Starting phenix.real_space_refine on Sat Mar 16 06:43:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/03_2024/7oo8_13007.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/03_2024/7oo8_13007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/03_2024/7oo8_13007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/03_2024/7oo8_13007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/03_2024/7oo8_13007.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/03_2024/7oo8_13007.pdb" } resolution = 3.7 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= 0.000 sd= 0.006 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 42 5.16 5 C 8932 2.51 5 N 2436 2.21 5 O 2513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13923 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "B" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "C" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "D" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "E" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "G" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Time building chain proxies: 6.64, per 1000 atoms: 0.48 Number of scatterers: 13923 At special positions: 0 Unit cell: (98.9055, 98.9055, 141.446, 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 42 16.00 O 2513 8.00 N 2436 7.00 C 8932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.30 Conformation dependent library (CDL) restraints added in 2.6 seconds 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 55.9% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 22 through 59 removed outlier: 3.508A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 93 through 128 removed outlier: 4.700A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 22 through 59 removed outlier: 3.508A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 Processing helix chain 'B' and resid 93 through 128 removed outlier: 4.700A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 22 through 59 removed outlier: 3.508A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 90 Processing helix chain 'C' and resid 93 through 128 removed outlier: 4.700A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 22 through 59 removed outlier: 3.509A pdb=" N ARG D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Processing helix chain 'D' and resid 93 through 128 removed outlier: 4.700A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 22 through 59 removed outlier: 3.509A pdb=" N ARG E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 90 Processing helix chain 'E' and resid 93 through 128 removed outlier: 4.701A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 22 through 59 removed outlier: 3.509A pdb=" N ARG F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 90 Processing helix chain 'F' and resid 93 through 128 removed outlier: 4.699A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 22 through 59 removed outlier: 3.509A pdb=" N ARG G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 90 Processing helix chain 'G' and resid 93 through 128 removed outlier: 4.699A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N SER G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.679A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.808A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278 removed outlier: 8.288A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N MET C 273 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N MET D 273 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP C 274 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASN C 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE D 277 