Starting phenix.real_space_refine on Sat Mar 16 06:40:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/03_2024/7onl_12997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/03_2024/7onl_12997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/03_2024/7onl_12997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/03_2024/7onl_12997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/03_2024/7onl_12997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/03_2024/7onl_12997.pdb" } resolution = 3.9 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= 0.007 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: 7.44, per 1000 atoms: 0.53 Number of scatterers: 13923 At special positions: 0 Unit cell: (98.9055, 96.7785, 142.509, 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: 5.23 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, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 22 through 59 removed outlier: 3.502A 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: 4.729A pdb=" N GLY A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 5.014A 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 removed outlier: 3.564A pdb=" N GLU A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 22 through 59 removed outlier: 3.502A 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: 4.730A pdb=" N GLY B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.014A 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 removed outlier: 3.564A pdb=" N GLU B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 22 through 59 removed outlier: 3.503A 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: 4.729A pdb=" N GLY C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 5.014A 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 removed outlier: 3.563A pdb=" N GLU C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 22 through 59 removed outlier: 3.502A 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: 4.729A pdb=" N GLY D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.014A 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 removed outlier: 3.564A pdb=" N GLU D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 22 through 59 removed outlier: 3.502A 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: 4.729A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 5.013A 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 removed outlier: 3.563A pdb=" N GLU E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 22 through 59 removed outlier: 3.502A 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: 4.729A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 5.014A 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 removed outlier: 3.563A pdb=" N GLU F 212 " --> pdb=" O ILE F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 22 through 59 removed outlier: 3.503A 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: 4.728A pdb=" N GLY G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 5.013A 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 removed outlier: 3.563A pdb=" N GLU G 212 " --> pdb=" O ILE G 208 " (cutoff:3.500A) 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: 3.842A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.974A 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: 7.035A 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 276 removed outlier: 8.093A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N MET C 273 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS B 278 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N MET D 273 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP C 274 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN C 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N MET F 273 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASP E 274 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS E 278 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N MET G 273 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 275 " --> pdb=" O ASN G 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 7.036A 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: 7.035A 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: 7.035A 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: 7.035A 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: 7.035A 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: 7.035A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 