Starting phenix.real_space_refine on Mon Dec 30 00:35:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c1z_16385/12_2024/8c1z_16385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c1z_16385/12_2024/8c1z_16385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c1z_16385/12_2024/8c1z_16385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c1z_16385/12_2024/8c1z_16385.map" model { file = "/net/cci-nas-00/data/ceres_data/8c1z_16385/12_2024/8c1z_16385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c1z_16385/12_2024/8c1z_16385.cif" } resolution = 3.8 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= 0.014 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 32 5.16 5 C 7851 2.51 5 N 1916 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11863 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3042 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 347} Chain breaks: 1 Chain: "B" Number of atoms: 3035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3035 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "C" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2988 Classifications: {'peptide': 361} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain breaks: 4 Chain: "D" Number of atoms: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2798 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 318} Chain breaks: 11 Time building chain proxies: 7.91, per 1000 atoms: 0.67 Number of scatterers: 11863 At special positions: 0 Unit cell: (95.418, 92.907, 127.224, 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 32 16.00 O 2064 8.00 N 1916 7.00 C 7851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 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: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 44.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 4.301A pdb=" N ASN A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.521A pdb=" N ASP A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 227 through 243 removed outlier: 3.722A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 273 removed outlier: 3.565A pdb=" N PHE A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 287 through 311 removed outlier: 3.504A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.850A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TRP A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 459 Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.550A pdb=" N HIS B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.859A pdb=" N ASP B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.909A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 273 removed outlier: 3.753A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 284 through 307 removed outlier: 4.000A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 Processing helix chain 'B' and resid 422 through 462 Processing helix chain 'C' and resid 10 through 22 removed outlier: 4.283A pdb=" N ASN C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 removed outlier: 3.602A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 227 through 244 removed outlier: 3.518A pdb=" N SER C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 273 removed outlier: 3.678A pdb=" N VAL C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 309 removed outlier: 4.048A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.995A pdb=" N TRP C 320 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 426 through 462 removed outlier: 3.580A pdb=" N SER C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.502A pdb=" N SER D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE D 93 " --> pdb=" O THR D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 170 through 177 removed outlier: 3.938A pdb=" N ASP D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 224 Processing helix chain 'D' and resid 227 through 243 removed outlier: 3.671A pdb=" N SER D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 273 removed outlier: 4.240A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 310 removed outlier: 3.594A pdb=" N PHE D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 4.038A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 461 removed outlier: 4.314A pdb=" N ASP D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.907A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 removed outlier: 6.995A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 101 removed outlier: 4.621A pdb=" N THR A 152 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 134 removed outlier: 7.174A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 44 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 164 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 88 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.083A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR B 207 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 198 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU B 209 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B 196 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS B 211 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR B 213 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 192 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 215 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 10.883A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 116 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 10.883A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 116 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 