Starting phenix.real_space_refine on Thu Mar 13 16:43:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jln_36401/03_2025/8jln_36401.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jln_36401/03_2025/8jln_36401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jln_36401/03_2025/8jln_36401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jln_36401/03_2025/8jln_36401.map" model { file = "/net/cci-nas-00/data/ceres_data/8jln_36401/03_2025/8jln_36401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jln_36401/03_2025/8jln_36401.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 C 5814 2.51 5 N 1560 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9117 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1972 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 1 Chain: "S" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1767 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.63 Number of scatterers: 9117 At special positions: 0 Unit cell: (107.95, 118.15, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 68 16.00 O 1674 8.00 N 1560 7.00 C 5814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.978A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.546A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.086A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.864A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.995A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.623A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.262A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 50 removed outlier: 3.891A pdb=" N HIS R 50 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 84 removed outlier: 3.503A pdb=" N SER R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 127 removed outlier: 3.914A pdb=" N THR R 100 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER R 101 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 176 Processing helix chain 'R' and resid 178 through 182 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 232 Processing helix chain 'R' and resid 247 through 277 removed outlier: 4.439A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 300 removed outlier: 3.559A pdb=" N ILE R 290 " --> pdb=" O ASN R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 removed outlier: 3.814A pdb=" N TYR R 304 " --> pdb=" O ASN R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 318 removed outlier: 3.572A pdb=" N MET R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.338A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.118A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 29 through 45 removed outlier: 4.060A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.333A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.617A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.903A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.607A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.754A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.671A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.991A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 320 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.573A pdb=" N MET S 83 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 59 removed outlier: 6.567A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.765A pdb=" N THR S 141 " --> pdb=" O ARG S 160 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 174 through 176 Processing sheet with id=AB5, first strand: chain 'S' and resid 189 through 190 409 hydrogen bonds defined for protein. 1179 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: 2.41 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 3889 1.40 - 1.58: 5330 1.58 - 1.76: 0 1.76 - 1.93: 102 1.93 - 2.11: 1 Bond restraints: 9322 Sorted by residual: bond pdb=" N ASP R 103 " pdb=" CA ASP R 103 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.61e+00 bond pdb=" C01 UJF R 401 " pdb=" O01 UJF R 401 " ideal model delta sigma weight residual 1.370 1.396 -0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" C ASP B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.25e-02 6.40e+03 1.42e+00 bond pdb=" C07 UJF R 401 " pdb=" O02 UJF R 401 " ideal model delta sigma weight residual 1.379 1.402 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.34e-02 5.57e+03 1.20e+00 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12416 2.01 - 4.03: 166 4.03 - 6.04: 27 6.04 - 8.06: 9 8.06 - 10.07: 1 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C LYS Y 20 " pdb=" N MET Y 21 " pdb=" CA MET Y 21 " ideal model delta sigma weight residual 121.58 114.90 6.68 1.95e+00 