3054 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: 4.09 Time building geometry restraints manager: 5.71 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: 4655 1.34 - 1.46: 2538 1.46 - 1.57: 6821 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 14098 Sorted by residual: bond pdb=" CA ARG B 128 " pdb=" CB ARG B 128 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.36e+00 bond pdb=" CA ARG F 128 " pdb=" CB ARG F 128 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.34e+00 bond pdb=" CA ARG E 128 " pdb=" CB ARG E 128 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.29e+00 bond pdb=" CA ARG C 128 " pdb=" CB ARG C 128 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.23e+00 bond pdb=" CA ARG G 128 " pdb=" CB ARG G 128 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.20e+00 ... (remaining 14093 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.06: 230 107.06 - 113.80: 8265 113.80 - 120.53: 5314 120.53 - 127.26: 5245 127.26 - 134.00: 63 Bond angle restraints: 19117 Sorted by residual: angle pdb=" C ARG F 128 " pdb=" CA ARG F 128 " pdb=" CB ARG F 128 " ideal model delta sigma weight residual 111.00 109.34 1.66 8.70e-01 1.32e+00 3.63e+00 angle pdb=" C ARG G 128 " pdb=" CA ARG G 128 " pdb=" CB ARG G 128 " ideal model delta sigma weight residual 111.00 109.35 1.65 8.70e-01 1.32e+00 3.59e+00 angle pdb=" C ARG D 128 " pdb=" CA ARG D 128 " pdb=" CB ARG D 128 " ideal model delta sigma weight residual 111.00 109.36 1.64 8.70e-01 1.32e+00 3.54e+00 angle pdb=" C ARG C 128 " pdb=" CA ARG C 128 " pdb=" CB ARG C 128 " ideal model delta sigma weight residual 111.00 109.37 1.63 8.70e-01 1.32e+00 3.52e+00 angle pdb=" C ARG E 128 " pdb=" CA ARG E 128 " pdb=" CB ARG E 128 " ideal model delta sigma weight residual 111.00 109.37 1.63 8.70e-01 1.32e+00 3.50e+00 ... (remaining 19112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.34: 7296 8.34 - 16.69: 789 16.69 - 25.03: 238 25.03 - 33.38: 119 33.38 - 41.72: 42 Dihedral angle restraints: 8484 sinusoidal: 3248 harmonic: 5236 Sorted by residual: dihedral pdb=" N LEU B 72 " pdb=" CA LEU B 72 " pdb=" CB LEU B 72 " pdb=" CG LEU B 72 " ideal model delta sinusoidal sigma weight residual -60.00 -101.72 41.72 3 1.50e+01 4.44e-03 7.47e+00 dihedral pdb=" N LEU G 72 " pdb=" CA LEU G 72 " pdb=" CB LEU G 72 " pdb=" CG LEU G 72 " ideal model delta sinusoidal sigma weight residual -60.00 -101.70 41.70 3 1.50e+01 4.44e-03 7.47e+00 dihedral pdb=" N LEU E 72 " pdb=" CA LEU E 72 " pdb=" CB LEU E 72 " pdb=" CG LEU E 72 " ideal model delta sinusoidal sigma weight residual -60.00 -101.70 41.70 3 1.50e+01 4.44e-03 7.47e+00 ... (remaining 8481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1543 0.027 - 0.055: 500 0.055 - 0.082: 140 0.082 - 0.109: 106 0.109 - 0.137: 56 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CA ILE C 175 " pdb=" N ILE C 175 " pdb=" C ILE C 175 " pdb=" CB ILE C 175 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE D 165 " pdb=" N ILE D 165 " pdb=" C ILE D 165 " pdb=" CB ILE D 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2342 not shown) Planarity restraints: 2429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 111 " 0.005 2.00e-02 2.50e+03 9.22e-03 8.49e-01 pdb=" C LEU D 111 " -0.016 2.00e-02 2.50e+03 pdb=" O LEU D 111 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN D 112 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 111 " 0.005 2.00e-02 2.50e+03 9.14e-03 8.35e-01 pdb=" C LEU F 111 " -0.016 2.00e-02 2.50e+03 pdb=" O LEU F 111 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN F 112 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 111 " 0.004 2.00e-02 2.50e+03 9.04e-03 8.16e-01 pdb=" C LEU A 111 " -0.016 2.00e-02 2.50e+03 pdb=" O LEU A 111 " 0.006 2.00e-02 2.50e+03 pdb=" N GLN A 112 " 0.005 2.00e-02 2.50e+03 ... (remaining 2426 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 626 2.72 - 3.27: 14169 3.27 - 3.81: 22931 3.81 - 4.36: 24538 4.36 - 4.90: 45458 Nonbonded interactions: 107722 Sorted by model distance: nonbonded pdb=" OD1 ASP B 199 " pdb=" NH2 ARG C 259 " model vdw 2.180 2.520 nonbonded pdb=" OD1 ASN B 174 " pdb=" NZ LYS C 169 " model vdw 2.206 2.520 nonbonded pdb=" OD1 ASN A 276 " pdb=" NE2 GLN B 272 " model vdw 2.214 2.520 nonbonded pdb=" OD1 ASP D 199 " pdb=" NH2 ARG E 259 " model vdw 2.285 2.520 nonbonded pdb=" O ALA B 22 " pdb=" OG SER B 26 " model vdw 2.292 2.440 ... (remaining 107717 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: 