Starting phenix.real_space_refine on Wed Jan 15 19:06:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjk_38399/01_2025/8xjk_38399.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjk_38399/01_2025/8xjk_38399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjk_38399/01_2025/8xjk_38399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjk_38399/01_2025/8xjk_38399.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjk_38399/01_2025/8xjk_38399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjk_38399/01_2025/8xjk_38399.cif" } resolution = 2.63 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: 5 Type Number sf(0) Gaussians S 62 5.16 5 Cl 1 4.86 5 C 5626 2.51 5 N 1513 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8850 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1821 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2171 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'A1D5A': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.57 Number of scatterers: 8850 At special positions: 0 Unit cell: (108.07, 118.77, 109.14, 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) Cl 1 17.00 S 62 16.00 O 1648 8.00 N 1513 7.00 C 5626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " 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: 2.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 40.6% alpha, 23.4% 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 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.605A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.166A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.109A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.551A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 245 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.508A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.374A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.547A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 59 removed outlier: 4.106A pdb=" N SER R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 97 through 102 Processing helix chain 'R' and resid 106 through 139 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 148 through 173 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 195 through 232 removed outlier: 3.999A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 276 Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.523A pdb=" N TRP R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 6.183A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 86 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU A 38 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 9.547A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.621A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.808A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.891A 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: 5.910A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.070A 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 151 removed outlier: 6.388A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.853A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.309A 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: 6.500A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.677A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.805A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.326A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.525A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 178 through 179 487 hydrogen bonds defined for protein. 1356 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: 2.67 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2876 1.34 - 1.46: 2181 1.46 - 1.58: 3877 1.58 - 1.70: 3 1.70 - 1.81: 91 Bond restraints: 9028 Sorted by residual: bond pdb=" C10 A1D5A R 601 " pdb=" C11 A1D5A R 601 " ideal model delta sigma weight residual 1.543 1.318 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C14 A1D5A R 601 " pdb=" C15 A1D5A R 601 " ideal model delta sigma weight residual 1.523 1.335 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C10 A1D5A R 601 " pdb=" C15 A1D5A R 601 " ideal model delta sigma weight residual 1.535 1.694 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" C21 A1D5A R 601 " pdb=" O20 A1D5A R 601 " ideal model delta sigma weight residual 1.342 1.422 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C11 A1D5A R 601 " pdb=" C13 A1D5A R 601 " ideal model delta sigma weight residual 1.538 1.617 -0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 