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS C 278 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N MET F 273 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP E 274 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LYS E 278 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N MET G 273 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.809A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.809A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.808A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.808A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.809A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.808A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 1055 hydrogen bonds defined for protein. 3081 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: 5.74 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4654 1.34 - 1.46: 2133 1.46 - 1.57: 7227 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 14098 Sorted by residual: bond pdb=" C ARG C 128 " pdb=" O ARG C 128 " ideal model delta sigma weight residual 1.235 1.231 0.003 4.70e-03 4.53e+04 5.50e-01 bond pdb=" C ARG G 128 " pdb=" O ARG G 128 " ideal model delta sigma weight residual 1.235 1.232 0.003 4.70e-03 4.53e+04 4.64e-01 bond pdb=" C ARG E 128 " pdb=" O ARG E 128 " ideal model delta sigma weight residual 1.235 1.232 0.003 4.70e-03 4.53e+04 4.48e-01 bond pdb=" N ILE D 165 " pdb=" CA ILE D 165 " ideal model delta sigma weight residual 1.460 1.454 0.006 9.30e-03 1.16e+04 4.42e-01 bond pdb=" C ARG F 128 " pdb=" O ARG F 128 " ideal model delta sigma weight residual 1.235 1.232 0.003 4.70e-03 4.53e+04 4.12e-01 ... (remaining 14093 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.30: 237 107.30 - 113.96: 8450 113.96 - 120.63: 5556 120.63 - 127.29: 4811 127.29 - 133.95: 63 Bond angle restraints: 19117 Sorted by residual: angle pdb=" N ILE B 83 " pdb=" CA ILE B 83 " pdb=" CB ILE B 83 " ideal model delta sigma weight residual 110.77 113.99 -3.22 1.81e+00 3.05e-01 3.16e+00 angle pdb=" N ILE D 83 " pdb=" CA ILE D 83 " pdb=" CB ILE D 83 " ideal model delta sigma weight residual 110.77 113.96 -3.19 1.81e+00 3.05e-01 3.12e+00 angle pdb=" N ILE C 83 " pdb=" CA ILE C 83 " pdb=" CB ILE C 83 " ideal model delta sigma weight residual 110.77 113.95 -3.18 1.81e+00 3.05e-01 3.08e+00 angle pdb=" N ILE E 83 " pdb=" CA ILE E 83 " pdb=" CB ILE E 83 " ideal model delta sigma weight residual 110.77 113.91 -3.14 1.81e+00 3.05e-01 3.02e+00 angle pdb=" N ILE F 83 " pdb=" CA ILE F 83 " pdb=" CB ILE F 83 " ideal model delta sigma weight residual 110.77 113.91 -3.14 1.81e+00 3.05e-01 3.00e+00 ... (remaining 19112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.84: 7336 9.84 - 19.68: 805 19.68 - 29.51: 238 29.51 - 39.35: 91 39.35 - 49.19: 14 Dihedral angle restraints: 8484 sinusoidal: 3248 harmonic: 5236 Sorted by residual: dihedral pdb=" C ILE C 83 " pdb=" N ILE C 83 " pdb=" CA ILE C 83 " pdb=" CB ILE C 83 " ideal model delta harmonic sigma weight residual -122.00 -130.26 8.26 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" C ILE A 83 " pdb=" N ILE A 83 " pdb=" CA ILE A 83 " pdb=" CB ILE A 83 " ideal model delta harmonic sigma weight residual -122.00 -130.24 8.24 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" C ILE B 83 " pdb=" N ILE B 83 " pdb=" CA ILE B 83 " pdb=" CB ILE B 83 " ideal model delta harmonic sigma weight residual -122.00 -130.22 8.22 0 2.50e+00 1.60e-01 1.08e+01 ... (remaining 8481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1774 0.042 - 0.083: 410 0.083 - 0.125: 140 0.125 - 0.166: 14 0.166 - 0.208: 7 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CA ILE