0.890 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: 4.440 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 37.940 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.002 0.020 14098 Z= 0.156 Angle : 0.379 4.573 19117 Z= 0.224 Chirality : 0.039 0.137 2345 Planarity : 0.002 0.010 2429 Dihedral : 9.172 41.722 5110 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.41 % Allowed : 4.81 % Favored : 94.79 % 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: 2.97 (0.20), residues: 1813 helix: 3.44 (0.15), residues: 1001 sheet: 0.27 (0.27), residues: 308 loop : -0.03 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 240 PHE 0.006 0.001 PHE C 68 TYR 0.005 0.001 TYR E 135 ARG 0.002 0.000 ARG C 184 *********************** 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 403 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 397 time to evaluate : 1.575 Fit side-chains REVERT: A 43 ILE cc_start: 0.8326 (mm) cc_final: 0.7999 (pt) REVERT: A 131 ARG cc_start: 0.7178 (ptp-170) cc_final: 0.6967 (ptm-80) REVERT: A 203 GLN cc_start: 0.8127 (pp30) cc_final: 0.7672 (pp30) REVERT: A 220 GLU cc_start: 0.7630 (pp20) cc_final: 0.7353 (pp20) REVERT: A 272 GLN cc_start: 0.7864 (tt0) cc_final: 0.7640 (tt0) REVERT: A 273 MET cc_start: 0.7755 (ptp) cc_final: 0.7328 (ptm) REVERT: B 48 ILE cc_start: 0.7904 (tp) cc_final: 0.7653 (tp) REVERT: B 86 LEU cc_start: 0.8513 (tp) cc_final: 0.8196 (tp) REVERT: B 134 GLU cc_start: 0.7071 (tt0) cc_final: 0.6832 (tt0) REVERT: B 197 ASP cc_start: 0.7704 (t70) cc_final: 0.7384 (t70) REVERT: B 206 THR cc_start: 0.8791 (m) cc_final: 0.8587 (p) REVERT: B 272 GLN cc_start: 0.8481 (tt0) cc_final: 0.7844 (tt0) REVERT: C 48 ILE cc_start: 0.7801 (tp) cc_final: 0.7580 (tp) REVERT: C 134 GLU cc_start: 0.7297 (tt0) cc_final: 0.6912 (tt0) REVERT: C 255 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7654 (tt0) REVERT: C 272 GLN cc_start: 0.8072 (tt0) cc_final: 0.7568 (tt0) REVERT: D 203 GLN cc_start: 0.8022 (pp30) cc_final: 0.7720 (pp30) REVERT: D 220 GLU cc_start: 0.7495 (pp20) cc_final: 0.7241 (pp20) REVERT: D 272 GLN cc_start: 0.7993 (tt0) cc_final: 0.7570 (tt0) REVERT: E 135 TYR cc_start: 0.7958 (t80) cc_final: 0.7637 (t80) REVERT: F 47 MET cc_start: 0.2489 (mmt) cc_final: 0.2254 (mmt) REVERT: F 131 ARG cc_start: 0.7180 (ptp-170) cc_final: 0.6980 (ptm-80) REVERT: F 197 ASP cc_start: 0.7180 (t70) cc_final: 0.6825 (t70) REVERT: F 272 GLN cc_start: 0.8291 (tt0) cc_final: 0.7622 (tt0) REVERT: G 47 MET cc_start: 0.2640 (mmt) cc_final: 0.2398 (mmt) REVERT: G 134 GLU cc_start: 0.6834 (tt0) cc_final: 0.6539 (tt0) REVERT: G 135 TYR cc_start: 0.7805 (t80) cc_final: 0.7546 (t80) REVERT: G 197 ASP cc_start: 0.7083 (t70) cc_final: 0.6686 (t70) REVERT: G 203 GLN cc_start: 0.7920 (pp30) cc_final: 0.7579 (pp30) outliers start: 6 outliers final: 0 residues processed: 403 average time/residue: 0.2252 time to fit residues: 132.8378 Evaluate side-chains 270 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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: 10.0000 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.4980 chunk 142 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14098 Z= 0.295 Angle : 0.564 6.676 19117 Z= 0.299 Chirality : 0.041 0.144 2345 Planarity : 0.004 0.067 2429 Dihedral : 3.878 12.639 1988 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.66 % Allowed : 9.28 % Favored : 87.07 % 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: 2.67 (0.20), residues: 1813 helix: 3.05 (0.16), residues: 1001 sheet: 0.72 (0.31), residues: 259 loop : -0.17 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 240 PHE 0.019 0.002 PHE B 127 TYR 0.005 0.001 TYR A 27 ARG 0.004 0.000 ARG C 74 *********************** 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 329 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 275 time to evaluate : 1.557 Fit side-chains REVERT: A 43 ILE cc_start: 0.8367 (mm) cc_final: 0.7964 (pt) REVERT: A 131 ARG cc_start: 0.7133 (ptp-170) cc_final: 0.6921 (ptm-80) REVERT: A 203 GLN cc_start: 0.8205 (pp30) cc_final: 0.7831 (pp30) REVERT: A 220 GLU cc_start: 0.7673 (pp20) cc_final: 0.7350 (pp20) REVERT: B 86 LEU cc_start: 0.8500 (tp) cc_final: 0.8230 (tp) REVERT: B 134 GLU cc_start: 0.7185 (tt0) cc_final: 0.6913 (tt0) REVERT: B 161 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8421 (mtmm) REVERT: B 197 ASP cc_start: 0.7727 (t70) cc_final: 0.7452 (t70) REVERT: B 272 GLN cc_start: 0.8302 (tt0) cc_final: 