Starting phenix.real_space_refine on Fri Nov 15 13:07:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fee_50339/11_2024/9fee_50339.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fee_50339/11_2024/9fee_50339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fee_50339/11_2024/9fee_50339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fee_50339/11_2024/9fee_50339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fee_50339/11_2024/9fee_50339.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fee_50339/11_2024/9fee_50339.cif" } resolution = 3.03 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= 0.002 sd= 0.033 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 48 5.16 5 C 5818 2.51 5 N 1568 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9112 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2291 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 21, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2267 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2262 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 285} Chain breaks: 1 Chain: "D" Number of atoms: 2292 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 310, 2286 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 310, 2286 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 288} Chain breaks: 1 bond proxies already assigned to first conformer: 2318 Time building chain proxies: 7.08, per 1000 atoms: 0.78 Number of scatterers: 9112 At special positions: 0 Unit cell: (91.16, 103.2, 103.2, 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 48 16.00 O 1678 8.00 N 1568 7.00 C 5818 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.5 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2242 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 48.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.607A pdb=" N GLN A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.077A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 171 removed outlier: 4.283A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.508A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.521A pdb=" N GLU A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.578A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 removed outlier: 3.806A pdb=" N SER B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.830A pdb=" N ASP B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.759A pdb=" N THR B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.676A pdb=" N GLY B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 Proline residue: B 135 - end of helix removed outlier: 3.505A pdb=" N ALA B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 156 through 169 removed outlier: 4.402A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.640A pdb=" N GLN B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.949A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 252 removed outlier: 3.684A pdb=" N MET B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 319 removed outlier: 3.800A pdb=" N GLY B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 removed outlier: 4.163A pdb=" N SER C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.715A pdb=" N ASP C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.596A pdb=" N THR C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.573A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C 109 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix removed outlier: 3.560A pdb=" N LYS C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 4.347A pdb=" N GLY C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.856A pdb=" N ILE C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.503A pdb=" N GLU C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 removed outlier: 3.698A pdb=" N HIS C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 318 removed outlier: 3.599A pdb=" N GLY C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 25 removed outlier: 4.013A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.850A pdb=" N ASP D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.857A pdb=" N GLU D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 76' Processing helix chain 'D' and resid 100 through 118 removed outlier: 3.614A pdb=" N GLY D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 145 Proline residue: D 135 - end of helix removed outlier: 3.692A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 206 through 225 removed outlier: 3.802A pdb=" N GLN D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 252 removed outlier: 3.533A pdb=" N MET D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 317 removed outlier: 3.811A pdb=" N MET D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 60 removed outlier: 6.292A pdb=" N LEU A 31 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ALA A 59 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 33 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN A 3 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL A 83 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA A 5 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 123 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 260 removed outlier: 3.878A pdb=" N ALA A 260 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 275 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG A 287 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 278 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 55 through 59 removed outlier: 3.690A pdb=" N LEU B 33 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE B 82 " --> pdb=" O CYS B 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'B' and resid 257 through 261 removed outlier: 3.778A pdb=" N ALA B 260 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 60 removed outlier: 6.325A pdb=" N LEU C 31 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA C 59 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 33 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA9, first strand: chain 'C' and resid 257 through 261 removed outlier: 3.557A pdb=" N ALA C 260 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ARG C 287 