2.63e-01 1.18e+01 angle pdb=" N VAL R 176 " pdb=" CA VAL R 176 " pdb=" C VAL R 176 " ideal model delta sigma weight residual 112.98 108.92 4.06 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N VAL R 94 " pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 111.81 109.08 2.73 8.60e-01 1.35e+00 1.01e+01 angle pdb=" C ASP R 103 " pdb=" N ILE R 104 " pdb=" CA ILE R 104 " ideal model delta sigma weight residual 120.55 125.28 -4.73 1.60e+00 3.91e-01 8.74e+00 angle pdb=" CA MET Y 21 " pdb=" CB MET Y 21 " pdb=" CG MET Y 21 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 4949 18.14 - 36.29: 478 36.29 - 54.43: 81 54.43 - 72.57: 10 72.57 - 90.72: 9 Dihedral angle restraints: 5527 sinusoidal: 2176 harmonic: 3351 Sorted by residual: dihedral pdb=" CA GLY A 225 " pdb=" C GLY A 225 " pdb=" N ALA A 226 " pdb=" CA ALA A 226 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 911 0.034 - 0.068: 326 0.068 - 0.102: 116 0.102 - 0.136: 46 0.136 - 0.170: 4 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA MET Y 21 " pdb=" N MET Y 21 " pdb=" C MET Y 21 " pdb=" CB MET Y 21 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CB ILE R 280 " pdb=" CA ILE R 280 " pdb=" CG1 ILE R 280 " pdb=" CG2 ILE R 280 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB THR A 350 " pdb=" CA THR A 350 " pdb=" OG1 THR A 350 " pdb=" CG2 THR A 350 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1400 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 310 " -0.014 2.00e-02 2.50e+03 1.55e-02 6.03e+00 pdb=" CG TRP R 310 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP R 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP R 310 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 310 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 310 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 310 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 310 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 310 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO S 151 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO S 107 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " -0.024 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1441 2.76 - 3.31: 8896 3.31 - 3.86: 15061 3.86 - 4.41: 17457 4.41 - 4.96: 30913 Nonbonded interactions: 73768 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLU A 21 " pdb=" OG SER S 52 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.288 3.040 ... (remaining 73763 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9322 Z= 0.152 Angle : 0.637 10.073 12619 Z= 0.365 Chirality : 0.043 0.170 1403 Planarity : 0.004 0.051 1597 Dihedral : 14.364 90.715 3358 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1136 helix: 1.76 (0.27), residues: 396 sheet: -0.03 (0.34), residues: 246 loop : -1.73 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 310 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE S 80 TYR 0.014 0.001 TYR S 103 ARG 0.006 0.000 ARG R 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.044 Fit side-chains REVERT: B 42 ARG cc_start: 0.7311 (ptm-80) cc_final: 0.6910 (tmt170) REVERT: R 262 ILE cc_start: 0.7961 (tt) cc_final: 0.7675 (tt) REVERT: S 20 LEU cc_start: 0.6905 (mt) cc_final: 0.6616 (mt) REVERT: Y 21 MET cc_start: 0.5427 (pmm) cc_final: 0.4650 (mtp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1800 time to fit residues: 39.0283 Evaluate side-chains 127 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 HIS S 35 HIS S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.206998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143279 restraints weight = 9439.688| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.01 r_work: 0.3316 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9322 Z= 0.436 Angle : 0.735 9.344 12619 Z= 0.387 Chirality : 0.050 0.175 1403 Planarity : 0.005 0.052 1597 Dihedral : 6.052 72.148 1264 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.62 % Allowed : 9.40 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.68 (0.24), residues: 1136 helix: 1.27 (0.25), residues: 397 sheet: -0.44 (0.33), residues: 251 loop : -1.95 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 310 HIS 0.008 0.002 HIS B 311 PHE 0.033 0.003 PHE R 165 TYR 0.019 0.002 TYR S 103 ARG 0.006 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7278 (tt0) cc_final: 0.6874 (tm-30) REVERT: B 42 ARG cc_start: 0.7542 (ptm-80) cc_final: 0.7017 (tmt170) REVERT: B 153 ASP cc_start: 0.8413 (t0) cc_final: 0.8156 (t0) REVERT: B 212 ASP cc_start: 0.7763 (t0) cc_final: 0.7334 (p0) REVERT: B 247 ASP cc_start: 0.8392 (t70) cc_final: 0.8074 (t0) REVERT: R 91 PHE cc_start: 0.8360 (m-80) cc_final: 0.8115 (m-80) REVERT: S 20 LEU cc_start: 0.6895 (mt) cc_final: 0.6604 (mt) REVERT: S 172 THR cc_start: 0.8179 (m) cc_final: 0.7728 (t) REVERT: S 233 LEU cc_start: 0.4743 (tp) cc_final: 0.4430 (tp) outliers start: 16 outliers final: 13 residues processed: 146 average time/residue: 0.2139 time to fit residues: 45.0494 Evaluate side-chains 144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS R 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.210750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141527 restraints weight = 9757.082| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.04 r_work: 0.3398 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9322 Z= 0.200 Angle : 0.579 10.955 12619 Z= 0.301 Chirality : 0.043 0.152 1403 Planarity : 0.004 0.051 1597 Dihedral : 5.807 75.115 1264 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.52 % Allowed : 13.45 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.45 (0.24), residues: 1136 helix: 1.58 (0.25), residues: 398 sheet: -0.43 (0.33), residues: 257 loop : -1.88 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 310 HIS 0.004 0.001 HIS B 311 PHE 0.022 0.001 PHE S 80 TYR 0.015 0.001 TYR S 190 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7294 (tt0) cc_final: 0.6888 (tm-30) REVERT: B 42 ARG cc_start: 0.7607 (ptm-80) cc_final: 0.7150 (tmt170) REVERT: B 153 ASP cc_start: 0.7865 (t0) cc_final: 0.7585 (t0) REVERT: B 247 ASP cc_start: 0.8370 (t70) cc_final: 0.7956 (t0) REVERT: R 23 ARG cc_start: 0.8111 (mpt-90) cc_final: 0.7731 (mpp-170) REVERT: R 69 ASP cc_start: 0.7707 (m-30) cc_final: 0.7471 (m-30) REVERT: S 20 LEU cc_start: 0.6963 (mt) cc_final: 0.6636 (mt) REVERT: S 172 THR cc_start: 0.8174 (m) cc_final: 0.7562 (t) outliers start: 15 outliers final: 11 residues processed: 147 average time/residue: 0.1908 time to fit residues: 40.8476 Evaluate side-chains 142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS S 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.209676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144544 restraints weight = 9350.101| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.79 r_work: 0.3370 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9322 Z= 0.229 Angle : 0.569 7.447 12619 Z= 0.299 Chirality : 0.043 0.153 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.761 79.737 1264 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.02 % Allowed : 16.38 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.37 (0.25), residues: 1136 helix: 1.66 (0.26), residues: 399 sheet: -0.38 (0.33), residues: 257 loop : -1.87 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 310 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.002 PHE R 165 TYR 0.016 0.001 TYR S 190 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7354 (tt0) cc_final: 0.6927 (tm-30) REVERT: B 42 ARG cc_start: 0.7663 (ptm-80) cc_final: 0.7210 (tmt170) REVERT: B 153 ASP cc_start: 0.8082 (t0) cc_final: 0.7806 (t0) REVERT: B 247 ASP cc_start: 0.8355 (t70) cc_final: 0.7795 (t0) REVERT: R 23 ARG cc_start: 0.8165 (mpt-90) cc_final: 0.7898 (mpt180) REVERT: R 69 ASP cc_start: 0.7795 (m-30) cc_final: 0.7533 (m-30) REVERT: R 75 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6541 (tt) REVERT: R 165 PHE cc_start: 0.8699 (p90) cc_final: 0.8267 (p90) REVERT: S 20 LEU cc_start: 0.7041 (mt) cc_final: 0.6691 (mt) REVERT: S 172 THR cc_start: 0.8128 (m) cc_final: 0.7520 (t) outliers start: 20 outliers final: 16 residues processed: 144 average time/residue: 0.2372 time to fit residues: 48.6461 Evaluate side-chains 144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 35 optimal weight: 0.0030 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 17 optimal weight: 0.0030 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN S 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.214531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143150 restraints weight = 9136.298| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.54 r_work: 0.3457 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9322 Z= 0.136 Angle : 0.518 8.781 12619 Z= 0.268 Chirality : 0.041 0.146 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.531 79.989 1264 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.82 % Allowed : 17.59 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1136 helix: 1.95 (0.26), residues: 395 sheet: -0.21 (0.34), residues: 252 loop : -1.78 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 310 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE S 80 TYR 0.015 0.001 TYR S 190 