154 removed outlier: 3.580A pdb=" N PHE C 193 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 124 through 128 Processing sheet with id=AB2, first strand: chain 'D' and resid 124 through 128 removed outlier: 7.412A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 146 through 153 removed outlier: 6.524A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 3.30 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: 3610 1.34 - 1.46: 2707 1.46 - 1.58: 5827 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 12192 Sorted by residual: bond pdb=" N VAL D 83 " pdb=" CA VAL D 83 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.68e+00 bond pdb=" N ILE D 278 " pdb=" CA ILE D 278 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.19e-02 7.06e+03 5.97e+00 bond pdb=" N GLN A 147 " pdb=" CA GLN A 147 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.19e-02 7.06e+03 4.98e+00 bond pdb=" N ASP C 105 " pdb=" CA ASP C 105 " ideal model delta sigma weight residual 1.457 1.431 0.027 1.29e-02 6.01e+03 4.29e+00 bond pdb=" N ASN D 82 " pdb=" CA ASN D 82 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.46e-02 4.69e+03 3.88e+00 ... (remaining 12187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 16301 1.59 - 3.17: 298 3.17 - 4.76: 62 4.76 - 6.35: 3 6.35 - 7.94: 5 Bond angle restraints: 16669 Sorted by residual: angle pdb=" N GLY D 279 " pdb=" CA GLY D 279 " pdb=" C GLY D 279 " ideal model delta sigma weight residual 115.21 107.27 7.94 1.30e+00 5.92e-01 3.73e+01 angle pdb=" N GLN A 147 " pdb=" CA GLN A 147 " pdb=" C GLN A 147 " ideal model delta sigma weight residual 108.41 115.63 -7.22 1.63e+00 3.76e-01 1.96e+01 angle pdb=" N VAL C 106 " pdb=" CA VAL C 106 " pdb=" CB VAL C 106 " ideal model delta sigma weight residual 111.50 105.02 6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" N ASP D 81 " pdb=" CA ASP D 81 " pdb=" C ASP D 81 " ideal model delta sigma weight residual 112.58 108.17 4.41 1.22e+00 6.72e-01 1.31e+01 angle pdb=" CA ASN D 82 " pdb=" C ASN D 82 " pdb=" O ASN D 82 " ideal model delta sigma weight residual 121.28 117.33 3.95 1.19e+00 7.06e-01 1.10e+01 ... (remaining 16664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 6181 16.04 - 32.08: 707 32.08 - 48.13: 211 48.13 - 64.17: 38 64.17 - 80.21: 9 Dihedral angle restraints: 7146 sinusoidal: 2877 harmonic: 4269 Sorted by residual: dihedral pdb=" CA TYR A 286 " pdb=" C TYR A 286 " pdb=" N PHE A 287 " pdb=" CA PHE A 287 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 136.48 -43.48 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA PHE A 144 " pdb=" C PHE A 144 " pdb=" N ASP A 145 " pdb=" CA ASP A 145 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 7143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1564 0.048 - 0.096: 288 0.096 - 0.143: 86 0.143 - 0.191: 6 0.191 - 0.239: 3 Chirality restraints: 1947 Sorted by residual: chirality pdb=" CA VAL A 106 " pdb=" N VAL A 106 " pdb=" C VAL A 106 " pdb=" CB VAL A 106 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP C 105 " pdb=" N ASP C 105 " pdb=" C ASP C 105 " pdb=" CB ASP C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL C 106 " pdb=" N VAL C 106 " pdb=" C VAL C 106 " pdb=" CB VAL C 106 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 1944 not shown) Planarity restraints: 2030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 88 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO D 89 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 89 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 89 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 277 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ALA D 277 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA D 277 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE D 278 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 82 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C ASN D 82 " -0.026 2.00e-02 2.50e+03 pdb=" O ASN D 82 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL D 83 " 0.009 2.00e-02 2.50e+03 ... (remaining 2027 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 65 2.49 - 3.10: 8813 3.10 - 3.70: 18034 3.70 - 4.30: 25423 4.30 - 4.90: 42966 Nonbonded interactions: 95301 Sorted by model distance: nonbonded pdb=" O VAL C 104 " pdb=" OD1 ASP C 105 " model vdw 1.892 3.040 nonbonded pdb=" O VAL A 104 " pdb=" OD1 ASP A 105 " model vdw 2.009 3.040 nonbonded pdb=" OG SER C 170 " pdb=" OE1 GLU C 173 " model vdw 2.219 3.040 nonbonded pdb=" N GLN B 74 " pdb=" OE1 GLN B 74 " model vdw 2.225 3.120 nonbonded pdb=" O LEU C 293 " pdb=" OH TYR C 441 " model vdw 2.230 3.040 ... (remaining 95296 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 12 through 22 or resid 27 through 29 or resid 33 or resid \ 39 through 69 or resid 72 through 94 or resid 99 through 106 or resid 109 throug \ h 110 or resid 113 through 116 or resid 118 through 160 or resid 165 through 195 \ or resid 197 through 198 or resid 205 through 462)) selection = (chain 'B' and (resid 12 through 22 or resid 27 through 29 or resid 33 or resid \ 39 through 69 or resid 72 through 94 or resid 99 through 106 or resid 109 throug \ h 110 or resid 113 through 116 or resid 118 through 160 or resid 165 through 195 \ or resid 197 through 198 or resid 205 through 462)) selection = (chain 'C' and (resid 12 through 22 or resid 27 through 29 or resid 33 or resid \ 39 through 69 or resid 72 through 94 or resid 99 through 110 or resid 113 throug \ h 116 or resid 118 through 160 or resid 165 through 195 or resid 197 through 