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 278 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 55 through 59 removed outlier: 3.964A pdb=" N LEU D 33 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 261 removed outlier: 3.577A pdb=" N ALA D 260 " --> pdb=" O MET D 275 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ARG D 287 " --> pdb=" O PRO D 276 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL D 278 " --> pdb=" O GLU D 285 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3006 1.34 - 1.46: 1397 1.46 - 1.58: 4786 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 9269 Sorted by residual: bond pdb=" C HIS A 172 " pdb=" N PRO A 173 " ideal model delta sigma weight residual 1.332 1.354 -0.022 8.20e-03 1.49e+04 6.89e+00 bond pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta sigma weight residual 1.465 1.490 -0.025 2.03e-02 2.43e+03 1.53e+00 bond pdb=" C LEU B 63 " pdb=" N PRO B 64 " ideal model delta sigma weight residual 1.329 1.343 -0.014 1.18e-02 7.18e+03 1.44e+00 bond pdb=" C ARG C 68 " pdb=" N ASP C 69 " ideal model delta sigma weight residual 1.333 1.363 -0.031 2.74e-02 1.33e+03 1.26e+00 bond pdb=" CG GLU A 303 " pdb=" CD GLU A 303 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.17e-01 ... (remaining 9264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12293 1.50 - 3.01: 274 3.01 - 4.51: 41 4.51 - 6.01: 16 6.01 - 7.52: 6 Bond angle restraints: 12630 Sorted by residual: angle pdb=" C GLU B 267 " pdb=" CA GLU B 267 " pdb=" CB GLU B 267 " ideal model delta sigma weight residual 116.54 109.64 6.90 1.15e+00 7.56e-01 3.60e+01 angle pdb=" CA GLU B 267 " pdb=" C GLU B 267 " pdb=" N HIS B 268 " ideal model delta sigma weight residual 119.52 116.27 3.25 7.90e-01 1.60e+00 1.69e+01 angle pdb=" N VAL C 126 " pdb=" CA VAL C 126 " pdb=" C VAL C 126 " ideal model delta sigma weight residual 113.47 109.49 3.98 1.01e+00 9.80e-01 1.55e+01 angle pdb=" C VAL B 191 " pdb=" CA VAL B 191 " pdb=" CB VAL B 191 " ideal model delta sigma weight residual 110.16 113.37 -3.21 1.01e+00 9.80e-01 1.01e+01 angle pdb=" C HIS D 185 " pdb=" N BSER D 186 " pdb=" CA BSER D 186 " ideal model delta sigma weight residual 121.54 115.61 5.93 1.91e+00 2.74e-01 9.65e+00 ... (remaining 12625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4900 17.85 - 35.69: 579 35.69 - 53.54: 136 53.54 - 71.39: 18 71.39 - 89.23: 5 Dihedral angle restraints: 5638 sinusoidal: 2142 harmonic: 3496 Sorted by residual: dihedral pdb=" CA PRO B 64 " pdb=" C PRO B 64 " pdb=" N PRO B 65 " pdb=" CA PRO B 65 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PRO A 64 " pdb=" C PRO A 64 " pdb=" N PRO A 65 " pdb=" CA PRO A 65 " ideal model delta harmonic sigma weight residual 180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LEU B 63 " pdb=" C LEU B 63 " pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta harmonic sigma weight residual -180.00 -154.80 -25.20 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 764 0.027 - 0.054: 471 0.054 - 0.081: 159 0.081 - 0.108: 121 0.108 - 0.135: 44 Chirality restraints: 1559 Sorted by residual: chirality pdb=" CA VAL C 66 " pdb=" N VAL C 66 " pdb=" C VAL C 66 " pdb=" CB VAL C 66 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ASN B 128 " pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CB ASN B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 1556 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 66 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO C 67 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 191 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO B 192 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 66 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 67 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " -0.022 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1490 2.76 - 3.29: 8341 3.29 - 3.83: 13738 3.83 - 4.36: 16069 4.36 - 4.90: 29062 Nonbonded interactions: 68700 Sorted by model distance: nonbonded pdb=" OD1 ASN B 131 " pdb=" OG SER B 186 " model vdw 2.225 3.040 nonbonded pdb=" O LEU B 112 " pdb=" OG SER B 116 " model vdw 2.242 3.040 nonbonded pdb=" O SER A 156 " pdb=" OG SER A 156 " model vdw 2.248 3.040 nonbonded pdb=" O ALA D 76 " pdb=" OG SER D 118 " model vdw 2.253 3.040 nonbonded pdb=" O ALA A 313 " pdb=" OG1 THR A 317 " model vdw 2.266 3.040 ... (remaining 68695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 88 or resid 100 through 185 or resid 187 through \ 318)) selection = (chain 'B' and (resid 1 through 185 or resid 187 through 318)) selection = (chain 'C' and (resid 1 through 185 or resid 187 through 318)) selection = (chain 'D' and (resid 1 through 88 or resid 100 through 185 or resid 187 through \ 318)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.790 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.004 0.045 9269 Z= 0.242 Angle : 0.582 7.517 12630 Z= 0.311 Chirality : 0.046 0.135 1559 Planarity : 0.005 0.043 1621 Dihedral : 15.800 89.231 3396 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.20 % Allowed : 25.55 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.23), residues: 1223 helix: 0.10 (0.22), residues: 534 sheet: -1.24 (0.42), residues: 151 loop : -1.88 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 58 PHE 0.012 0.001 PHE D 27 TYR 0.010 0.001 TYR D 261 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 1.297 Fit side-chains REVERT: B 263 ASP cc_start: 0.7936 (t70) cc_final: 0.7667 (t70) outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 0.2181 time to fit residues: 25.0193 Evaluate side-chains 74 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN C 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9269 Z= 0.290 Angle : 0.633 6.042 12630 Z= 0.336 Chirality : 0.048 0.146 1559 Planarity : 0.005 0.044 1621 Dihedral : 4.736 28.261 1308 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.32 % Allowed : 23.04 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1223 helix: 1.13 (0.23), residues: 542 sheet: -0.77 (0.40), residues: 171 loop : -2.00 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 245 PHE 0.013 0.002 PHE D 27 TYR 0.008 0.001 TYR D 261 ARG 0.004 