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7262 (tt0) cc_final: 0.6889 (tm-30) REVERT: A 333 ARG cc_start: 0.8920 (mmm-85) cc_final: 0.8696 (mtp85) REVERT: B 42 ARG cc_start: 0.7688 (ptm-80) cc_final: 0.7234 (tmt170) REVERT: B 153 ASP cc_start: 0.7689 (t0) cc_final: 0.7428 (t0) REVERT: B 247 ASP cc_start: 0.8257 (t70) cc_final: 0.7666 (t0) REVERT: R 23 ARG cc_start: 0.8095 (mpt-90) cc_final: 0.7857 (mpt180) REVERT: R 69 ASP cc_start: 0.7659 (m-30) cc_final: 0.7313 (m-30) REVERT: R 75 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6280 (tt) REVERT: R 161 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7819 (tt) REVERT: S 20 LEU cc_start: 0.7046 (mt) cc_final: 0.6688 (mt) REVERT: S 172 THR cc_start: 0.8016 (m) cc_final: 0.7463 (t) outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 0.1812 time to fit residues: 38.0385 Evaluate side-chains 140 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS S 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.209860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131636 restraints weight = 8945.413| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.79 r_work: 0.3402 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9322 Z= 0.218 Angle : 0.559 7.635 12619 Z= 0.291 Chirality : 0.044 0.267 1403 Planarity : 0.004 0.049 1597 Dihedral : 5.614 83.003 1264 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.02 % Allowed : 18.30 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1136 helix: 1.91 (0.26), residues: 395 sheet: -0.34 (0.33), residues: 259 loop : -1.77 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 310 HIS 0.003 0.001 HIS S 35 PHE 0.022 0.002 PHE R 165 TYR 0.016 0.001 TYR A 37 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7232 (tt0) cc_final: 0.6880 (tm-30) REVERT: A 333 ARG cc_start: 0.8959 (mmm-85) cc_final: 0.8750 (mtp85) REVERT: B 42 ARG cc_start: 0.7688 (ptm-80) cc_final: 0.7253 (tmt170) REVERT: B 153 ASP cc_start: 0.8047 (t0) cc_final: 0.7813 (t0) REVERT: B 247 ASP cc_start: 0.8280 (t70) cc_final: 0.7692 (t0) REVERT: R 23 ARG cc_start: 0.8099 (mpt-90) cc_final: 0.7795 (mpt-90) REVERT: R 69 ASP cc_start: 0.7872 (m-30) cc_final: 0.7571 (m-30) REVERT: R 161 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7881 (tt) REVERT: R 262 ILE cc_start: 0.8885 (tp) cc_final: 0.8453 (tp) REVERT: R 273 MET cc_start: 0.7304 (mtp) cc_final: 0.7087 (mtp) REVERT: S 20 LEU cc_start: 0.6997 (mt) cc_final: 0.6629 (mt) REVERT: S 172 THR cc_start: 0.8138 (m) cc_final: 0.7630 (t) outliers start: 20 outliers final: 16 residues processed: 137 average time/residue: 0.2005 time to fit residues: 39.1920 Evaluate side-chains 143 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.0170 chunk 18 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** 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 = 0.4406 r_free = 0.4406 target = 0.214597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151650 restraints weight = 9432.407| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.75 r_work: 0.3487 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9322 Z= 0.138 Angle : 0.532 9.503 12619 Z= 0.273 Chirality : 0.042 0.189 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.534 83.102 1264 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.33 % Allowed : 18.50 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1136 helix: 2.03 (0.26), residues: 395 sheet: -0.13 (0.34), residues: 252 loop : -1.73 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 310 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE S 80 TYR 0.015 0.001 TYR A 37 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7179 (tt0) cc_final: 0.6841 (tm-30) REVERT: A 333 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8711 (mtp85) REVERT: B 42 ARG cc_start: 0.7687 (ptm-80) cc_final: 0.7294 (tmt170) REVERT: B 153 ASP cc_start: 0.7723 (t0) cc_final: 0.7485 (t0) REVERT: B 247 ASP cc_start: 0.8236 (t70) cc_final: 0.7655 (t0) REVERT: R 23 ARG cc_start: 0.7981 (mpt-90) cc_final: 0.7763 (mpt180) REVERT: R 69 ASP cc_start: 0.7666 (m-30) cc_final: 0.7322 (m-30) REVERT: R 75 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6318 (tt) REVERT: R 161 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7857 (tt) REVERT: R 262 ILE cc_start: 0.8859 (tp) cc_final: 0.8440 (tp) REVERT: Y 21 MET cc_start: 0.6294 (pmm) cc_final: 0.4757 (mtm) outliers start: 23 outliers final: 15 residues processed: 141 average time/residue: 0.2061 time to fit residues: 42.1352 Evaluate side-chains 142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.207254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138417 