Starting phenix.real_space_refine on Thu Mar 13 06:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjk_38399/03_2025/8xjk_38399.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjk_38399/03_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_38399/03_2025/8xjk_38399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjk_38399/03_2025/8xjk_38399.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjk_38399/03_2025/8xjk_38399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjk_38399/03_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-5624/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: 4.81, per 1000 atoms: 0.54 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: 2.00 Conformation dependent library (CDL) restraints added in 967.2 milliseconds 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: 0.96 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: 2.40 Time building geometry restraints manager: 2.37 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: 0.300 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.940 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:10.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.850 ------------------------------------------------------------------------------- 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 : 0.913 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: 1.4077 time to fit residues: 334.4652 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 : 0.929 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100824 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: 0.2902 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- 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 : 1.020 Fit side-chains REVERT: A 163 TYR cc_start: 0.8236 (m-80) cc_final: 0.7931 (m-80) REVERT: A 170 TYR cc_start: 0.8609 (t80) cc_final: 0.8382 (t80) REVERT: A 222 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8002 (mm-30) REVERT: A 242 GLU cc_start: 0.8580 (tt0) cc_final: 0.8332 (tm-30) REVERT: B 17 GLN cc_start: 0.8229 (tt0) cc_final: 0.7975 (tp-100) REVERT: B 45 MET cc_start: 0.9019 (mtt) cc_final: 0.8666 (mtt) REVERT: B 46 ARG cc_start: 0.8342 (mtp-110) cc_final: 0.7737 (mmm160) REVERT: B 59 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8428 (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: 0.8429 (pt0) REVERT: B 303 ASP cc_start: 0.8145 (m-30) cc_final: 0.7796 (m-30) REVERT: C 38 MET cc_start: 0.8684 (ttp) cc_final: 0.8480 (ttp) REVERT: R 246 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: R 255 MET cc_start: 0.8319 (mtp) cc_final: 0.8112 (mtp) outliers start: 27 outliers final: 13 residues processed: 178 average time/residue: 1.4405 time to fit residues: 270.4770 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 : 0.914 ------------------------------------------------------------------------------- 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: 0.9990 chunk 69 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.139257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.103019 restraints weight = 10862.444| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.90 r_work: 0.3057 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9028 Z= 0.170 Angle : 0.459 4.896 12230 Z= 0.253 Chirality : 0.040 0.140 1398 Planarity : 0.003 0.040 1549 Dihedral : 4.657 50.625 1267 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.64 % Allowed : 12.76 % Favored : 84.60 % 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: 2.29 (0.25), residues: 1122 helix: 2.97 (0.24), residues: 415 sheet: 0.96 (0.30), residues: 279 loop : 0.51 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE R 101 TYR 0.017 0.001 TYR E 190 ARG 0.005 0.000 ARG A 135 *********************** 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: 25 poor density : 153 time to evaluate : 0.975 Fit side-chains REVERT: A 20 ASP cc_start: 0.8144 (m-30) cc_final: 0.7639 (m-30) REVERT: A 132 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7624 (ptp90) REVERT: A 163 TYR cc_start: 0.8223 (m-80) cc_final: 0.7930 (m-80) REVERT: A 222 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8000 (mm-30) REVERT: B 45 MET cc_start: 0.9019 (mtt) cc_final: 0.8634 (mtt) REVERT: B 46 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.7723 (mmm160) REVERT: B 59 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8397 (t80) REVERT: B 130 GLU cc_start: 0.8575 (mp0) cc_final: 0.8353 (mp0) REVERT: B 176 GLN cc_start: 0.8678 (pt0) cc_final: 0.8391 (pt0) REVERT: B 303 ASP cc_start: 0.8113 (m-30) cc_final: 0.7795 (m-30) REVERT: C 38 MET cc_start: 0.8523 (ttp) cc_final: 0.8308 (ttp) outliers start: 25 outliers final: 13 residues processed: 166 average time/residue: 1.7429 time to fit residues: 306.4281 Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 107 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 13 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.138421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102086 restraints weight = 10741.075| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.87 