C 83 " pdb=" N ILE C 83 " pdb=" C ILE C 83 " pdb=" CB ILE C 83 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE B 83 " pdb=" N ILE B 83 " pdb=" C ILE B 83 " pdb=" CB ILE B 83 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 83 " pdb=" N ILE A 83 " pdb=" C ILE A 83 " pdb=" CB ILE A 83 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2342 not shown) Planarity restraints: 2429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 275 " 0.004 2.00e-02 2.50e+03 7.56e-03 5.71e-01 pdb=" C VAL G 275 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL G 275 " 0.005 2.00e-02 2.50e+03 pdb=" N ASN G 276 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 275 " 0.004 2.00e-02 2.50e+03 7.54e-03 5.69e-01 pdb=" C VAL D 275 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL D 275 " 0.005 2.00e-02 2.50e+03 pdb=" N ASN D 276 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 275 " 0.004 2.00e-02 2.50e+03 7.52e-03 5.65e-01 pdb=" C VAL E 275 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL E 275 " 0.005 2.00e-02 2.50e+03 pdb=" N ASN E 276 " 0.004 2.00e-02 2.50e+03 ... (remaining 2426 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3570 2.81 - 3.33: 14071 3.33 - 3.85: 23177 3.85 - 4.38: 25652 4.38 - 4.90: 45696 Nonbonded interactions: 112166 Sorted by model distance: nonbonded pdb=" NZ LYS B 202 " pdb=" OE1 GLU C 255 " model vdw 2.286 2.520 nonbonded pdb=" NH2 ARG E 88 " pdb=" O GLY F 90 " model vdw 2.291 2.520 nonbonded pdb=" NH2 ARG D 88 " pdb=" O GLY E 90 " model vdw 2.292 2.520 nonbonded pdb=" NH2 ARG C 88 " pdb=" O GLY D 90 " model vdw 2.293 2.520 nonbonded pdb=" NH2 ARG F 88 " pdb=" O GLY G 90 " model vdw 2.310 2.520 ... (remaining 112161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.410 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: 0.000 Extract box with map and model: 6.150 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 37.000 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 14098 Z= 0.185 Angle : 0.399 4.564 19117 Z= 0.228 Chirality : 0.041 0.208 2345 Planarity : 0.002 0.018 2429 Dihedral : 9.895 49.189 5110 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % 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: 2.79 (0.19), residues: 1813 helix: 3.46 (0.15), residues: 1008 sheet: 0.09 (0.28), residues: 294 loop : -0.47 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 240 PHE 0.005 0.001 PHE G 188 TYR 0.006 0.001 TYR D 135 ARG 0.002 0.000 ARG F 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 1.560 Fit side-chains REVERT: A 43 ILE cc_start: 0.7702 (tp) cc_final: 0.7461 (tp) REVERT: A 47 MET cc_start: 0.7030 (mmt) cc_final: 0.6676 (mmt) REVERT: A 50 ASN cc_start: 0.7164 (m-40) cc_final: 0.6843 (t0) REVERT: A 144 THR cc_start: 0.8965 (m) cc_final: 0.8337 (p) REVERT: A 199 ASP cc_start: 0.8183 (p0) cc_final: 0.7824 (p0) REVERT: A 212 GLU cc_start: 0.6741 (tp30) cc_final: 0.6307 (tp30) REVERT: B 40 VAL cc_start: 0.8419 (t) cc_final: 0.7842 (m) REVERT: B 78 ILE cc_start: 0.8065 (pt) cc_final: 0.7447 (mt) REVERT: C 50 ASN cc_start: 0.7503 (m-40) cc_final: 0.7158 (t0) REVERT: C 78 ILE cc_start: 0.8329 (pt) cc_final: 0.7673 (mt) REVERT: D 199 ASP cc_start: 0.8112 (p0) cc_final: 0.7859 (p0) REVERT: E 78 ILE cc_start: 0.8410 (pt) cc_final: 0.7836 (mt) REVERT: F 31 ILE cc_start: 0.9023 (tp) cc_final: 0.8605 (mm) REVERT: F 78 ILE cc_start: 0.8463 (pt) cc_final: 0.7859 (mt) REVERT: F 155 MET cc_start: 0.8772 (ptp) cc_final: 0.8571 (ptm) REVERT: G 40 VAL cc_start: 0.8501 (t) cc_final: 0.8209 (m) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.2400 time to fit residues: 148.9548 Evaluate side-chains 311 