Starting phenix.real_space_refine on Wed Apr 30 22:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zh8_60096/04_2025/8zh8_60096.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zh8_60096/04_2025/8zh8_60096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zh8_60096/04_2025/8zh8_60096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zh8_60096/04_2025/8zh8_60096.map" model { file = "/net/cci-nas-00/data/ceres_data/8zh8_60096/04_2025/8zh8_60096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zh8_60096/04_2025/8zh8_60096.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 1.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6422 2.51 5 N 1720 2.21 5 O 1838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10048 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2635 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2473 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1704 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 62 Chain: "S" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Q" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 187 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.60, per 1000 atoms: 0.56 Number of scatterers: 10048 At special positions: 0 Unit cell: (87.849, 132.795, 148.117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1838 8.00 N 1720 7.00 C 6422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 201 " distance=2.03 Simple disulfide: pdb=" SG CYS R 285 " - pdb=" SG CYS R 327 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 15 sheets defined 37.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'R' and resid 7 through 18 removed outlier: 4.108A pdb=" N ARG R 16 " --> pdb=" O SER R 12 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP R 17 " --> pdb=" O ARG R 13 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 30 Processing helix chain 'R' and resid 41 through 73 removed outlier: 3.506A pdb=" N THR R 71 " --> pdb=" O PHE R 67 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 removed outlier: 3.649A pdb=" N ARG R 77 " --> pdb=" O LYS R 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 74 through 77' Processing helix chain 'R' and resid 78 through 98 Processing helix chain 'R' and resid 98 through 107 Processing helix chain 'R' and resid 113 through 149 removed outlier: 4.019A pdb=" N ILE R 117 " --> pdb=" O GLY R 113 " (cutoff:3.500A) Proline residue: R 122 - end of helix removed outlier: 3.644A pdb=" N THR R 137 " --> pdb=" O ILE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.676A pdb=" N LYS R 154 " --> pdb=" O PHE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 177 removed outlier: 3.599A pdb=" N ALA R 162 " --> pdb=" O THR R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 183 removed outlier: 4.175A pdb=" N HIS R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 195 Processing helix chain 'R' and resid 207 through 223 removed outlier: 3.805A pdb=" N GLN R 211 " --> pdb=" O SER R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 243 Processing helix chain 'R' and resid 264 through 299 removed outlier: 3.814A pdb=" N ALA R 283 " --> pdb=" O VAL R 279 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.579A pdb=" N SER R 299 " --> pdb=" O MET R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 306 through 323 Processing helix chain 'R' and resid 323 through 335 Proline residue: R 329 - end of helix Processing helix chain 'R' and resid 336 through 346 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.559A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.987A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.781A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.584A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.649A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.318A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.890A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.643A pdb=" N TYR A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.591A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.082A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 14 removed outlier: 4.269A pdb=" N GLY Q 14 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 191 Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.926A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.181A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.904A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.085A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.923A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.931A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.036A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.660A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 72 through 76 removed outlier: 3.976A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.724A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.565A