9023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 12192 2.74 - 5.48: 34 5.48 - 8.22: 2 8.22 - 10.96: 1 10.96 - 13.70: 1 Bond angle restraints: 12230 Sorted by residual: angle pdb=" C06 A1D5A R 601 " pdb=" C07 A1D5A R 601 " pdb=" C08 A1D5A R 601 " ideal model delta sigma weight residual 127.33 113.63 13.70 3.00e+00 1.11e-01 2.08e+01 angle pdb=" C07 A1D5A R 601 " pdb=" C08 A1D5A R 601 " pdb=" C09 A1D5A R 601 " ideal model delta sigma weight residual 127.18 117.71 9.47 3.00e+00 1.11e-01 9.96e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.62 -4.08 1.91e+00 2.74e-01 4.55e+00 angle pdb=" O01 A1D5A R 601 " pdb=" C02 A1D5A R 601 " pdb=" O03 A1D5A R 601 " ideal model delta sigma weight residual 126.47 120.17 6.30 3.00e+00 1.11e-01 4.41e+00 angle pdb=" C14 A1D5A R 601 " pdb=" C15 A1D5A R 601 " pdb=" C16 A1D5A R 601 " ideal model delta sigma weight residual 116.30 110.03 6.27 3.00e+00 1.11e-01 4.36e+00 ... (remaining 12225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 5118 16.64 - 33.28: 193 33.28 - 49.92: 46 49.92 - 66.56: 9 66.56 - 83.20: 2 Dihedral angle restraints: 5368 sinusoidal: 2073 harmonic: 3295 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PHE E 31 " pdb=" C PHE E 31 " pdb=" N GLY E 32 " pdb=" CA GLY E 32 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1089 0.043 - 0.085: 227 0.085 - 0.128: 77 0.128 - 0.171: 3 0.171 - 0.213: 2 Chirality restraints: 1398 Sorted by residual: chirality pdb=" C11 A1D5A R 601 " pdb=" C10 A1D5A R 601 " pdb=" C13 A1D5A R 601 " pdb=" O12 A1D5A R 601 " both_signs ideal model delta sigma weight residual False 2.65 2.44 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C15 A1D5A R 601 " pdb=" C10 A1D5A R 601 " pdb=" C14 A1D5A R 601 " pdb=" C16 A1D5A R 601 " both_signs ideal model delta sigma weight residual False 2.59 2.78 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" C10 A1D5A R 601 " pdb=" C09 A1D5A R 601 " pdb=" C11 A1D5A R 601 " pdb=" C15 A1D5A R 601 " both_signs ideal model delta sigma weight residual False -2.56 -2.71 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1395 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO B 236 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO B 194 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " -0.016 5.00e-02 4.00e+02 2.48e-02 9.82e-01 pdb=" N PRO E 74 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.014 5.00e-02 4.00e+02 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1450 2.77 - 3.30: 8436 3.30 - 3.83: 14888 3.83 - 4.37: 18541 4.37 - 4.90: 31865 Nonbonded interactions: 75180 Sorted by model distance: nonbonded pdb=" O VAL R 303 " pdb=" NH2 ARG R 308 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.268 3.040 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.271 3.120 nonbonded pdb=" O SER E 29 " pdb=" OG SER E 52 " model vdw 2.289 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ALA A 218 " model vdw 2.294 3.120 ... (remaining 75175 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: 0.320 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 21.940 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 9028 Z= 0.259 Angle : 0.432 13.696 12230 Z= 0.212 Chirality : 0.039 0.213 1398 Planarity : 0.003 0.037 1549 Dihedral : 9.763 83.201 3231 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.84 % Allowed : 2.95 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1122 helix: 1.92 (0.24), residues: 414 sheet: 0.79 (0.30), residues: 286 loop : 0.45 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 133 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE R 58 TYR 0.014 0.001 TYR E 190 ARG 0.003 0.000 ARG R 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 1.038 Fit side-chains REVERT: A 10 LYS cc_start: 0.8696 (mttt) cc_final: 0.8486 (mtmm) REVERT: A 21 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8219 (ttmt) REVERT: A 26 ASP cc_start: 0.8426 (m-30) cc_final: 0.8184 (m-30) REVERT: A 116 ASN cc_start: 0.7940 (t0) cc_final: 0.7639 (p0) REVERT: A 163 TYR cc_start: 0.8214 (m-80) cc_final: 0.7943 (m-80) REVERT: A 170 TYR cc_start: 0.8527 (t80) cc_final: 0.8242 (t80) REVERT: A 222 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7748 (mm-30) REVERT: A 230 ASP cc_start: 0.8516 (m-30) cc_final: 0.8301 (m-30) REVERT: A 242 GLU cc_start: 0.8722 (tt0) cc_final: 0.8515 (tt0) REVERT: B 17 GLN cc_start: 0.8133 (tt0) cc_final: 0.7933 (tp-100) REVERT: B 45 MET cc_start: 0.9039 (mtt) cc_final: 0.8568 (mtt) REVERT: B 46 ARG cc_start: 0.7840 (mtp-110) cc_final: 0.7556 (mtp85) REVERT: B 130 GLU cc_start: 0.8568 (mp0) cc_final: 0.8307 (mp0) REVERT: B 188 MET cc_start: 0.9095 (mmm) cc_final: 0.8684 (mmm) REVERT: B 325 MET cc_start: 0.8931 (tpp) cc_final: 0.8636 (mmt) REVERT: C 38 MET cc_start: 0.8724 (ttp) cc_final: 0.8209 (ttp) REVERT: E 18 LYS cc_start: 0.8619 (tptm) cc_final: 0.8308 (tptm) REVERT: R 207 PHE cc_start: 0.8348 (t80) cc_final: 0.8100 (t80) REVERT: R 255 MET cc_start: 0.8631 (mtp) cc_final: 0.8246 (mtp) outliers start: 8 outliers final: 3 residues processed: 225 average time/residue: 1.4328 time to fit residues: 340.4361 Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100823 restraints weight = 10785.509| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.87 r_work: 0.3018 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9028 Z= 0.275 Angle : 0.531 5.745 12230 Z= 0.291 Chirality : 0.043 0.153 1398 Planarity : 0.004 0.044 1549 Dihedral : 5.247 56.999 1269 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.85 % Allowed : 10.55 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.25), residues: 1122 helix: 2.69 (0.24), residues: 416 sheet: 0.94 (0.30), residues: 287 loop : 0.54 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.012 0.001 PHE B 151 TYR 0.019 0.001 TYR E 190 ARG 0.007 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.053 Fit side-chains REVERT: A 163 TYR cc_start: 0.8235 (m-80) cc_final: 0.7931 (m-80) REVERT: A 170 TYR cc_start: 0.8597 (t80) cc_final: 0.8370 (t80) REVERT: A 222 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8005 (mm-30) REVERT: A 242 GLU cc_start: 0.8580 (tt0) cc_final: 0.8331 (tm-30) REVERT: B 17 GLN cc_start: 0.8223 (tt0) cc_final: 0.7967 (tp-100) REVERT: B 45 MET cc_start: 0.9021 (mtt) cc_final: 0.8668 (mtt) REVERT: B 46 ARG cc_start: 0.8339 (mtp-110) cc_final: 0.7735 (mmm160) REVERT: B 59 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8427 (t80) REVERT: B 153 ASP cc_start: 0.8929 (p0) cc_final: 0.8551 (p0) REVERT: B 176 GLN cc_start: 0.8686 (pt0) cc_final: 0.8430 (pt0) REVERT: B 303 ASP cc_start: 0.8145 (m-30) cc_final: 0.7796 (m-30) REVERT: C 38 MET cc_start: 0.8685 (ttp) cc_final: 0.8481 (ttp) REVERT: R 246 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: R 255 MET cc_start: 0.8318 (mtp) cc_final: 0.8111 (mtp) outliers start: 27 outliers final: 13 residues processed: 178 average time/residue: 1.5327 time to fit residues: 287.4471 Evaluate side-chains 166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101469 restraints weight = 10866.222| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.90 r_work: 0.3028 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9028 Z= 0.217 Angle : 0.484 5.433 12230 Z= 0.265 Chirality : 0.041 0.143 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.796 50.680 1267 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.95 % Allowed : 12.55 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1122 helix: 2.87 (0.24), residues: 415 sheet: 0.90 (0.30), residues: 269 loop : 0.46 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE R 207 TYR 0.017 0.001 TYR E 190 ARG 0.005 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.960 Fit side-chains REVERT: A 20 ASP cc_start: 0.8184 (m-30) cc_final: 0.7645 (m-30) REVERT: A 71 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7782 (mt-10) REVERT: A 163 TYR cc_start: 0.8258 (m-80) cc_final: 0.7957 (m-80) REVERT: A 222 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8024 (mm-30) REVERT: B 45 MET cc_start: 0.9054 (mtt) cc_final: 0.8702 (mtt) REVERT: B 46 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.7794 (mmm160) REVERT: B 59 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8427 (t80) REVERT: B 130 GLU cc_start: 0.8582 (mp0) cc_final: 0.8365 (mp0) REVERT: B 176 GLN cc_start: 0.8710 (pt0) cc_final: 0.8425 (pt0) REVERT: B 303 ASP cc_start: 0.8082 (m-30) cc_final: 0.7767 (m-30) REVERT: C 38 MET cc_start: 0.8558 (ttp) cc_final: 0.8334 (ttp) REVERT: R 139 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8111 (mtpt) outliers start: 28 outliers final: 15 residues processed: 164 average time/residue: 1.4037 time to fit residues: 243.3442 Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 139 LYS Chi-restraints excluded: chain R residue 149 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.102844 restraints weight = 10738.168| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.87 r_work: 0.3059 