r_work: 0.3045 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9028 Z= 0.196 Angle : 0.476 5.036 12230 Z= 0.259 Chirality : 0.041 0.142 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.379 29.742 1265 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.06 % Allowed : 13.82 % 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: 2.30 (0.25), residues: 1122 helix: 3.13 (0.25), residues: 412 sheet: 0.81 (0.30), residues: 269 loop : 0.50 (0.31), residues: 441 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 0.013 0.001 PHE R 101 TYR 0.016 0.001 TYR E 190 ARG 0.009 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 178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8130 (m-30) cc_final: 0.7680 (m-30) REVERT: A 132 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7649 (ptp90) REVERT: A 163 TYR cc_start: 0.8254 (m-80) cc_final: 0.8017 (m-80) REVERT: A 222 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7981 (mm-30) REVERT: B 33 ILE cc_start: 0.8353 (mp) cc_final: 0.8113 (mt) REVERT: B 45 MET cc_start: 0.9033 (mtt) cc_final: 0.8661 (mtt) REVERT: B 46 ARG cc_start: 0.8381 (mtp-110) cc_final: 0.7772 (mmm160) REVERT: B 59 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8425 (t80) REVERT: B 130 GLU cc_start: 0.8561 (mp0) cc_final: 0.8339 (mp0) REVERT: B 176 GLN cc_start: 0.8697 (pt0) cc_final: 0.8434 (pt0) REVERT: B 303 ASP cc_start: 0.8116 (m-30) cc_final: 0.7810 (m-30) REVERT: R 139 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8116 (mtpt) REVERT: R 246 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8138 (tt0) outliers start: 29 outliers final: 15 residues processed: 165 average time/residue: 1.4257 time to fit residues: 248.9090 Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain R residue 139 LYS 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: 7.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.140485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108155 restraints weight = 10829.066| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.78 r_work: 0.3088 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9028 Z= 0.135 Angle : 0.450 9.082 12230 Z= 0.241 Chirality : 0.040 0.137 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.099 29.364 1265 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.74 % Allowed : 14.14 % 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: 2.42 (0.26), residues: 1122 helix: 3.32 (0.25), residues: 412 sheet: 0.74 (0.30), residues: 279 loop : 0.56 (0.32), residues: 431 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 0.016 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 173 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8159 (m-30) cc_final: 0.7797 (m-30) REVERT: A 132 ARG cc_start: 0.8056 (ttp-110) cc_final: 0.7609 (ptp90) REVERT: A 163 TYR cc_start: 0.8224 (m-80) cc_final: 0.7999 (m-80) REVERT: A 222 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7892 (mm-30) REVERT: B 45 MET cc_start: 0.9029 (mtt) cc_final: 0.8638 (mtt) REVERT: B 46 ARG cc_start: 0.8292 (mtp-110) cc_final: 0.7666 (mtp-110) REVERT: B 59 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.8398 (t80) REVERT: B 130 GLU cc_start: 0.8550 (mp0) cc_final: 0.8325 (mp0) REVERT: B 176 GLN cc_start: 0.8593 (pt0) cc_final: 0.8326 (pt0) REVERT: B 303 ASP cc_start: 0.8116 (m-30) cc_final: 0.7810 (m-30) REVERT: B 325 MET cc_start: 0.8986 (mmt) cc_final: 0.8490 (mmt) REVERT: E 112 GLN cc_start: 0.8417 (mm110) cc_final: 0.8095 (mm-40) outliers start: 26 outliers final: 15 residues processed: 162 average time/residue: 1.3653 time to fit residues: 234.1660 Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 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 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 197 SER Chi-restraints excluded: chain R residue 28 LEU 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: 9.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.137688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.101098 restraints weight = 10747.542| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.88 r_work: 0.3030 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9028 Z= 0.244 Angle : 0.506 7.662 12230 Z= 0.269 Chirality : 0.042 0.138 1398 Planarity : 0.003 0.038 1549 Dihedral : 4.340 28.717 1265 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.95 % Allowed : 14.45 % 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: 2.26 (0.26), residues: 1122 helix: 3.13 (0.25), residues: 412 sheet: 0.63 (0.30), residues: 274 loop : 0.56 (0.32), residues: 436 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 0.015 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 175 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8275 (m-30) cc_final: 0.7896 (m-30) REVERT: A 132 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7668 (ptp90) REVERT: A 163 TYR cc_start: 0.8292 (m-80) cc_final: 0.8087 (m-80) REVERT: A 222 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7996 (mm-30) REVERT: B 45 MET cc_start: 0.9101 (mtt) cc_final: 0.8773 (mtt) REVERT: B 46 