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN D 149 GLN E 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14098 Z= 0.294 Angle : 0.500 4.798 19117 Z= 0.275 Chirality : 0.042 0.175 2345 Planarity : 0.004 0.033 2429 Dihedral : 3.991 13.102 1988 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.05 % Allowed : 14.62 % Favored : 82.33 % 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: 2.50 (0.19), residues: 1813 helix: 3.16 (0.14), residues: 1008 sheet: -0.08 (0.27), residues: 294 loop : -0.41 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 251 PHE 0.022 0.002 PHE A 277 TYR 0.008 0.001 TYR F 250 ARG 0.008 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 317 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7376 (mm) REVERT: A 47 MET cc_start: 0.7038 (mmt) cc_final: 0.6713 (mmt) REVERT: A 199 ASP cc_start: 0.8240 (p0) cc_final: 0.7774 (p0) REVERT: C 50 ASN cc_start: 0.7363 (m-40) cc_final: 0.7087 (t0) REVERT: C 78 ILE cc_start: 0.8135 (pt) cc_final: 0.7666 (mt) REVERT: C 273 MET cc_start: 0.8661 (tpp) cc_final: 0.8151 (tpp) REVERT: D 199 ASP cc_start: 0.8138 (p0) cc_final: 0.7825 (p0) REVERT: E 81 THR cc_start: 0.9070 (m) cc_final: 0.8811 (t) REVERT: E 255 GLU cc_start: 0.8544 (tt0) cc_final: 0.8317 (tt0) REVERT: F 78 ILE cc_start: 0.8417 (pt) cc_final: 0.7867 (mt) REVERT: G 81 THR cc_start: 0.9060 (m) cc_final: 0.8810 (t) outliers start: 45 outliers final: 31 residues processed: 328 average time/residue: 0.2207 time to fit residues: 109.2172 Evaluate side-chains 309 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 277 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 0.0980 chunk 137 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14098 Z= 0.144 Angle : 0.422 4.884 19117 Z= 0.232 Chirality : 0.041 0.196 2345 Planarity : 0.003 0.037 2429 Dihedral : 3.810 13.243 1988 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.17 % Allowed : 18.01 % Favored : 79.82 % 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: 2.70 (0.19), residues: 1813 helix: 3.36 (0.15), residues: 1008 sheet: 0.55 (0.29), residues: 259 loop : -0.74 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 251 PHE 0.028 0.002 PHE D 277 TYR 0.004 0.001 TYR C 250 ARG 0.010 0.000 ARG E 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 339 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 50 ASN cc_start: 0.7002 (m110) cc_final: 0.6612 (t0) REVERT: A 81 THR cc_start: 0.9172 (m) cc_final: 0.8829 (t) REVERT: A 199 ASP cc_start: 0.8180 (p0) cc_final: 0.7778 (p0) REVERT: B 44 ILE cc_start: 0.8534 (mt) cc_final: 0.8330 (mm) REVERT: B 81 THR cc_start: 0.9077 (m) cc_final: 0.8873 (t) REVERT: C 50 ASN cc_start: 0.7274 (m-40) cc_final: 0.7052 (t0) REVERT: C 78 ILE cc_start: 0.8157 (pt) cc_final: 0.7817 (mt) REVERT: C 81 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8758 (t) REVERT: C 273 MET cc_start: 0.8649 (tpp) cc_final: 0.8427 (tpp) REVERT: D 199 ASP cc_start: 0.8065 (p0) cc_final: 0.7755 (p0) REVERT: D 247 GLN cc_start: 0.7888 (tp40) cc_final: 0.7588 (tp-100) REVERT: D 277 PHE cc_start: 0.6064 (m-10) cc_final: 0.5551 (m-10) REVERT: E 81 THR cc_start: 0.8997 (m) cc_final: 0.8696 (t) REVERT: E 255 GLU cc_start: 0.8505 (tt0) cc_final: 0.8284 (tt0) REVERT: F 31 ILE cc_start: 0.8958 (tp) cc_final: 0.8616 (mm) REVERT: F 78 ILE cc_start: 0.8390 (pt) cc_final: 0.7841 (mt) REVERT: G 46 ARG cc_start: 0.5653 (ttp-170) cc_final: 0.5209 (mtm180) REVERT: G 81 THR cc_start: 0.9063 (m) cc_final: 0.8823 (t) outliers start: 32 outliers final: 21 residues processed: 349 average time/residue: 0.2105 time to fit residues: 112.4481 Evaluate side-chains 320 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 