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.977 Fit side-chains REVERT: B 7 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8139 (mm) REVERT: C 303 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: D 51 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.7697 (tpt-90) outliers start: 33 outliers final: 20 residues processed: 100 average time/residue: 0.1960 time to fit residues: 28.4611 Evaluate side-chains 90 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9269 Z= 0.237 Angle : 0.585 6.157 12630 Z= 0.307 Chirality : 0.046 0.141 1559 Planarity : 0.005 0.044 1621 Dihedral : 4.664 28.298 1307 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.53 % Allowed : 21.23 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1223 helix: 1.43 (0.23), residues: 541 sheet: -0.69 (0.40), residues: 166 loop : -1.96 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 58 PHE 0.011 0.001 PHE D 27 TYR 0.007 0.001 TYR D 261 ARG 0.002 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.998 Fit side-chains REVERT: B 7 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8040 (mm) REVERT: B 74 GLU cc_start: 0.7690 (pm20) cc_final: 0.6871 (tp30) REVERT: B 77 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: B 267 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: C 73 THR cc_start: 0.8738 (p) cc_final: 0.8484 (t) REVERT: C 303 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: D 51 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7695 (tpt-90) REVERT: D 169 ASN cc_start: 0.8885 (m-40) cc_final: 0.8635 (m110) outliers start: 45 outliers final: 22 residues processed: 116 average time/residue: 0.2008 time to fit residues: 33.7680 Evaluate side-chains 102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 overall best weight: 1.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9269 Z= 0.231 Angle : 0.582 6.478 12630 Z= 0.304 Chirality : 0.046 0.137 1559 Planarity : 0.005 0.044 1621 Dihedral : 4.647 27.890 1307 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.33 % Allowed : 21.53 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1223 helix: 1.55 (0.23), residues: 542 sheet: -0.65 (0.41), residues: 161 loop : -1.95 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 58 PHE 0.011 0.001 PHE D 27 TYR 0.007 0.001 TYR C 261 ARG 0.002 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 82 time to evaluate : 1.031 Fit side-chains REVERT: B 7 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8024 (mm) REVERT: B 68 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6411 (mtp180) REVERT: B 74 GLU cc_start: 0.7560 (pm20) cc_final: 0.6862 (tp30) REVERT: B 77 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: B 267 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: C 303 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: D 7 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.7995 (mm) REVERT: D 51 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7673 (tpt-90) REVERT: D 169 ASN cc_start: 0.8886 (m-40) cc_final: 0.8647 (m110) outliers start: 43 outliers final: 28 residues processed: 117 average time/residue: 0.2097 time to fit residues: 34.5549 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9269 Z= 0.294 Angle : 0.617 6.942 12630 Z= 0.323 Chirality : 0.048 0.146 1559 Planarity : 0.005 0.044 1621 Dihedral : 4.795 27.560 1307 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.63 % Allowed : 21.43 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1223 helix: 1.48 (0.23), residues: 541 sheet: -0.73 (0.39), residues: 176 loop : -2.04 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 58 PHE 0.013 0.002 PHE D 27 TYR 0.008 0.001 TYR D 259 ARG 0.002 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 75 time to evaluate : 1.021 Fit side-chains REVERT: B 7 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8091 (mm) REVERT: B 68 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6403 (mtp180) REVERT: B 74 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: B 77 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: B 267 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: C 73 THR cc_start: 0.8729 (p) cc_final: 0.8494 (t) REVERT: C 303 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: D 7 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8021 (mm) REVERT: D 51 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7684 (tpt-90) REVERT: D 169 ASN cc_start: 0.8921 (m-40) cc_final: 0.8679 (m110) outliers start: 46 outliers final: 30 residues processed: 111 average time/residue: 0.2077 time to fit residues: 32.9884 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9269 Z= 0.183 Angle : 0.556 7.624 12630 Z= 0.289 Chirality : 0.045 0.137 1559 Planarity : 0.005 0.044 1621 Dihedral : 4.555 27.935 1307 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.12 % Allowed : 22.23 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1223 helix: 1.70 (0.23), residues: 540 sheet: -0.57 (0.41), residues: 161 loop : -1.88 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 58 PHE 0.010 0.001 PHE D 27 TYR 0.006 0.001 TYR C 261 ARG 0.002 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 82 time to evaluate : 0.936 Fit side-chains REVERT: B 7 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8035 (mm) REVERT: B 68 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6361 (mtp180) REVERT: B 74 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6821 (tp30) REVERT: B 77 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: B 267 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: C 303 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: D 7 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.7925 (mm) REVERT: D 51 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7640 (tpt-90) outliers start: 40 outliers final: 23 residues processed: 114 average time/residue: 0.2158 time to fit residues: 34.7026 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 117 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9269 Z= 0.266 Angle : 0.597 8.281 12630 Z= 0.312 Chirality : 0.047 0.138 1559 Planarity : 0.005 0.043 1621 Dihedral : 4.687 27.276 1307 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.23 % Allowed : 22.23 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1223 helix: 1.60 (0.23), residues: 542 sheet: -0.63 (0.40), residues: 166 loop : -1.97 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 58 PHE 0.013 0.001 PHE D 27 TYR 0.008 0.001 TYR C 261 ARG 0.002 0.000 ARG D 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 0.953 Fit side-chains REVERT: B 7 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8056 (mm) REVERT: B 68 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.6388 (mtp180) REVERT: B 74 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: B 77 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: B 267 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 293 ILE cc_start: 0.9230 (pt) cc_final: 0.8938 (pt) REVERT: C 303 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: D 7 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.7994 (mm) REVERT: D 51 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7677 (tpt-90) outliers start: 41 outliers final: 30 residues processed: 108 average time/residue: 0.2208 time to fit residues: 33.3870 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9269 Z= 0.167 Angle : 0.540 6.921 12630 Z= 0.280 Chirality : 0.045 0.137 1559 Planarity : 0.005 0.044 1621 Dihedral : 4.450 27.739 1307 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.72 % Allowed : 23.34 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1223 helix: 1.81 (0.23), residues: 540 sheet: -0.51 (0.42), residues: 156 loop : -1.81 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 58 PHE 0.009 0.001 PHE D 27 TYR 0.006 0.001 TYR C 261 ARG 0.002 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 1.138 Fit side-chains REVERT: B 7 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8048 (mm) REVERT: B 68 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6326 (mtp180) REVERT: B 74 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7049 (tp30) REVERT: B 77 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: B 267 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 303 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: D 7 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.7913 (mm) REVERT: D 51 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7596 (tpt-90) outliers start: 36 outliers final: 22 residues processed: 116 average time/residue: 0.2128 time to fit residues: 35.2777 Evaluate side-chains 106 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9269 Z= 0.277 Angle : 0.613 9.895 12630 Z= 0.318 Chirality : 0.047 0.139 1559 Planarity : 0.005 0.043 1621 Dihedral : 4.688 27.779 1307 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.23 % Allowed : 23.04 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1223 helix: 1.65 (0.23), residues: 542 sheet: -0.59 (0.40), residues: 166 loop : -1.98 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS D 58 PHE 0.012 0.001 PHE D 27 TYR 0.008 0.001 TYR C 261 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 73 time to evaluate : 1.122 Fit side-chains REVERT: B 7 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8045 (mm) REVERT: B 68 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.6330 (mtp180) REVERT: B 74 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: B 77 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: B 267 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: B 293 ILE cc_start: 0.9239 (pt) cc_final: 0.8956 (pt) REVERT: C 303 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: D 7 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.7997 (mm) REVERT: D 51 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7648 (tpt-90) outliers start: 41 outliers final: 30 residues processed: 105 average time/residue: 0.2092 time to fit residues: 31.4314 Evaluate side-chains 109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 275 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9269 Z= 0.160 Angle : 0.547 9.250 12630 Z= 0.281 Chirality : 0.045 0.136 1559 Planarity : 0.005 0.044 1621 Dihedral : 4.402 27.678 1307 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.52 % Allowed : 23.44 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1223 helix: 1.85 (0.23), residues: 539 sheet: -0.38 (0.43), residues: 151 loop : -1.80 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 58 PHE 0.008 0.001 PHE D 27 TYR 0.007 0.001 TYR C 261 ARG 0.002 0.000 ARG D 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 1.083 Fit side-chains REVERT: B 7 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8006 (mm) REVERT: B 30 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8542 (m) REVERT: B 68 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6224 (mtp180) REVERT: B 74 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: B 77 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: B 267 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: C 303 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: D 7 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.7904 (mm) REVERT: D 51 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7559 (tpt-90) outliers start: 34 outliers final: 20 residues processed: 112 average time/residue: 0.2094 time to fit residues: 33.5266 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 51 ARG Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 248 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100047 restraints weight = 26720.443| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.23 r_work: 0.3086 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9269 Z= 0.193 Angle : 0.569 8.767 12630 Z= 0.292 Chirality : 0.045 0.135 1559 Planarity : 0.005 0.043 1621 Dihedral : 4.423 27.336 1307 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.22 % Allowed : 23.84 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1223 helix: 1.83 (0.23), residues: 540 sheet: -0.40 (0.41), residues: 161 loop : -1.82 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 58 PHE 0.009 0.001 PHE D 27 TYR 0.007 0.001 TYR C 261 ARG 0.002 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1909.31 seconds wall clock time: 35 minutes 46.13 seconds (2146.13 seconds total)