198 \ or resid 205 through 333 or resid 421 through 462)) selection = (chain 'D' and (resid 12 through 22 or resid 27 through 94 or resid 99 through 1 \ 06 or resid 109 through 333 or resid 421 through 462)) } 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 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.900 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12192 Z= 0.204 Angle : 0.554 7.935 16669 Z= 0.309 Chirality : 0.043 0.239 1947 Planarity : 0.004 0.040 2030 Dihedral : 15.091 80.208 4344 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.03 % Favored : 94.61 % Rotamer: Outliers : 0.22 % Allowed : 11.94 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % 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: -0.33 (0.24), residues: 1392 helix: 1.81 (0.23), residues: 552 sheet: -1.86 (0.27), residues: 334 loop : -1.25 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 156 HIS 0.005 0.001 HIS D 309 PHE 0.023 0.001 PHE D 233 TYR 0.012 0.001 TYR C 67 ARG 0.002 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 145 average time/residue: 0.2499 time to fit residues: 52.2216 Evaluate side-chains 87 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 278 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 50.0000 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 128 optimal weight: 0.0030 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12192 Z= 0.211 Angle : 0.574 6.865 16669 Z= 0.296 Chirality : 0.042 0.154 1947 Planarity : 0.004 0.044 2030 Dihedral : 4.453 47.441 1566 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.45 % Favored : 95.33 % Rotamer: Outliers : 1.87 % Allowed : 14.18 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % 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: 0.16 (0.24), residues: 1392 helix: 2.33 (0.22), residues: 558 sheet: -1.73 (0.28), residues: 331 loop : -1.10 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 PHE 0.033 0.001 PHE D 233 TYR 0.021 0.001 TYR C 67 ARG 0.006 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7781 (tpp) outliers start: 25 outliers final: 11 residues processed: 112 average time/residue: 0.2261 time to fit residues: 38.2061 Evaluate side-chains 88 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 307 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 0.0770 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 102 optimal weight: 0.0470 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12192 Z= 0.165 Angle : 0.550 8.764 16669 Z= 0.279 Chirality : 0.042 0.180 1947 Planarity : 0.004 0.044 2030 Dihedral : 4.051 22.477 1563 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.09 % Favored : 95.69 % Rotamer: Outliers : 1.87 % Allowed : 15.82 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1392 helix: 2.77 (0.22), residues: 551 sheet: -1.55 (0.28), residues: 341 loop : -1.07 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 PHE 0.024 0.001 PHE D 233 TYR 0.021 0.001 TYR C 67 ARG 0.004 0.000 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 109 average time/residue: 0.2250 time to fit residues: 37.4134 Evaluate side-chains 100 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 433 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 0.0670 chunk 61 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12192 Z= 0.155 Angle : 0.546 9.668 16669 Z= 0.274 Chirality : 0.041 0.146 1947 Planarity : 0.004 0.043 2030 Dihedral : 3.929 20.921 1563 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.38 % Favored : 95.40 % Rotamer: Outliers : 2.46 % Allowed : 16.04 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % 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: 0.71 (0.24), residues: 1392 helix: 2.95 (0.22), residues: 551 sheet: -1.42 (0.28), residues: 330 loop : -0.98 (0.30), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 PHE 0.022 0.001 PHE D 233 TYR 0.020 0.001 TYR C 67 ARG 0.003 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 238 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6411 (m-30) REVERT: D 441 TYR cc_start: 0.7434 (t80) cc_final: 0.7121 (t80) outliers start: 33 outliers final: 23 residues processed: 114 average time/residue: 0.2291 time to fit residues: 40.1229 Evaluate side-chains 105 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12192 Z= 0.216 Angle : 0.557 9.871 16669 Z= 0.277 Chirality : 0.041 0.154 1947 Planarity : 0.004 0.043 2030 Dihedral : 3.916 21.251 1563 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.60 % Favored : 95.19 % Rotamer: Outliers : 2.46 % Allowed : 17.46 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % 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: 0.77 (0.24), residues: 1392 helix: 3.02 (0.22), residues: 552 sheet: -1.40 (0.28), residues: 332 loop : -0.97 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 331 HIS 0.003 0.001 HIS B 119 PHE 0.016 0.001 PHE D 233 TYR 0.020 0.001 TYR C 67 ARG 0.003 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 ASP cc_start: 0.6376 (t0) cc_final: 0.6135 (t0) REVERT: D 441 TYR cc_start: 0.7415 (t80) cc_final: 0.6917 (t80) outliers start: 33 outliers final: 20 residues processed: 106 average time/residue: 0.2103 time to fit residues: 34.7301 Evaluate side-chains 94 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 307 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.1980 chunk 11 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12192 Z= 0.229 Angle : 0.566 9.647 16669 Z= 0.281 Chirality : 0.041 0.149 1947 Planarity : 0.004 0.043 2030 Dihedral : 3.951 21.418 1563 