 % 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: 0.44 (0.24), residues: 1254 helix: 2.22 (0.28), residues: 375 sheet: 0.01 (0.32), residues: 255 loop : -0.79 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.010 0.002 PHE B 238 TYR 0.013 0.001 TYR A 274 ARG 0.001 0.000 ARG C 415 *********************** 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 44 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 1.043 Fit side-chains REVERT: A 146 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7537 (mmm) REVERT: B 390 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8198 (tp) REVERT: B 426 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8309 (tt) REVERT: C 390 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8272 (tp) outliers start: 15 outliers final: 8 residues processed: 42 average time/residue: 1.2799 time to fit residues: 58.8395 Evaluate side-chains 41 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 209 ILE 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 390 ILE Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 390 ILE 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: 5.9990 chunk 121 optimal weight: 7.9990 chunk 118 optimal weight: 0.0270 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 0.0570 chunk 64 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.070636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.057191 restraints weight = 22171.973| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.49 r_work: 0.2736 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2934 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= 0.123 Angle : 0.465 12.842 13224 Z= 0.254 Chirality : 0.042 0.126 1614 Planarity : 0.003 0.031 1695 Dihedral : 4.196 16.474 1350 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.55 % Allowed : 8.82 % Favored : 90.63 % 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: 0.74 (0.24), residues: 1254 helix: 2.33 (0.28), residues: 375 sheet: 0.27 (0.30), residues: 288 loop : -0.59 (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 C 28 PHE 0.005 0.001 PHE B 375 TYR 0.009 0.001 TYR C 274 ARG 0.001 0.000 ARG B 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 36 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 1.170 Fit side-chains REVERT: B 390 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8075 (tp) REVERT: B 426 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8210 (tt) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.3052 time to fit residues: 51.6444 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 : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 393 CYS Chi-restraints excluded: chain B residue 426 ILE 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 105 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.0020 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4866 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.071477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057989 restraints weight = 22402.352| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.51 r_work: 0.2754 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3029 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= 0.113 Angle : 0.449 10.198 13224 Z= 0.246 Chirality : 0.042 0.124 1614 Planarity : 0.003 0.031 1695 Dihedral : 4.034 16.597 1350 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.28 % Allowed : 9.27 % Favored : 90.45 % 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: 0.86 (0.24), residues: 1254 helix: 2.48 (0.27), residues: 375 sheet: 0.42 (0.33), residues: 258 loop : -0.56 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 307 HIS 0.001 0.000 HIS C 134 PHE 0.005 0.001 PHE B 375 TYR 0.011 0.001 TYR C 206 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 32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 1.253 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 1.3815 time to fit residues: 48.5346 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 : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain B residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 125 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054855 restraints weight = 22588.651| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.53 r_work: 0.2682 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9726 Z= 0.223 Angle : 0.524 11.659 13224 Z= 0.283 Chirality : 0.043 0.131 1614 Planarity : 0.003 0.034 1695 Dihedral : 4.197 16.829 1350 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.37 % Allowed : 9.37 % Favored : 90.27 % 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: 0.83 (0.24), residues: 1254 helix: 2.48 (0.28), residues: 375 sheet: 0.28 (0.30), residues: 288 loop : -0.57 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 307 HIS 0.002 0.001 HIS C 134 PHE 0.010 0.002 PHE C 281 TYR 0.013 0.001 TYR A 274 ARG 0.001 0.000 ARG B 415 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.32 seconds wall clock time: 78 minutes 26.11 seconds (4706.11 seconds total)