pdb=" N THR S 129 " --> pdb=" O ARG S 148 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG S 148 " --> pdb=" O THR S 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.837A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1452 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: 2.98 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2254 1.33 - 1.46: 2824 1.46 - 1.58: 5086 1.58 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 10265 Sorted by residual: bond pdb=" CA PRO R 329 " pdb=" CB PRO R 329 " ideal model delta sigma weight residual 1.534 1.477 0.056 1.52e-02 4.33e+03 1.37e+01 bond pdb=" CA ARG Q 25 " pdb=" C ARG Q 25 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.36e+00 bond pdb=" C GLN R 125 " pdb=" O GLN R 125 " ideal model delta sigma weight residual 1.236 1.204 0.033 1.15e-02 7.56e+03 8.21e+00 bond pdb=" C GLN R 125 " pdb=" N SER R 126 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 7.86e+00 bond pdb=" C VAL R 121 " pdb=" N PRO R 122 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.89e+00 ... (remaining 10260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 13498 1.69 - 3.39: 383 3.39 - 5.08: 46 5.08 - 6.77: 12 6.77 - 8.47: 3 Bond angle restraints: 13942 Sorted by residual: angle pdb=" C ASN R 328 " pdb=" N PRO R 329 " pdb=" CA PRO R 329 " ideal model delta sigma weight residual 119.32 114.52 4.80 1.14e+00 7.69e-01 1.77e+01 angle pdb=" C PRO R 329 " pdb=" CA PRO R 329 " pdb=" CB PRO R 329 " ideal model delta sigma weight residual 112.64 106.17 6.47 1.74e+00 3.30e-01 1.38e+01 angle pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta sigma weight residual 120.39 125.45 -5.06 1.39e+00 5.18e-01 1.33e+01 angle pdb=" N SER S 194 " pdb=" CA SER S 194 " pdb=" C SER S 194 " ideal model delta sigma weight residual 108.38 112.67 -4.29 1.35e+00 5.49e-01 1.01e+01 angle pdb=" CA TRP A 96 " pdb=" CB TRP A 96 " pdb=" CG TRP A 96 " ideal model delta sigma weight residual 113.60 119.50 -5.90 1.90e+00 2.77e-01 9.65e+00 ... (remaining 13937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 5496 16.17 - 32.33: 452 32.33 - 48.50: 82 48.50 - 64.66: 13 64.66 - 80.83: 14 Dihedral angle restraints: 6057 sinusoidal: 2247 harmonic: 3810 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -22.52 -63.48 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CA ARG A 94 " pdb=" C ARG A 94 " pdb=" N LYS A 95 " pdb=" CA LYS A 95 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1139 0.041 - 0.082: 345 0.082 - 0.123: 95 0.123 - 0.163: 14 0.163 - 0.204: 3 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA ILE R 199 " pdb=" N ILE R 199 " pdb=" C ILE R 199 " pdb=" CB ILE R 199 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN R 328 " pdb=" N ASN R 328 " pdb=" C ASN R 328 " pdb=" CB ASN R 328 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CA ILE R 188 " pdb=" N ILE R 188 " pdb=" C ILE R 188 " pdb=" CB ILE R 188 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 1593 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 155 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C ASN B 155 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 155 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN B 156 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 328 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C ASN R 328 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN R 328 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO R 329 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 225 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO R 226 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 226 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 226 " 0.026 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 887 2.75 - 3.28: 9883 3.28 - 3.82: 17145 3.82 - 4.36: 19973 4.36 - 4.90: 34978 Nonbonded interactions: 82866 Sorted by model distance: nonbonded pdb=" OE2 GLU R 142 " pdb=" OH TYR R 157 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR N 117 " pdb=" O CYS B 204 " model vdw 2.218 3.040 nonbonded pdb=" O ASN B 155 " pdb=" ND2 ASN B 155 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.237 3.040 nonbonded pdb=" O SER N 63 " pdb=" NH2 ARG N 67 " model vdw 2.239 3.120 ... (remaining 82861 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: 1.400 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 10272 Z= 0.192 Angle : 0.670 8.466 13954 Z= 0.388 Chirality : 0.043 0.204 1596 Planarity : 0.004 0.046 1766 Dihedral : 12.775 80.825 3583 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.57 (0.24), residues: 1294 helix: 1.54 (0.26), residues: 426 sheet: 0.16 (0.29), residues: 330 loop : -0.33 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 47 HIS 0.006 0.001 HIS B 54 PHE 0.017 0.002 PHE R 314 TYR 0.017 0.001 TYR S 60 ARG 0.005 