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.67 % Favored : 95.11 % Rotamer: Outliers : 2.84 % Allowed : 17.46 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1392 helix: 3.01 (0.22), residues: 554 sheet: -1.41 (0.28), residues: 342 loop : -0.97 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 PHE 0.013 0.001 PHE D 233 TYR 0.021 0.001 TYR C 67 ARG 0.002 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 ASP cc_start: 0.6314 (t0) cc_final: 0.6113 (t0) REVERT: D 441 TYR cc_start: 0.7306 (t80) cc_final: 0.6812 (t80) outliers start: 38 outliers final: 24 residues processed: 110 average time/residue: 0.2250 time to fit residues: 38.4007 Evaluate side-chains 94 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12192 Z= 0.171 Angle : 0.546 9.148 16669 Z= 0.274 Chirality : 0.041 0.170 1947 Planarity : 0.003 0.045 2030 Dihedral : 3.927 19.974 1563 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.45 % Favored : 95.33 % Rotamer: Outliers : 2.39 % Allowed : 18.28 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1392 helix: 3.08 (0.22), residues: 548 sheet: -1.36 (0.27), residues: 350 loop : -0.93 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 PHE 0.020 0.001 PHE D 80 TYR 0.020 0.001 TYR C 67 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 ASP cc_start: 0.6269 (t0) cc_final: 0.6054 (t0) REVERT: D 441 TYR cc_start: 0.7274 (t80) cc_final: 0.6806 (t80) outliers start: 32 outliers final: 22 residues processed: 107 average time/residue: 0.2181 time to fit residues: 36.3355 Evaluate side-chains 98 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.0270 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS B 184 GLN ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 12192 Z= 0.152 Angle : 0.555 9.817 16669 Z= 0.276 Chirality : 0.041 0.152 1947 Planarity : 0.003 0.043 2030 Dihedral : 3.879 18.337 1563 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 2.24 % Allowed : 18.81 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % 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: 0.88 (0.25), residues: 1392 helix: 3.13 (0.22), residues: 547 sheet: -1.29 (0.27), residues: 348 loop : -0.90 (0.31), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 PHE 0.020 0.001 PHE D 80 TYR 0.020 0.001 TYR C 67 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 ILE cc_start: 0.7885 (mm) cc_final: 0.7683 (pt) REVERT: D 441 TYR cc_start: 0.7283 (t80) cc_final: 0.6902 (t80) outliers start: 30 outliers final: 23 residues processed: 101 average time/residue: 0.2412 time to fit residues: 37.7056 Evaluate side-chains 97 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 114 optimal weight: 30.0000 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12192 Z= 0.181 Angle : 0.581 9.772 16669 Z= 0.286 Chirality : 0.041 0.163 1947 Planarity : 0.003 0.045 2030 Dihedral : 3.871 18.677 1563 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.45 % Favored : 95.40 % Rotamer: Outliers : 1.72 % Allowed : 19.48 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % 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: 0.89 (0.24), residues: 1392 helix: 3.11 (0.22), residues: 548 sheet: -1.27 (0.27), residues: 350 loop : -0.88 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 331 HIS 0.006 0.001 HIS D 309 PHE 0.010 0.001 PHE A 153 TYR 0.020 0.001 TYR C 67 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 21 residues processed: 97 average time/residue: 0.2316 time to fit residues: 35.2447 Evaluate side-chains 93 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12192 Z= 0.182 Angle : 0.593 14.900 16669 Z= 0.292 Chirality : 0.041 0.219 1947 Planarity : 0.003 0.045 2030 Dihedral : 3.874 19.032 1563 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 1.87 % Allowed : 19.18 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % 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: 0.88 (0.24), residues: 1392 helix: 3.05 (0.22), residues: 549 sheet: -1.23 (0.27), residues: 350 loop : -0.86 (0.31), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 331 HIS 0.004 0.001 HIS D 309 PHE 0.030 0.001 PHE B 303 TYR 0.020 0.001 TYR C 67 ARG 0.003 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 95 average time/residue: 0.2058 time to fit residues: 30.7653 Evaluate side-chains 91 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 168 TRP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.0470 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.090790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.064976 restraints weight = 45074.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.066395 restraints weight = 21062.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067066 restraints weight = 14395.891| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12192 Z= 0.206 Angle : 0.604 14.830 16669 Z= 0.299 Chirality : 0.042 0.236 1947 Planarity : 0.003 0.045 2030 Dihedral : 3.908 20.429 1563 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.74 % Favored : 95.11 % Rotamer: Outliers : 1.79 % Allowed : 19.78 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.58 % 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: 0.88 (0.24), residues: 1392 helix: 3.07 (0.22), residues: 548 sheet: -1.25 (0.27), residues: 350 loop : -0.86 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 331 HIS 0.004 0.001 HIS B 119 PHE 0.029 0.001 PHE B 303 TYR 0.021 0.001 TYR B 64 ARG 0.003 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2053.15 seconds wall clock time: 39 minutes 19.30 seconds (2359.30 seconds total)