298 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 227 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14098 Z= 0.171 Angle : 0.425 5.398 19117 Z= 0.232 Chirality : 0.041 0.192 2345 Planarity : 0.003 0.041 2429 Dihedral : 3.785 14.174 1988 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.98 % Allowed : 19.23 % Favored : 77.79 % 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: 2.71 (0.19), residues: 1813 helix: 3.33 (0.15), residues: 1015 sheet: 0.65 (0.28), residues: 273 loop : -0.80 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 251 PHE 0.028 0.002 PHE D 277 TYR 0.005 0.001 TYR C 250 ARG 0.011 0.000 ARG E 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 319 time to evaluate : 1.673 Fit side-chains REVERT: A 50 ASN cc_start: 0.7065 (m110) cc_final: 0.6626 (t0) REVERT: A 81 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8842 (t) REVERT: A 199 ASP cc_start: 0.8271 (p0) cc_final: 0.7877 (p0) REVERT: B 44 ILE cc_start: 0.8563 (mt) cc_final: 0.8363 (mm) REVERT: C 50 ASN cc_start: 0.7281 (m-40) cc_final: 0.7059 (t0) REVERT: C 78 ILE cc_start: 0.8178 (pt) cc_final: 0.7827 (mt) REVERT: C 81 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8732 (t) REVERT: C 273 MET cc_start: 0.8585 (tpp) cc_final: 0.8100 (tpp) REVERT: D 199 ASP cc_start: 0.8085 (p0) cc_final: 0.7758 (p0) REVERT: D 277 PHE cc_start: 0.5901 (m-10) cc_final: 0.5427 (m-10) REVERT: E 81 THR cc_start: 0.9080 (m) cc_final: 0.8821 (t) REVERT: E 255 GLU cc_start: 0.8517 (tt0) cc_final: 0.8274 (tt0) REVERT: F 78 ILE cc_start: 0.8374 (pt) cc_final: 0.7834 (mt) REVERT: F 273 MET cc_start: 0.8861 (tpp) cc_final: 0.8452 (tpp) REVERT: G 46 ARG cc_start: 0.5669 (ttp-170) cc_final: 0.5211 (mtm180) REVERT: G 81 THR cc_start: 0.9111 (m) cc_final: 0.8882 (t) outliers start: 44 outliers final: 33 residues processed: 335 average time/residue: 0.2031 time to fit residues: 104.6416 Evaluate side-chains 329 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 294 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 227 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.0050 chunk 99 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 0.0030 chunk 72 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14098 Z= 0.124 Angle : 0.411 6.035 19117 Z= 0.222 Chirality : 0.041 0.212 2345 Planarity : 0.003 0.040 2429 Dihedral : 3.683 15.292 1988 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.17 % Allowed : 20.24 % Favored : 77.59 % 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: 2.79 (0.19), residues: 1813 helix: 3.40 (0.15), residues: 1015 sheet: 1.10 (0.30), residues: 238 loop : -0.91 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 251 PHE 0.030 0.001 PHE A 277 TYR 0.003 0.001 TYR D 250 ARG 0.009 0.000 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 345 time to evaluate : 1.699 Fit side-chains REVERT: A 50 ASN cc_start: 0.7020 (m110) cc_final: 0.6593 (t0) REVERT: A 81 THR cc_start: 0.9171 (m) cc_final: 0.8840 (t) REVERT: C 50 ASN cc_start: 0.7335 (m-40) cc_final: 0.7064 (t0) REVERT: C 78 ILE cc_start: 0.8193 (pt) cc_final: 0.7800 (mt) REVERT: C 81 THR cc_start: 0.9130 (m) cc_final: 0.8888 (t) REVERT: C 273 MET cc_start: 0.8515 (tpp) cc_final: 0.8036 (tpp) REVERT: D 199 ASP cc_start: 0.8055 (p0) cc_final: 0.7759 (p0) REVERT: D 277 PHE cc_start: 0.5779 (m-10) cc_final: 0.5322 (m-10) REVERT: E 81 THR cc_start: 0.9080 (m) cc_final: 0.8835 (t) REVERT: E 255 GLU cc_start: 0.8487 (tt0) cc_final: 0.8260 (tt0) REVERT: F 78 ILE cc_start: 0.8298 (pt) cc_final: 0.7789 (mt) REVERT: F 273 MET cc_start: 0.8848 (tpp) cc_final: 0.8459 (tpp) REVERT: G 46 ARG cc_start: 0.5616 (ttp-170) cc_final: 0.5185 (mtm180) REVERT: G 81 THR cc_start: 0.9097 (m) cc_final: 0.8870 (t) REVERT: G 277 PHE cc_start: 0.5979 (m-10) cc_final: 0.5707 (m-10) outliers start: 32 outliers final: 16 residues processed: 358 average time/residue: 0.2068 time to fit residues: 113.8159 Evaluate side-chains 323 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 307 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 227 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 0.1980 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14098 Z= 0.135 Angle : 0.421 6.681 19117 Z= 0.224 Chirality : 0.041 0.218 2345 Planarity : 0.002 0.048 2429 Dihedral : 3.651 14.311 1988 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.51 % Allowed : 19.91 % Favored : 77.59 % 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: 2.79 (0.19), residues: 1813 helix: 3.38 (0.15), residues: 1015 sheet: 1.13 (0.30), residues: 238 loop : -0.88 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 251 PHE 0.018 0.001 PHE F 277 TYR 0.005 0.001 TYR A 250 ARG 0.008 0.000 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 321 time to evaluate : 1.615 Fit side-chains REVERT: A 50 ASN cc_start: 0.7023 (m110) cc_final: 0.6588 (t0) REVERT: A 81 THR cc_start: 0.9179 (m) cc_final: 0.8866 (t) REVERT: A 199 ASP cc_start: 0.8261 (p0) cc_final: 0.7850 (p0) REVERT: B 100 LEU cc_start: 0.8725 (tp) cc_final: 0.8491 (mm) REVERT: C 50 ASN cc_start: 0.7281 (m-40) cc_final: 0.7049 (t0) REVERT: C 78 ILE cc_start: 0.8197 (pt) cc_final: 0.7794 (mt) REVERT: C 81 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8865 (t) REVERT: C 273 MET cc_start: 0.8540 (tpp) cc_final: 0.8066 (tpp) REVERT: D 199 ASP cc_start: 0.8163 (p0) cc_final: 0.7790 (p0) REVERT: D 277 PHE cc_start: 0.5748 (m-10) cc_final: 0.5282 (m-10) REVERT: E 81 THR cc_start: 0.9063 (m) cc_final: 0.8813 (t) REVERT: E 255 GLU cc_start: 0.8476 (tt0) cc_final: 0.8271 (tt0) REVERT: F 78 ILE cc_start: 0.8300 (pt) cc_final: 0.7787 (mt) REVERT: F 273 MET cc_start: 0.8853 (tpp) cc_final: 0.8495 (tpp) REVERT: G 46 ARG cc_start: 0.5642 (ttp-170) cc_final: 0.5209 (mtm180) REVERT: G 81 THR cc_start: 0.9123 (m) cc_final: 0.8890 (t) REVERT: G 277 PHE cc_start: 0.6154 (m-10) cc_final: 0.5679 (m-10) outliers start: 37 outliers final: 30 residues processed: 335 average time/residue: 0.2113 time to fit residues: 109.3284 Evaluate side-chains 327 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 296 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 227 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 0.0170 chunk 148 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 14098 Z= 0.133 Angle : 0.424 6.301 19117 Z= 0.226 Chirality : 0.041 0.229 2345 Planarity : 0.002 0.049 2429 Dihedral : 3.593 13.877 1988 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.51 % Allowed : 20.24 % Favored : 77.25 % 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: 2.77 (0.19), residues: 1813 helix: 3.35 (0.15), residues: 1015 sheet: 1.12 (0.30), residues: 238 loop : -0.87 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 251 PHE 0.013 0.001 PHE F 277 TYR 0.005 0.000 TYR C 250 ARG 0.010 0.000 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 314 time to evaluate : 1.660 Fit side-chains REVERT: A 50 ASN cc_start: 0.7019 (m110) cc_final: 0.6584 (t0) REVERT: A 81 THR cc_start: 0.9175 (m) cc_final: 0.8858 (t) REVERT: C 50 ASN cc_start: 0.7330 (m-40) cc_final: 0.7081 (t0) REVERT: C 78 ILE cc_start: 0.8197 (pt) cc_final: 0.7797 (mt) REVERT: C 81 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8846 (t) REVERT: C 273 MET cc_start: 0.8492 (tpp) cc_final: 0.8074 (tpp) REVERT: D 277 PHE