0.7404 (tt0) REVERT: C 134 GLU cc_start: 0.7158 (tt0) cc_final: 0.6867 (tt0) REVERT: C 255 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7739 (tt0) REVERT: C 272 GLN cc_start: 0.8133 (tt0) cc_final: 0.7718 (tt0) REVERT: D 135 TYR cc_start: 0.7984 (t80) cc_final: 0.7733 (t80) REVERT: D 203 GLN cc_start: 0.8067 (pp30) cc_final: 0.7823 (pp30) REVERT: D 220 GLU cc_start: 0.7632 (pp20) cc_final: 0.7194 (pp20) REVERT: D 272 GLN cc_start: 0.8185 (tt0) cc_final: 0.7736 (tt0) REVERT: D 273 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8075 (ptm) REVERT: E 134 GLU cc_start: 0.7054 (tt0) cc_final: 0.6774 (tt0) REVERT: E 135 TYR cc_start: 0.8004 (t80) cc_final: 0.7784 (t80) REVERT: E 272 GLN cc_start: 0.8115 (tt0) cc_final: 0.7752 (tt0) REVERT: F 134 GLU cc_start: 0.7006 (tt0) cc_final: 0.6721 (tt0) REVERT: F 197 ASP cc_start: 0.7396 (t70) cc_final: 0.7133 (t70) REVERT: F 272 GLN cc_start: 0.8217 (tt0) cc_final: 0.7531 (tt0) REVERT: F 273 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8535 (ttm) REVERT: G 134 GLU cc_start: 0.6782 (tt0) cc_final: 0.6577 (tt0) REVERT: G 197 ASP cc_start: 0.7244 (t70) cc_final: 0.6858 (t70) REVERT: G 203 GLN cc_start: 0.7926 (pp30) cc_final: 0.7651 (pp30) outliers start: 54 outliers final: 26 residues processed: 305 average time/residue: 0.2141 time to fit residues: 99.0009 Evaluate side-chains 277 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 249 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 273 MET Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 233 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14098 Z= 0.236 Angle : 0.513 5.205 19117 Z= 0.275 Chirality : 0.041 0.148 2345 Planarity : 0.003 0.029 2429 Dihedral : 3.869 13.420 1988 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.32 % Allowed : 12.05 % Favored : 84.63 % 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: 2.62 (0.19), residues: 1813 helix: 2.97 (0.16), residues: 1001 sheet: 1.71 (0.31), residues: 224 loop : -0.52 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 240 PHE 0.012 0.001 PHE G 178 TYR 0.009 0.001 TYR D 135 ARG 0.005 0.000 ARG B 74 *********************** 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 319 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 270 time to evaluate : 1.569 Fit side-chains REVERT: A 43 ILE cc_start: 0.8342 (mm) cc_final: 0.7926 (pt) REVERT: A 203 GLN cc_start: 0.8167 (pp30) cc_final: 0.7827 (pp30) REVERT: A 220 GLU cc_start: 0.7718 (pp20) cc_final: 0.7334 (pp20) REVERT: A 255 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7772 (tm-30) REVERT: B 86 LEU cc_start: 0.8512 (tp) cc_final: 0.8232 (tp) REVERT: B 161 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8313 (mtmm) REVERT: B 197 ASP cc_start: 0.7682 (t70) cc_final: 0.7453 (t70) REVERT: B 272 GLN cc_start: 0.8207 (tt0) cc_final: 0.7252 (tt0) REVERT: C 134 GLU cc_start: 0.7099 (tt0) cc_final: 0.6868 (tt0) REVERT: C 255 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7873 (tt0) REVERT: C 272 GLN cc_start: 0.8127 (tt0) cc_final: 0.7532 (tt0) REVERT: D 149 GLN cc_start: 0.7903 (mp10) cc_final: 0.7647 (mp10) REVERT: D 203 GLN cc_start: 0.8033 (pp30) cc_final: 0.7806 (pp30) REVERT: D 220 GLU cc_start: 0.7513 (pp20) cc_final: 0.7068 (pp20) REVERT: D 272 GLN cc_start: 0.8110 (tt0) cc_final: 0.7514 (tt0) REVERT: D 273 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8082 (ptm) REVERT: E 134 GLU cc_start: 0.7022 (tt0) cc_final: 0.6798 (tt0) REVERT: E 211 SER cc_start: 0.8463 (m) cc_final: 0.8244 (t) REVERT: E 272 GLN cc_start: 0.8055 (tt0) cc_final: 0.7648 (tt0) REVERT: F 134 GLU cc_start: 0.7007 (tt0) cc_final: 0.6627 (tt0) REVERT: F 149 GLN cc_start: 0.7978 (mp10) cc_final: 0.7441 (mp10) REVERT: F 197 ASP cc_start: 0.7393 (t70) cc_final: 0.7125 (t70) REVERT: F 272 GLN cc_start: 0.8122 (tt0) cc_final: 0.7335 (tt0) REVERT: F 273 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8360 (ttm) REVERT: G 134 GLU cc_start: 0.6831 (tt0) cc_final: 0.6621 (tt0) REVERT: G 197 ASP cc_start: 0.7345 (t70) cc_final: 0.6981 (t70) REVERT: G 203 GLN cc_start: 0.7955 (pp30) cc_final: 0.7557 (pp30) REVERT: G 220 GLU cc_start: 0.7269 (pp20) cc_final: 0.6981 (pp20) outliers start: 49 outliers final: 34 residues processed: 297 average time/residue: 0.2200 time to fit residues: 99.0962 Evaluate side-chains 281 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 273 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14098 Z= 0.216 Angle : 0.502 5.567 19117 Z= 0.268 Chirality : 0.040 0.145 2345 Planarity : 0.003 0.023 2429 Dihedral : 3.853 12.576 1988 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.52 % Allowed : 12.53 % Favored : 83.95 % 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: 2.60 (0.19), residues: 1813 helix: 2.94 (0.15), residues: 1001 sheet: 1.81 (0.30), residues: 224 loop : -0.56 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.011 0.001 PHE C 178 TYR 0.005 0.001 TYR C 135 ARG 0.003 0.000 ARG B 74 *********************** 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 311 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 259 time to evaluate : 1.429 Fit side-chains REVERT: A 43 ILE cc_start: 0.8253 (mm) cc_final: 0.7912 (pt) REVERT: A 203 GLN cc_start: 0.8121 (pp30) cc_final: 0.7834 (pp30) REVERT: A 220 GLU cc_start: 0.7784 (pp20) cc_final: 0.7419 (pp20) REVERT: B 86 LEU cc_start: 0.8518 (tp) cc_final: 0.8234 (tp) REVERT: B 161 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8378 (mtmm) REVERT: B 197 ASP cc_start: 0.7667 (t70) cc_final: 0.7410 (t70) REVERT: B 272 GLN cc_start: 0.8134 (tt0) cc_final: 0.7244 (tt0) REVERT: C 134 GLU cc_start: 0.7034 (tt0) cc_final: 0.6804 (tt0) REVERT: C 255 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7890 (tt0) REVERT: C 272 GLN cc_start: 0.8118 (tt0) cc_final: 0.7482 (tt0) REVERT: D 149 GLN cc_start: 0.7988 (mp10) cc_final: 0.7662 (mp10) REVERT: D 203 GLN cc_start: 0.7974 (pp30) cc_final: 0.7758 (pp30) REVERT: D 220 GLU cc_start: 0.7512 (pp20) cc_final: 0.7101 (pp20) REVERT: D 272 GLN cc_start: 0.8018 (tt0) cc_final: 0.7453 (tt0) REVERT: D 273 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8154 (ptm) REVERT: E 272 GLN cc_start: 0.7986 (tt0) cc_final: 0.7608 (tt0) REVERT: F 134 GLU cc_start: 0.7047 (tt0) cc_final: 0.6674 (tt0) REVERT: F 149 GLN cc_start: 0.8014 (mp10) cc_final: 0.7463 (mp10) REVERT: F 197 ASP cc_start: 0.7403 (t70) cc_final: 0.7132 (t70) REVERT: F 272 GLN cc_start: 0.8109 (tt0) cc_final: 0.7291 (tt0) REVERT: G 134 GLU cc_start: 0.6806 (tt0) cc_final: 0.6566 (tt0) REVERT: G 197 ASP cc_start: 0.7360 (t70) cc_final: 0.7023 (t70) REVERT: G 203 GLN cc_start: 0.7932 (pp30) cc_final: 0.7540 (pp30) outliers start: 52 outliers final: 36 residues processed: 288 average time/residue: 0.2103 time to fit residues: 93.0841 Evaluate side-chains 278 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 241 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 257 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.1980 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN F 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14098 Z= 0.165 Angle : 0.499 10.321 19117 Z= 0.264 Chirality : 0.040 0.180 2345 Planarity : 0.002 0.017 2429 Dihedral : 3.781 12.665 1988 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.27 % Allowed : 13.34 % Favored : 82.40 % 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: 2.61 (0.19), residues: 1813 helix: 2.96 (0.15), residues: 1001 sheet: 1.17 (0.30), residues: 273 loop : -0.42 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 251 PHE 0.009 0.001 PHE C 178 TYR 0.005 0.001 TYR A 270 ARG 0.002 0.000 ARG C 74 *********************** 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 320 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 257 time to evaluate : 1.539 Fit side-chains REVERT: A 43 ILE cc_start: 0.8309 (mm) cc_final: 0.7878 (pt) REVERT: A 203 GLN cc_start: 0.8147 (pp30) cc_final: 0.7926 (pp30) REVERT: A 220 GLU cc_start: 0.7751 (pp20) cc_final: 0.7449 (pp20) REVERT: A 255 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 86 LEU cc_start: 0.8511 (tp) cc_final: 0.8234 (tp) REVERT: B 197 ASP cc_start: 0.7616 (t70) cc_final: 0.7344 (t70) REVERT: B 272 GLN cc_start: 0.8117 (tt0) cc_final: 0.7211 (tt0) REVERT: C 134 GLU cc_start: 0.7057 (tt0) cc_final: 0.6827 (tt0) REVERT: C 161 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7838 (mtmm) REVERT: C 220 GLU cc_start: 0.7612 (pp20) cc_final: 0.7273 (pp20) REVERT: C 255 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7783 (tt0) REVERT: C 272 GLN cc_start: 0.8087 (tt0) cc_final: 0.7407 (tt0) REVERT: D 149 GLN cc_start: 0.7966 (mp10) cc_final: 0.7662 (mp10) REVERT: D 203 GLN cc_start: 0.7997 (pp30) cc_final: 0.7796 (pp30) REVERT: D 272 GLN cc_start: 0.8017 (tt0) cc_final: 0.7798 (tt0) REVERT: D 273 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8140 (ptm) REVERT: E 272 GLN cc_start: 0.7879 (tt0) cc_final: 0.7502 (tt0) REVERT: F 134 GLU cc_start: 0.7151 (tt0) cc_final: 0.6768 (tt0) REVERT: F 149 GLN cc_start: 0.7992 (mp10) cc_final: 0.7424 (mp10) REVERT: F 197 ASP cc_start: 0.7345 (t70) cc_final: 0.7077 (t70) REVERT: F 203 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8000 (tm130) REVERT: F 272 GLN cc_start: 0.8136 (tt0) cc_final: 0.7502 (tt0) REVERT: G 197 ASP cc_start: 0.7375 (t70) cc_final: 0.7048 (t70) REVERT: G 203 GLN cc_start: 0.7954 (pp30) cc_final: 0.7602 (pp30) REVERT: G 273 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8182 (ttm) outliers start: 63 outliers final: 33 residues processed: 296 average time/residue: 0.2098 time to fit residues: 94.9368 Evaluate side-chains 276 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 239 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN F 203 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14098 Z= 0.212 Angle : 0.516 8.564 19117 Z= 0.271 Chirality : 0.040 0.221 2345 Planarity : 0.002 0.015 2429 Dihedral : 3.826 12.282 1988 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.86 % Allowed : 13.88 % Favored : 82.26 % 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: 2.54 (0.19), residues: 1813 helix: 2.90 (0.15), residues: 1008 sheet: 1.12 (0.30), residues: 273 loop : -0.47 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 240 PHE 0.012 0.001 PHE D 80 TYR 0.007 0.001 TYR A 270 ARG 0.002 0.000 ARG C 74 *********************** 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 306 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 249 time to evaluate : 1.600 Fit side-chains REVERT: A 43 ILE cc_start: 0.8308 (mm) cc_final: 0.7886 (pt) REVERT: A 203 GLN cc_start: 0.8181 (pp30) cc_final: 0.7957 (pp30) REVERT: A 220 GLU cc_start: 0.7924 (pp20) cc_final: 0.7548 (pp20) REVERT: A 255 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7720 (tm-30) REVERT: A 273 MET cc_start: 0.7785 (ptm) cc_final: 0.7503 (ptm) REVERT: B 86 LEU cc_start: 0.8494 (tp) cc_final: 0.8213 (tp) REVERT: B 161 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8348 (mtmm) REVERT: B 197 ASP cc_start: 0.7601 (t70) cc_final: 0.7360 (t70) REVERT: C 134 GLU cc_start: 0.7025 (tt0) cc_final: 0.6802 (tt0) REVERT: C 161 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7849 (mtmm) REVERT: C 220 GLU cc_start: 0.7652 (pp20) cc_final: 0.7310 (pp20) REVERT: C 255 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7763 (tt0) REVERT: C 272 GLN cc_start: 0.8136 (tt0) cc_final: 0.7453 (tt0) REVERT: D 149 GLN cc_start: 0.7962 (mp10) cc_final: 0.7650 (mp10) REVERT: D 203 GLN cc_start: 0.7967 (pp30) cc_final: 0.7765 (pp30) REVERT: D 273 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8152 (ptm) REVERT: E 203 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8185 (tm130) REVERT: E 272 GLN cc_start: 0.7878 (tt0) cc_final: 0.7512 (tt0) REVERT: F 134 GLU cc_start: 0.7131 (tt0) cc_final: 0.6743 (tt0) REVERT: F 197 ASP cc_start: 0.7383 (t70) cc_final: 0.7116 (t70) REVERT: F 203 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8076 (tm130) REVERT: F 272 GLN cc_start: 0.8111 (tt0) cc_final: 0.7510 (tt0) REVERT: G 197 ASP cc_start: 0.7412 (t70) cc_final: 0.7087 (t70) REVERT: G 203 GLN cc_start: 0.7988 (pp30) cc_final: 0.7625 (pp30) REVERT: G 273 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8417 (ttp) outliers start: 57 outliers final: 39 residues processed: 284 average time/residue: 0.2064 time to fit residues: 89.8614 Evaluate side-chains 282 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 238 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN D 272 GLN F 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14098 Z= 0.309 Angle : 0.570 8.378 19117 Z= 0.299 Chirality : 0.041 0.193 2345 Planarity : 0.003 0.021 2429 Dihedral : 3.967 12.335 1988 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.13 % Allowed : 14.08 % Favored : 81.79 % 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: 2.38 (0.19), residues: 1813 helix: 2.79 (0.15), residues: 1008 sheet: 1.85 (0.30), residues: 238 loop : -0.91 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 240 PHE 0.013 0.001 PHE D 80 TYR 0.006 0.001 TYR A 270 ARG 0.004 0.000 ARG G 184 *********************** 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 312 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 251 time to evaluate : 1.632 Fit side-chains REVERT: A 43 ILE cc_start: 0.8300 (mm) cc_final: 0.7890 (pt) REVERT: A 203 GLN cc_start: 0.8097 (pp30) cc_final: 0.7870 (pp30) REVERT: A 255 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7779 (tm-30) REVERT: B 161 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8412 (mtmm) REVERT: B 197 ASP cc_start: 0.7653 (t70) cc_final: 0.7437 (t70) REVERT: B 255 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8045 (tm-30) REVERT: C 134 GLU cc_start: 0.7035 (tt0) cc_final: 0.6794 (tt0) REVERT: C 161 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7915 (mtmm) REVERT: C 220 GLU cc_start: 0.7774 (pp20) cc_final: 0.7511 (pp20) REVERT: C 272 GLN cc_start: 0.8244 (tt0) cc_final: 0.7562 (tt0) REVERT: D 149 GLN cc_start: 0.7977 (mp10) cc_final: 0.7695 (mp10) REVERT: D 203 GLN cc_start: 0.7979 (pp30) cc_final: 0.7768 (pp30) REVERT: D 273 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8079 (ptm) REVERT: E 272 GLN cc_start: 0.7914 (tt0) cc_final: 0.7545 (tt0) REVERT: F 134 GLU cc_start: 0.7121 (tt0) cc_final: 0.6730 (tt0) REVERT: F 220 GLU cc_start: 0.7660 (pp20) cc_final: 0.7305 (pp20) REVERT: F 272 GLN cc_start: 0.8106 (tt0) cc_final: 0.7436 (tt0) REVERT: G 197 ASP cc_start: 0.7401 (t70) cc_final: 0.7071 (t70) REVERT: G 203 GLN cc_start: 0.8009 (pp30) cc_final: 0.7798 (pp30) REVERT: G 273 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8468 (ptm) outliers start: 61 outliers final: 46 residues processed: 289 average time/residue: 0.2124 time to fit residues: 94.4606 Evaluate side-chains 286 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 237 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 203 GLN Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.0000 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 ASN E 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14098 Z= 0.183 Angle : 0.547 7.685 19117 Z= 0.284 Chirality : 0.041 0.155 2345 Planarity : 0.002 0.016 2429 Dihedral : 3.840 12.652 1988 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.98 % Allowed : 15.37 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.19), residues: 1813 helix: 2.83 (0.15), residues: 1008 sheet: 1.12 (0.30), residues: 273 loop : -0.58 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 251 PHE 0.013 0.001 PHE E 80 TYR 0.008 0.001 TYR C 270 ARG 0.003 0.000 ARG F 256 *********************** 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 292 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 248 time to evaluate : 1.541 Fit side-chains REVERT: A 43 ILE cc_start: 0.8305 (mm) cc_final: 0.7892 (pt) REVERT: A 255 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7694 (tm-30) REVERT: B 86 LEU cc_start: 0.8489 (tp) cc_final: 0.8253 (tp) REVERT: B 197 ASP cc_start: 0.7578 (t70) cc_final: 0.7340 (t70) REVERT: C 134 GLU cc_start: 0.6973 (tt0) cc_final: 0.6738 (tt0) REVERT: C 161 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7869 (mtmm) REVERT: C 220 GLU cc_start: 0.7697 (pp20) cc_final: 0.7493 (pp20) REVERT: C 272 GLN cc_start: 0.8136 (tt0) cc_final: 0.7461 (tt0) REVERT: D 149 GLN cc_start: 0.7961 (mp10) cc_final: 0.7693 (mp10) REVERT: D 273 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8216 (ptm) REVERT: E 221 MET cc_start: 0.6813 (ptt) cc_final: 0.6608 (ptt) REVERT: E 272 GLN cc_start: 0.7866 (tt0) cc_final: 0.7523 (tt0) REVERT: F 134 GLU cc_start: 0.7139 (tt0) cc_final: 0.6746 (tt0) REVERT: F 220 GLU cc_start: 0.7670 (pp20) cc_final: 0.7365 (pp20) REVERT: F 272 GLN cc_start: 0.8073 (tt0) cc_final: 0.7382 (tt0) REVERT: G 197 ASP cc_start: 0.7366 (t70) cc_final: 0.7062 (t70) REVERT: G 203 GLN cc_start: 0.7963 (pp30) cc_final: 0.7729 (pp30) REVERT: G 273 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8384 (ptm) outliers start: 44 outliers final: 36 residues processed: 278 average time/residue: 0.2111 time to fit residues: 90.2482 Evaluate side-chains 276 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 203 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14098 Z= 0.191 Angle : 0.568 12.897 19117 Z= 0.290 Chirality : 0.041 0.201 2345 Planarity : 0.002 0.015 2429 Dihedral : 3.835 12.774 1988 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.05 % Allowed : 15.84 % Favored : 81.11 % 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: 2.40 (0.19), residues: 1813 helix: 2.82 (0.15), residues: 1008 sheet: 1.09 (0.30), residues: 273 loop : -0.63 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 251 PHE 0.012 0.001 PHE D 80 TYR 0.008 0.001 TYR B 135 ARG 0.003 0.000 ARG E 219 *********************** 