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.7702 (mmm160) REVERT: B 59 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8424 (t80) REVERT: B 130 GLU cc_start: 0.8572 (mp0) cc_final: 0.8327 (mp0) REVERT: B 303 ASP cc_start: 0.8139 (m-30) cc_final: 0.7834 (m-30) REVERT: B 325 MET cc_start: 0.8951 (mmt) cc_final: 0.8642 (mmt) REVERT: E 112 GLN cc_start: 0.8442 (mm110) cc_final: 0.8111 (mm-40) REVERT: R 260 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8663 (mt) outliers start: 28 outliers final: 18 residues processed: 166 average time/residue: 1.4556 time to fit residues: 256.0554 Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 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 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 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=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: 5.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 102 optimal weight: 0.0970 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.139690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103510 restraints weight = 10821.138| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.88 r_work: 0.3070 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9028 Z= 0.156 Angle : 0.461 7.087 12230 Z= 0.247 Chirality : 0.040 0.137 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.173 29.797 1265 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.43 % Allowed : 14.98 % 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: 2.39 (0.26), residues: 1122 helix: 3.37 (0.24), residues: 406 sheet: 0.60 (0.29), residues: 286 loop : 0.62 (0.32), residues: 430 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 0.005 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 168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8149 (m-30) cc_final: 0.7838 (m-30) REVERT: A 132 ARG cc_start: 0.8113 (ttp-110) cc_final: 0.7675 (ptp90) REVERT: A 163 TYR cc_start: 0.8316 (m-80) cc_final: 0.8057 (m-80) REVERT: A 222 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7975 (mm-30) REVERT: B 45 MET cc_start: 0.9055 (mtt) cc_final: 0.8701 (mtt) REVERT: B 46 ARG cc_start: 0.8296 (mtp-110) cc_final: 0.7696 (mtp-110) REVERT: B 59 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8398 (t80) REVERT: B 130 GLU cc_start: 0.8573 (mp0) cc_final: 0.8351 (mp0) REVERT: B 303 ASP cc_start: 0.8172 (m-30) cc_final: 0.7848 (m-30) REVERT: B 325 MET cc_start: 0.9012 (mmt) cc_final: 0.8532 (mmt) REVERT: E 112 GLN cc_start: 0.8439 (mm110) cc_final: 0.8122 (mm-40) REVERT: R 260 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8599 (mt) outliers start: 23 outliers final: 18 residues processed: 159 average time/residue: 1.3515 time to fit residues: 227.4062 Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 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 79 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 15 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 79 optimal weight: 0.1980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.141831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105928 restraints weight = 10964.990| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.90 r_work: 0.3109 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9028 Z= 0.125 Angle : 0.443 6.778 12230 Z= 0.237 Chirality : 0.039 0.137 1398 Planarity : 0.003 0.040 1549 Dihedral : 3.999 30.813 1265 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.32 % Allowed : 15.19 % Favored : 82.49 % 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: 2.43 (0.26), residues: 1122 helix: 3.38 (0.25), residues: 412 sheet: 0.65 (0.29), residues: 285 loop : 0.60 (0.33), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS E 34 PHE 0.015 0.001 PHE R 101 TYR 0.015 0.001 TYR E 190 ARG 0.008 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 173 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8072 (ttp-110) cc_final: 0.7656 (ptp90) REVERT: A 163 TYR cc_start: 0.8297 (m-80) cc_final: 0.8055 (m-80) REVERT: A 222 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7959 (mm-30) REVERT: B 45 MET cc_start: 0.9031 (mtt) cc_final: 0.8707 (mtt) REVERT: B 46 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7671 (mtp-110) REVERT: B 59 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8363 (t80) REVERT: B 130 GLU cc_start: 0.8568 (mp0) cc_final: 0.8345 (mp0) REVERT: B 303 ASP cc_start: 0.8176 (m-30) cc_final: 0.7844 (m-30) REVERT: E 112 GLN cc_start: 0.8416 (mm110) cc_final: 0.8095 (mm-40) REVERT: R 260 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8554 (mt) outliers start: 22 outliers final: 18 residues processed: 164 average time/residue: 1.3844 time to fit residues: 240.8750 Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 154 LEU 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 234 PHE Chi-restraints excluded: chain B residue 277 SER 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 197 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: 7.9990 chunk 21 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.133238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097636 