cc_start: 0.5685 (m-10) cc_final: 0.5268 (m-10) REVERT: E 81 THR cc_start: 0.9046 (m) cc_final: 0.8798 (t) REVERT: E 255 GLU cc_start: 0.8433 (tt0) cc_final: 0.8023 (tt0) REVERT: F 78 ILE cc_start: 0.8295 (pt) cc_final: 0.7782 (mt) REVERT: F 273 MET cc_start: 0.8831 (tpp) cc_final: 0.8518 (tpp) REVERT: G 46 ARG cc_start: 0.5641 (ttp-170) cc_final: 0.5200 (mtm180) REVERT: G 81 THR cc_start: 0.9114 (m) cc_final: 0.8901 (t) outliers start: 37 outliers final: 29 residues processed: 330 average time/residue: 0.2086 time to fit residues: 105.6780 Evaluate side-chains 327 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 297 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 227 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 52 optimal weight: 0.0470 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14098 Z= 0.128 Angle : 0.421 6.361 19117 Z= 0.223 Chirality : 0.041 0.229 2345 Planarity : 0.002 0.056 2429 Dihedral : 3.570 13.411 1988 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.64 % Allowed : 20.11 % Favored : 77.25 % 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: 2.75 (0.19), residues: 1813 helix: 3.33 (0.15), residues: 1015 sheet: 1.14 (0.30), residues: 238 loop : -0.88 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 251 PHE 0.012 0.001 PHE A 80 TYR 0.003 0.000 TYR C 250 ARG 0.011 0.000 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 307 time to evaluate : 1.698 Fit side-chains REVERT: A 50 ASN cc_start: 0.7029 (m110) cc_final: 0.6587 (t0) REVERT: A 81 THR cc_start: 0.9228 (m) cc_final: 0.8913 (t) REVERT: B 81 THR cc_start: 0.9185 (m) cc_final: 0.8960 (t) REVERT: C 50 ASN cc_start: 0.7328 (m-40) cc_final: 0.7080 (t0) REVERT: C 78 ILE cc_start: 0.8195 (pt) cc_final: 0.7790 (mt) REVERT: C 81 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8860 (t) REVERT: C 273 MET cc_start: 0.8617 (tpp) cc_final: 0.8046 (tpp) REVERT: D 277 PHE cc_start: 0.5714 (m-10) cc_final: 0.5255 (m-10) REVERT: E 81 THR cc_start: 0.9056 (m) cc_final: 0.8800 (t) REVERT: E 255 GLU cc_start: 0.8430 (tt0) cc_final: 0.8025 (tt0) REVERT: F 78 ILE cc_start: 0.8295 (pt) cc_final: 0.7781 (mt) REVERT: F 273 MET cc_start: 0.8816 (tpp) cc_final: 0.8528 (tpp) REVERT: G 46 ARG cc_start: 0.5577 (ttp-170) cc_final: 0.5170 (mtm180) REVERT: G 81 THR cc_start: 0.9107 (m) cc_final: 0.8892 (t) outliers start: 39 outliers final: 34 residues processed: 321 average time/residue: 0.2101 time to fit residues: 103.8365 Evaluate side-chains 339 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 304 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 227 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14098 Z= 0.169 Angle : 0.435 5.922 19117 Z= 0.231 Chirality : 0.041 0.233 2345 Planarity : 0.003 0.055 2429 Dihedral : 3.648 12.903 1988 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.71 % Allowed : 19.97 % Favored : 77.32 % 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: 2.66 (0.19), residues: 1813 helix: 3.25 (0.15), residues: 1015 sheet: 1.09 (0.30), residues: 238 loop : -0.89 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 240 PHE 0.012 0.001 PHE B 80 TYR 0.005 0.001 TYR C 250 ARG 0.012 0.000 ARG G 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 305 time to evaluate : 1.699 Fit side-chains REVERT: A 50 ASN cc_start: 0.7003 (m110) cc_final: 0.6554 (t0) REVERT: A 81 THR cc_start: 0.9188 (m) cc_final: 0.8861 (t) REVERT: A 199 ASP cc_start: 0.8300 (p0) cc_final: 0.7920 (p0) REVERT: B 81 THR cc_start: 0.9247 (m) cc_final: 0.8955 (t) REVERT: C 50 ASN cc_start: 0.7296 (m-40) cc_final: 0.7064 (t0) REVERT: C 78 ILE cc_start: 0.8151 (pt) cc_final: 0.7785 (mt) REVERT: C 81 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8857 (t) REVERT: C 273 MET cc_start: 0.8522 (tpp) cc_final: 0.7936 (tpp) REVERT: D 277 PHE cc_start: 0.5952 (m-10) cc_final: 0.5321 (m-10) REVERT: E 81 THR cc_start: 0.9088 (m) cc_final: 0.8816 (t) REVERT: F 78 ILE cc_start: 0.8309 (pt) cc_final: 0.7798 (mt) REVERT: F 80 PHE cc_start: 0.8614 (m-10) cc_final: 0.8306 (m-10) REVERT: F 273 MET cc_start: 0.8788 (tpp) cc_final: 0.8537 (tpp) REVERT: G 46 ARG cc_start: 0.5637 (ttp-170) cc_final: 0.5192 (mtm180) REVERT: G 81 THR cc_start: 0.9118 (m) cc_final: 0.8877 (t) outliers start: 40 outliers final: 32 residues processed: 321 average time/residue: 0.2277 time to fit residues: 112.9237 Evaluate side-chains 327 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 294 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 120 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 0.055 14098 Z= 0.152 Angle : 0.440 6.219 19117 Z= 0.234 Chirality : 0.042 0.240 2345 Planarity : 0.003 0.061 2429 Dihedral : 3.653 13.388 1988 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.37 % Allowed : 20.85 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.19), residues: 1813 helix: 3.25 (0.15), residues: 1015 sheet: 1.10 (0.30), residues: 238 loop : -0.90 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 240 PHE 0.013 0.001 PHE A 277 TYR 0.004 0.001 TYR C 250 ARG 0.014 0.000 ARG A 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 301 time to evaluate : 1.446 Fit side-chains REVERT: A 50 ASN cc_start: 0.7000 (m110) cc_final: 0.6556 (t0) REVERT: A 81 THR cc_start: 0.9228 (m) cc_final: 0.8912 (t) REVERT: A 273 MET cc_start: 0.8415 (tpp) cc_final: 0.8093 (tpp) REVERT: B 81 THR cc_start: 0.9239 (m) cc_final: 0.8940 (t) REVERT: C 50 ASN cc_start: 0.7293 (m-40) cc_final: 0.7067 (t0) REVERT: C 78 ILE cc_start: 0.8151 (pt) cc_final: 0.7788 (mt) REVERT: C 81 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8846 (t) REVERT: C 273 MET cc_start: 0.8554 (tpp) cc_final: 0.7981 (tpp) REVERT: D 277 PHE cc_start: 0.6071 (m-10) cc_final: 0.5397 (m-10) REVERT: E 81 THR cc_start: 0.9067 (m) cc_final: 0.8796 (t) REVERT: F 78 ILE cc_start: 0.8306 (pt) cc_final: 0.7796 (mt) REVERT: F 273 MET cc_start: 0.8776 (tpp) cc_final: 0.8525 (tpp) REVERT: G 46 ARG cc_start: 0.5634 (ttp-170) cc_final: 0.5185 (mtm180) REVERT: G 81 THR cc_start: 0.9115 (m) cc_final: 0.8881 (t) outliers start: 35 outliers final: 34 residues processed: 312 average time/residue: 0.2120 time to fit residues: 101.3550 Evaluate side-chains 333 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 298 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 227 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.108599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091460 restraints weight = 30436.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093783 restraints weight = 14868.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095442 restraints weight = 9116.589| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14098 Z= 0.222 Angle : 0.464 6.154 19117 Z= 0.249 Chirality : 0.042 0.228 2345 Planarity : 0.003 0.063 2429 Dihedral : 3.830 14.301 1988 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.51 % Allowed : 20.72 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.19), residues: 1813 helix: 3.09 (0.15), residues: 1015 sheet: 1.02 (0.30), residues: 238 loop : -0.90 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.015 0.001 PHE A 277 TYR 0.007 0.001 TYR F 250 ARG 0.013 0.000 ARG G 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2779.08 seconds wall clock time: 53 minutes 8.00 seconds (3188.00 seconds total)