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9028 Z= 0.163 Angle : 0.461 4.778 12230 Z= 0.252 Chirality : 0.040 0.140 1398 Planarity : 0.003 0.040 1549 Dihedral : 4.358 32.271 1265 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.85 % Allowed : 14.03 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.25), residues: 1122 helix: 3.05 (0.25), residues: 416 sheet: 0.88 (0.30), residues: 272 loop : 0.42 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS E 34 PHE 0.013 0.001 PHE R 101 TYR 0.017 0.001 TYR E 190 ARG 0.008 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8119 (m-30) cc_final: 0.7670 (m-30) REVERT: A 71 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 132 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7645 (ptp90) REVERT: A 163 TYR cc_start: 0.8248 (m-80) cc_final: 0.8016 (m-80) REVERT: A 222 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7979 (mm-30) REVERT: B 33 ILE cc_start: 0.8343 (mp) cc_final: 0.8099 (mt) REVERT: B 45 MET cc_start: 0.9026 (mtt) cc_final: 0.8652 (mtt) REVERT: B 46 ARG cc_start: 0.8380 (mtp-110) cc_final: 0.7795 (mmm160) REVERT: B 59 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 130 GLU cc_start: 0.8574 (mp0) cc_final: 0.8355 (mp0) REVERT: B 176 GLN cc_start: 0.8669 (pt0) cc_final: 0.8390 (pt0) REVERT: B 303 ASP cc_start: 0.8063 (m-30) cc_final: 0.7760 (m-30) REVERT: E 112 GLN cc_start: 0.8430 (mm110) cc_final: 0.8152 (mm-40) REVERT: E 174 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8887 (tp) REVERT: R 246 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8137 (tt0) outliers start: 27 outliers final: 14 residues processed: 162 average time/residue: 1.4346 time to fit residues: 246.1480 Evaluate side-chains 160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 79 optimal weight: 0.0270 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104031 restraints weight = 10846.977| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.88 r_work: 0.3059 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9028 Z= 0.145 Angle : 0.454 8.862 12230 Z= 0.244 Chirality : 0.040 0.137 1398 Planarity : 0.003 0.040 1549 Dihedral : 4.130 28.636 1265 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.06 % Allowed : 13.92 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.26), residues: 1122 helix: 3.27 (0.25), residues: 412 sheet: 0.69 (0.29), residues: 284 loop : 0.53 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS E 34 PHE 0.014 0.001 PHE R 101 TYR 0.016 0.001 TYR E 190 ARG 0.007 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8163 (m-30) cc_final: 0.7816 (m-30) REVERT: A 132 ARG cc_start: 0.8077 (ttp-110) cc_final: 0.7644 (ptp90) REVERT: A 163 TYR cc_start: 0.8290 (m-80) cc_final: 0.8064 (m-80) REVERT: A 222 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7940 (mm-30) REVERT: B 17 GLN cc_start: 0.8314 (tt0) cc_final: 0.8010 (tp40) REVERT: B 45 MET cc_start: 0.9017 (mtt) cc_final: 0.8631 (mtt) REVERT: B 46 ARG cc_start: 0.8307 (mtp-110) cc_final: 0.7705 (mtp-110) REVERT: B 59 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8412 (t80) REVERT: B 130 GLU cc_start: 0.8571 (mp0) cc_final: 0.8355 (mp0) REVERT: B 176 GLN cc_start: 0.8638 (pt0) cc_final: 0.8362 (pt0) REVERT: B 303 ASP cc_start: 0.8120 (m-30) cc_final: 0.7819 (m-30) REVERT: E 112 GLN cc_start: 0.8446 (mm110) cc_final: 0.8141 (mm-40) outliers start: 29 outliers final: 16 residues processed: 164 average time/residue: 1.4587 time to fit residues: 252.9995 Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 149 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101416 restraints weight = 10735.984| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.87 r_work: 0.3036 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9028 Z= 0.227 Angle : 0.494 7.599 12230 Z= 0.264 Chirality : 0.041 0.141 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.319 28.291 1265 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.06 % Allowed : 14.35 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.26), residues: 1122 helix: 3.14 (0.25), residues: 412 sheet: 0.62 (0.29), residues: 286 loop : 0.54 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS E 34 PHE 0.014 0.001 PHE R 101 TYR 0.015 0.001 TYR E 190 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8263 (m-30) cc_final: 0.7889 (m-30) REVERT: A 132 ARG cc_start: 0.8131 (ttp-110) cc_final: 0.7687 (ptp90) REVERT: A 163 TYR cc_start: 0.8292 (m-80) cc_final: 0.7995 (m-80) REVERT: A 222 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7994 (mm-30) REVERT: B 45 MET cc_start: 0.9100 (mtt) cc_final: 0.8782 (mtt) REVERT: B 46 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.7712 (mmm160) REVERT: B 59 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.8411 (t80) REVERT: B 130 GLU cc_start: 0.8569 (mp0) cc_final: 0.8323 (mp0) REVERT: B 303 ASP cc_start: 0.8153 (m-30) cc_final: 0.7831 (m-30) REVERT: B 325 MET cc_start: 0.9013 (mmt) cc_final: 0.8721 (mmt) REVERT: E 112 GLN cc_start: 0.8435 (mm110) cc_final: 0.8109 (mm-40) REVERT: E 174 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8924 (tp) REVERT: R 260 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8674 (mt) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 1.4354 time to fit residues: 253.5269 Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 260 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.100736 restraints weight = 10836.948| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.89 r_work: 0.3025 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9028 Z= 0.243 Angle : 0.504 6.928 12230 Z= 0.270 Chirality : 0.042 0.139 1398 Planarity : 0.004 0.047 1549 Dihedral : 4.409 28.333 1265 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.38 % Allowed : 14.35 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.26), residues: 1122 helix: 3.06 (0.25), residues: 412 sheet: 0.55 (0.30), residues: 276 loop : 0.58 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS E 34 PHE 0.014 0.001 PHE R 101 TYR 0.016 0.001 TYR E 190 ARG 0.009 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8303 (m-30) cc_final: 0.7920 (m-30) REVERT: A 71 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 132 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7687 (ptp90) REVERT: A 163 TYR cc_start: 0.8303 (m-80) cc_final: 0.8005 (m-80) REVERT: A 222 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8030 (mm-30) REVERT: B 45 MET cc_start: 0.9069 (mtt) cc_final: 0.8743 (mtt) REVERT: B 46 ARG cc_start: 0.8424 (mtp-110) cc_final: 0.7800 (mmm160) REVERT: B 59 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8416 (t80) REVERT: B 79 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8871 (mp) REVERT: B 130 GLU cc_start: 0.8549 (mp0) cc_final: 0.8308 (mp0) REVERT: B 153 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8601 (p0) REVERT: B 303 ASP cc_start: 0.8165 (m-30) cc_final: 0.7837 (m-30) REVERT: B 325 MET cc_start: 0.8987 (mmt) cc_final: 0.8772 (mmt) REVERT: E 112 GLN cc_start: 0.8455 (mm110) cc_final: 0.8140 (mm-40) REVERT: E 174 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8927 (tp) REVERT: R 260 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8678 (mt) outliers start: 32 outliers final: 21 residues processed: 165 average time/residue: 1.3822 time to fit residues: 241.5671 Evaluate side-chains 167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 260 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 92 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104397 restraints weight = 10955.978| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.90 r_work: 0.3083 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9028 Z= 0.137 Angle : 0.451 6.619 12230 Z= 0.242 Chirality : 0.040 0.136 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.120 30.382 1265 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.74 % Allowed : 15.08 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.26), residues: 1122 helix: 3.40 (0.24), residues: 406 sheet: 0.61 (0.29), residues: 286 loop : 0.58 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS E 34 PHE 0.014 0.001 PHE R 101 TYR 0.016 0.001 TYR E 190 ARG 0.009 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8154 (m-30) cc_final: 0.7874 (m-30) REVERT: A 132 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7685 (ptp90) REVERT: A 163 TYR cc_start: 0.8345 (m-80) cc_final: 0.8079 (m-80) REVERT: A 222 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7992 (mm-30) REVERT: B 45 MET cc_start: 0.9066 (mtt) cc_final: 0.8700 (mtt) REVERT: B 46 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7703 (mtp-110) REVERT: B 59 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8384 (t80) REVERT: B 130 GLU cc_start: 0.8550 (mp0) cc_final: 0.8292 (mp0) REVERT: B 303 ASP cc_start: 0.8196 (m-30) cc_final: 0.7879 (m-30) REVERT: B 325 MET cc_start: 0.9002 (mmt) cc_final: 0.8675 (mmt) REVERT: E 112 GLN cc_start: 0.8420 (mm110) cc_final: 0.8106 (mm-40) REVERT: R 260 