restraints weight = 10200.590| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.84 r_work: 0.2868 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2740 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= 0.283 Angle : 0.528 6.829 12230 Z= 0.281 Chirality : 0.042 0.137 1398 Planarity : 0.004 0.038 1549 Dihedral : 4.423 29.034 1265 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.53 % Allowed : 15.30 % 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: 2.22 (0.26), residues: 1122 helix: 3.09 (0.25), residues: 412 sheet: 0.59 (0.29), residues: 284 loop : 0.57 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE R 101 TYR 0.014 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 168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.918 Fit side-chains REVERT: A 132 ARG cc_start: 0.7983 (ttp-110) cc_final: 0.7540 (ptp90) REVERT: A 163 TYR cc_start: 0.8179 (m-80) cc_final: 0.7857 (m-80) REVERT: A 222 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7855 (mm-30) REVERT: B 45 MET cc_start: 0.9111 (mtt) cc_final: 0.8780 (mtt) REVERT: B 46 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.7542 (mmm160) REVERT: B 59 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.8437 (t80) REVERT: B 79 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8840 (mp) REVERT: B 130 GLU cc_start: 0.8482 (mp0) cc_final: 0.8196 (mp0) REVERT: B 303 ASP cc_start: 0.8202 (m-30) cc_final: 0.7825 (m-30) REVERT: B 325 MET cc_start: 0.8946 (mmt) cc_final: 0.8564 (mmt) REVERT: E 112 GLN cc_start: 0.8364 (mm110) cc_final: 0.8040 (mm-40) REVERT: R 260 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8552 (mt) outliers start: 24 outliers final: 19 residues processed: 158 average time/residue: 1.3211 time to fit residues: 221.3058 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU 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 212 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 0.0870 chunk 101 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.137323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102442 restraints weight = 10200.616| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.83 r_work: 0.2953 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9028 Z= 0.133 Angle : 0.461 7.005 12230 Z= 0.247 Chirality : 0.040 0.134 1398 Planarity : 0.003 0.039 1549 Dihedral : 4.093 30.691 1265 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.00 % Allowed : 16.03 % Favored : 81.96 % 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: 2.38 (0.26), residues: 1122 helix: 3.41 (0.24), residues: 406 sheet: 0.55 (0.29), residues: 286 loop : 0.60 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 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 0.012 0.000 ARG B 19 ********************** 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 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.006 Fit side-chains REVERT: A 132 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7484 (ptp90) REVERT: A 163 TYR cc_start: 0.8204 (m-80) cc_final: 0.7918 (m-80) REVERT: A 222 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7829 (mm-30) REVERT: B 45 MET cc_start: 0.9084 (mtt) cc_final: 0.8670 (mtt) REVERT: B 46 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7506 (mtp-110) REVERT: B 59 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8386 (t80) REVERT: B 130 GLU cc_start: 0.8464 (mp0) cc_final: 0.8179 (mp0) REVERT: B 262 MET cc_start: 0.8270 (ttp) cc_final: 0.8035 (ttm) REVERT: B 303 ASP cc_start: 0.8191 (m-30) cc_final: 0.7796 (m-30) REVERT: B 325 MET cc_start: 0.8910 (mmt) cc_final: 0.8621 (mmt) REVERT: E 112 GLN cc_start: 0.8340 (mm110) cc_final: 0.8013 (mm-40) REVERT: R 260 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8516 (mt) outliers start: 19 outliers final: 15 residues processed: 157 average time/residue: 1.7192 time to fit residues: 286.4777 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU 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 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU 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 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: 1.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.135333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.100024 restraints weight = 10146.212| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.85 r_work: 0.2900 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9028 Z= 0.199 Angle : 0.500 7.229 12230 Z= 0.266 Chirality : 0.041 0.138 1398 Planarity : 0.004 0.047 1549 Dihedral : 4.219 30.007 1265 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.22 % Allowed : 15.82 % Favored : 81.96 % 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: 2.28 (0.26), residues: 1122 helix: 3.17 (0.24), residues: 412 sheet: 0.63 (0.29), residues: 284 loop : 0.56 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS E 34 PHE 0.014 0.001 PHE R 101 TYR 0.015 0.001 TYR E 190 ARG 0.013 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 8085.00 seconds wall clock time: 141 minutes 16.85 seconds (8476.85 seconds total)