restraints weight = 9286.852| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.78 r_work: 0.3388 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9322 Z= 0.301 Angle : 0.620 8.738 12619 Z= 0.323 Chirality : 0.045 0.187 1403 Planarity : 0.004 0.049 1597 Dihedral : 5.721 86.604 1264 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.33 % Allowed : 19.21 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.23 (0.25), residues: 1136 helix: 1.81 (0.26), residues: 394 sheet: -0.24 (0.33), residues: 254 loop : -1.81 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 310 HIS 0.005 0.001 HIS R 63 PHE 0.022 0.002 PHE A 212 TYR 0.015 0.002 TYR A 37 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7537 (tt0) cc_final: 0.7042 (tm-30) REVERT: B 42 ARG cc_start: 0.7798 (ptm-80) cc_final: 0.7321 (tmt170) REVERT: B 153 ASP cc_start: 0.8261 (t0) cc_final: 0.7980 (t0) REVERT: B 247 ASP cc_start: 0.8409 (t70) cc_final: 0.7838 (t0) REVERT: R 23 ARG cc_start: 0.8150 (mpt-90) cc_final: 0.7854 (mpt180) REVERT: R 69 ASP cc_start: 0.8081 (m-30) cc_final: 0.7771 (m-30) REVERT: R 75 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6689 (tt) REVERT: R 161 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7762 (tt) REVERT: S 146 SER cc_start: 0.5167 (m) cc_final: 0.4621 (t) REVERT: Y 21 MET cc_start: 0.6442 (pmm) cc_final: 0.5026 (mtp) REVERT: Y 46 LYS cc_start: 0.9280 (tptm) cc_final: 0.9032 (ttpp) outliers start: 23 outliers final: 20 residues processed: 142 average time/residue: 0.1909 time to fit residues: 39.2897 Evaluate side-chains 149 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1968 > 50: distance: 13 - 19: 3.017 distance: 80 - 85: 8.891 distance: 81 - 112: 15.741 distance: 86 - 87: 3.282 distance: 87 - 88: 5.556 distance: 87 - 93: 10.240 distance: 89 - 90: 9.221 distance: 90 - 91: 16.716 distance: 91 - 92: 24.168 distance: 93 - 94: 6.201 distance: 94 - 95: 11.085 distance: 94 - 97: 17.182 distance: 95 - 96: 8.002 distance: 95 - 100: 21.177 distance: 97 - 98: 4.428 distance: 97 - 99: 14.219 distance: 100 - 101: 10.502 distance: 101 - 102: 12.122 distance: 101 - 104: 7.010 distance: 102 - 103: 13.592 distance: 102 - 112: 19.791 distance: 104 - 105: 7.834 distance: 105 - 106: 16.618 distance: 105 - 107: 17.686 distance: 106 - 108: 13.399 distance: 107 - 109: 12.589 distance: 108 - 110: 17.906 distance: 109 - 110: 9.393 distance: 110 - 111: 9.410 distance: 112 - 113: 18.845 distance: 113 - 114: 18.003 distance: 113 - 116: 16.685 distance: 114 - 115: 20.741 distance: 114 - 117: 19.839 distance: 117 - 118: 15.840 distance: 118 - 119: 10.811 distance: 118 - 121: 19.899 distance: 119 - 120: 31.953 distance: 119 - 128: 10.019 distance: 121 - 122: 10.623 distance: 122 - 123: 17.822 distance: 122 - 124: 14.076 distance: 123 - 125: 17.701 distance: 124 - 126: 18.213 distance: 125 - 127: 16.718 distance: 126 - 127: 17.503 distance: 128 - 129: 12.037 distance: 129 - 130: 7.927 distance: 129 - 132: 9.049 distance: 130 - 131: 27.295 distance: 130 - 139: 16.867 distance: 132 - 133: 11.132 distance: 133 - 134: 17.578 distance: 133 - 135: 13.544 distance: 134 - 136: 5.784 distance: 135 - 137: 4.105 distance: 136 - 138: 9.806 distance: 137 - 138: 18.415 distance: 139 - 140: 23.072 distance: 140 - 141: 11.963 distance: 140 - 143: 10.144 distance: 141 - 142: 10.204 distance: 141 - 151: 7.722 distance: 142 - 183: 31.703 distance: 143 - 144: 17.091 distance: 144 - 145: 13.759 distance: 144 - 146: 20.727 distance: 145 - 147: 18.946 distance: 146 - 148: 9.445 distance: 147 - 149: 18.697 distance: 148 - 149: 26.985 distance: 149 - 150: 42.973 distance: 151 - 152: 6.093 distance: 151 - 157: 13.686 distance: 152 - 153: 12.706 distance: 152 - 155: 16.907 distance: 153 - 154: 10.763 distance: 153 - 158: 3.731 distance: 154 - 193: 11.809 distance: 155 - 156: 9.238 distance: 156 - 157: 5.597 distance: 158 - 159: 5.158 distance: 159 - 160: 10.319 distance: 159 - 162: 9.502 distance: 160 - 161: 8.799 distance: 160 - 172: 3.795 distance: 161 - 201: 11.973 distance: 162 - 163: 3.013 distance: 163 - 164: 5.782 distance: 163 - 165: 5.837 distance: 164 - 166: 4.054 distance: 165 - 167: 17.393 distance: 165 - 168: 6.410 distance: 166 - 167: 13.630 distance: 167 - 169: 4.898 distance: 168 - 170: 6.126 distance: 169 - 171: 6.733 distance: 170 - 171: 3.858 distance: 172 - 173: 8.995 distance: 173 - 174: 5.324 distance: 173 - 176: 7.850 distance: 174 - 175: 5.638 distance: 174 - 183: 3.742 distance: 175 - 206: 6.744 distance: 176 - 177: 4.123 distance: 177 - 178: 7.804 distance: 179 - 181: 4.256 distance: 181 - 182: 5.320