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8602 (mt) outliers start: 26 outliers final: 17 residues processed: 162 average time/residue: 1.4105 time to fit residues: 241.9106 Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 260 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.103176 restraints weight = 10895.322| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.89 r_work: 0.3063 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9028 Z= 0.168 Angle : 0.470 6.889 12230 Z= 0.251 Chirality : 0.040 0.137 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.172 30.107 1265 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.32 % Allowed : 15.82 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.26), residues: 1122 helix: 3.24 (0.25), residues: 412 sheet: 0.59 (0.29), residues: 286 loop : 0.56 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 34 PHE 0.014 0.001 PHE R 101 TYR 0.015 0.001 TYR E 190 ARG 0.008 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8175 (m-30) cc_final: 0.7873 (m-30) REVERT: A 132 ARG cc_start: 0.8120 (ttp-110) cc_final: 0.7680 (ptp90) REVERT: A 163 TYR cc_start: 0.8362 (m-80) cc_final: 0.8108 (m-80) REVERT: A 222 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7992 (mm-30) REVERT: B 45 MET cc_start: 0.9070 (mtt) cc_final: 0.8725 (mtt) REVERT: B 46 ARG cc_start: 0.8323 (mtp-110) cc_final: 0.7710 (mtp-110) REVERT: B 59 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8401 (t80) REVERT: B 130 GLU cc_start: 0.8551 (mp0) cc_final: 0.8305 (mp0) REVERT: B 303 ASP cc_start: 0.8202 (m-30) cc_final: 0.7899 (m-30) REVERT: E 112 GLN cc_start: 0.8422 (mm110) cc_final: 0.8108 (mm-40) REVERT: R 260 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8641 (mt) outliers start: 22 outliers final: 18 residues processed: 155 average time/residue: 1.4540 time to fit residues: 238.0651 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 260 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101159 restraints weight = 10191.343| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.83 r_work: 0.2924 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9028 Z= 0.155 Angle : 0.463 7.131 12230 Z= 0.247 Chirality : 0.040 0.136 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.140 30.350 1265 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.00 % Allowed : 16.46 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.26), residues: 1122 helix: 3.39 (0.24), residues: 406 sheet: 0.59 (0.29), residues: 286 loop : 0.58 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.002 0.001 HIS E 34 PHE 0.014 0.001 PHE R 101 TYR 0.016 0.001 TYR E 190 ARG 0.008 0.000 ARG A 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8209 (m-30) cc_final: 0.7870 (m-30) REVERT: A 132 ARG cc_start: 0.7978 (ttp-110) cc_final: 0.7522 (ptp90) REVERT: A 163 TYR cc_start: 0.8214 (m-80) cc_final: 0.7926 (m-80) REVERT: A 222 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7873 (mm-30) REVERT: B 45 MET cc_start: 0.9115 (mtt) cc_final: 0.8763 (mtt) REVERT: B 46 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.7581 (mtp-110) REVERT: B 59 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8429 (t80) REVERT: B 130 GLU cc_start: 0.8462 (mp0) cc_final: 0.8194 (mp0) REVERT: B 303 ASP cc_start: 0.8207 (m-30) cc_final: 0.7868 (m-30) REVERT: E 112 GLN cc_start: 0.8370 (mm110) cc_final: 0.8001 (mm-40) REVERT: R 260 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8534 (mt) outliers start: 19 outliers final: 17 residues processed: 154 average time/residue: 1.4758 time to fit residues: 240.1364 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 260 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.097353 restraints weight = 10191.183| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.77 r_work: 0.2866 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9028 Z= 0.336 Angle : 0.554 7.140 12230 Z= 0.295 Chirality : 0.044 0.156 1398 Planarity : 0.004 0.038 1549 Dihedral : 4.567 29.348 1265 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.43 % Allowed : 15.51 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.26), residues: 1122 helix: 2.94 (0.25), residues: 411 sheet: 0.58 (0.29), residues: 286 loop : 0.56 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.003 0.001 HIS E 167 PHE 0.014 0.002 PHE R 101 TYR 0.014 0.002 TYR E 190 ARG 0.007 0.001 ARG A 135 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7982.72 seconds wall clock time: 141 minutes 4.41 seconds (8464.41 seconds total)