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 289 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 244 time to evaluate : 1.608 Fit side-chains REVERT: A 43 ILE cc_start: 0.8378 (mm) cc_final: 0.7938 (pt) REVERT: A 47 MET cc_start: 0.2750 (mmm) cc_final: 0.2535 (mmp) REVERT: A 255 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 86 LEU cc_start: 0.8522 (tp) cc_final: 0.8287 (tp) REVERT: B 197 ASP cc_start: 0.7581 (t70) cc_final: 0.7348 (t70) REVERT: C 134 GLU cc_start: 0.6956 (tt0) cc_final: 0.6714 (tt0) REVERT: C 161 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7879 (mtmm) REVERT: C 272 GLN cc_start: 0.8198 (tt0) cc_final: 0.7528 (tt0) REVERT: D 149 GLN cc_start: 0.7951 (mp10) cc_final: 0.7690 (mp10) REVERT: D 220 GLU cc_start: 0.7655 (pp20) cc_final: 0.7411 (pp20) REVERT: D 273 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8265 (ptm) REVERT: E 272 GLN cc_start: 0.7861 (tt0) cc_final: 0.7513 (tt0) REVERT: F 134 GLU cc_start: 0.7165 (tt0) cc_final: 0.6812 (tt0) REVERT: F 272 GLN cc_start: 0.8087 (tt0) cc_final: 0.7404 (tt0) REVERT: G 273 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8406 (ptm) outliers start: 45 outliers final: 35 residues processed: 272 average time/residue: 0.2149 time to fit residues: 89.2930 Evaluate side-chains 274 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 0.0770 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN F 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14098 Z= 0.264 Angle : 0.601 8.558 19117 Z= 0.309 Chirality : 0.042 0.221 2345 Planarity : 0.003 0.018 2429 Dihedral : 3.925 12.403 1988 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.25 % Allowed : 15.84 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.19), residues: 1813 helix: 2.76 (0.15), residues: 1008 sheet: 1.03 (0.29), residues: 273 loop : -0.69 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 240 PHE 0.013 0.001 PHE D 80 TYR 0.007 0.001 TYR C 270 ARG 0.010 0.000 ARG E 74 ********************** 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 289 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 241 time to evaluate : 1.650 Fit side-chains REVERT: A 43 ILE cc_start: 0.8379 (mm) cc_final: 0.7945 (pt) REVERT: A 47 MET cc_start: 0.2839 (mmm) cc_final: 0.2607 (mmp) REVERT: A 255 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 273 MET cc_start: 0.7631 (ptm) cc_final: 0.7197 (ptm) REVERT: B 86 LEU cc_start: 0.8476 (tp) cc_final: 0.8223 (tp) REVERT: B 197 ASP cc_start: 0.7613 (t70) cc_final: 0.7373 (t70) REVERT: B 255 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8115 (tm-30) REVERT: C 134 GLU cc_start: 0.6984 (tt0) cc_final: 0.6705 (tt0) REVERT: C 161 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7931 (mtmm) REVERT: C 272 GLN cc_start: 0.8206 (tt0) cc_final: 0.7537 (tt0) REVERT: D 149 GLN cc_start: 0.7968 (mp10) cc_final: 0.7700 (mp10) REVERT: D 273 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8552 (ptm) REVERT: E 272 GLN cc_start: 0.7873 (tt0) cc_final: 0.7490 (tt0) REVERT: F 134 GLU cc_start: 0.7135 (tt0) cc_final: 0.6810 (tt0) REVERT: F 272 GLN cc_start: 0.8051 (tt0) cc_final: 0.7377 (tt0) REVERT: G 197 ASP cc_start: 0.7401 (t70) cc_final: 0.7101 (t70) outliers start: 48 outliers final: 42 residues processed: 272 average time/residue: 0.2099 time to fit residues: 88.1201 Evaluate side-chains 279 residues out of total 1477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 MET Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 273 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108208 restraints weight = 23632.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110658 restraints weight = 13881.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112186 restraints weight = 9278.771| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.181 14098 Z= 0.277 Angle : 0.823 59.199 19117 Z= 0.459 Chirality : 0.043 0.504 2345 Planarity : 0.003 0.022 2429 Dihedral : 3.920 12.381 1988 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.18 % Allowed : 15.84 % Favored : 80.97 % 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: 2.31 (0.19), residues: 1813 helix: 2.76 (0.15), residues: 1008 sheet: 1.03 (0.29), residues: 273 loop : -0.70 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 240 PHE 0.011 0.001 PHE A 178 TYR 0.006 0.001 TYR B 135 ARG 0.007 0.000 ARG E 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2601.52 seconds wall clock time: 48 minutes 54.13 seconds (2934.13 seconds total)