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.13456 ( 518) hydrogen bonds : angle 6.00369 ( 1452) SS BOND : bond 0.00603 ( 6) SS BOND : angle 0.99758 ( 12) covalent geometry : bond 0.00290 (10265) covalent geometry : angle 0.66953 (13942) Misc. bond : bond 0.10866 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 61 THR cc_start: 0.7475 (t) cc_final: 0.7110 (m) REVERT: A 10 LYS cc_start: 0.7900 (mttp) cc_final: 0.7523 (mttm) REVERT: A 199 ASP cc_start: 0.7787 (p0) cc_final: 0.7091 (p0) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.2643 time to fit residues: 125.4680 Evaluate side-chains 213 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.0060 chunk 117 optimal weight: 0.0770 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 5 ASN R 63 ASN R 81 ASN R 342 ASN B 259 GLN A 130 ASN A 131 ASN A 239 ASN S 82 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.126355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.103797 restraints weight = 25756.691| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 4.29 r_work: 0.3673 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10272 Z= 0.142 Angle : 0.666 6.959 13954 Z= 0.349 Chirality : 0.044 0.157 1596 Planarity : 0.005 0.051 1766 Dihedral : 4.454 24.540 1417 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.91 % Allowed : 14.07 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.46 (0.24), residues: 1294 helix: 1.53 (0.26), residues: 427 sheet: 0.06 (0.30), residues: 307 loop : -0.44 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 111 HIS 0.005 0.001 HIS A 209 PHE 0.020 0.002 PHE R 339 TYR 0.021 0.002 TYR S 95 ARG 0.009 0.001 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 518) hydrogen bonds : angle 5.17883 ( 1452) SS BOND : bond 0.00873 ( 6) SS BOND : angle 1.41879 ( 12) covalent geometry : bond 0.00306 (10265) covalent geometry : angle 0.66534 (13942) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.8824 (m-80) cc_final: 0.8422 (m-80) REVERT: R 34 LEU cc_start: 0.8648 (tp) cc_final: 0.8305 (mm) REVERT: R 74 LYS cc_start: 0.8864 (mptt) cc_final: 0.8636 (mmtm) REVERT: R 111 TRP cc_start: 0.7375 (t-100) cc_final: 0.7141 (t60) REVERT: R 323 SER cc_start: 0.8738 (t) cc_final: 0.8428 (t) REVERT: R 335 MET cc_start: 0.7690 (tpp) cc_final: 0.6527 (tpp) REVERT: N 32 TYR cc_start: 0.7942 (m-80) cc_final: 0.7176 (m-80) REVERT: N 53 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5924 (mp10) REVERT: N 61 THR cc_start: 0.8490 (t) cc_final: 0.7787 (m) REVERT: B 82 TRP cc_start: 0.8975 (m100) cc_final: 0.8634 (m-10) REVERT: B 262 MET cc_start: 0.7797 (tpp) cc_final: 0.7401 (tpp) REVERT: A 14 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7823 (mp0) REVERT: A 21 LYS cc_start: 0.6971 (tttm) cc_final: 0.6651 (ttpp) REVERT: A 25 GLU cc_start: 0.7383 (mp0) cc_final: 0.6924 (mp0) REVERT: A 28 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 131 ASN cc_start: 0.8139 (t0) cc_final: 0.7935 (t0) REVERT: A 199 ASP cc_start: 0.9291 (p0) cc_final: 0.8810 (p0) REVERT: A 230 ASP cc_start: 0.8523 (m-30) cc_final: 0.8320 (m-30) REVERT: S 218 MET cc_start: 0.5625 (ttp) cc_final: 0.5353 (ttp) outliers start: 20 outliers final: 8 residues processed: 259 average time/residue: 0.2497 time to fit residues: 88.8254 Evaluate side-chains 223 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 313 ILE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 GLN S 39 GLN S 182 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.120892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.098860 restraints weight = 26087.413| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 4.17 r_work: 0.3578 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10272 Z= 0.158 Angle : 0.644 7.304 13954 Z= 0.336 Chirality : 0.044 0.219 1596 Planarity : 0.004 0.038 1766 Dihedral : 4.301 22.061 1417 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 16.08 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.49 (0.24), residues: 1294 helix: 1.64 (0.26), residues: 423 sheet: 0.01 (0.29), residues: 317 loop : -0.44 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.005 0.001 HIS A 209 PHE 0.027 0.002 PHE A 192 TYR 0.019 0.002 TYR R 194 ARG 0.007 0.001 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 518) hydrogen bonds : angle 4.98597 ( 1452) SS BOND : bond 0.00487 ( 6) SS BOND : angle 2.27642 ( 12) covalent geometry : bond 0.00359 (10265) covalent geometry : angle 0.64071 (13942) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.8902 (m-80) cc_final: 0.8464 (m-80) REVERT: R 15 LEU cc_start: 0.9518 (mm) cc_final: 0.9192 (mm) REVERT: R 312 MET cc_start: 0.8691 (tpp) cc_final: 0.8459 (tpt) REVERT: N 27 PHE cc_start: 0.6105 (p90) cc_final: 0.5843 (p90) REVERT: N 53 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6179 (mp10) REVERT: N 61 THR cc_start: 0.8636 (t) cc_final: 0.7887 (m) REVERT: N 68 PHE cc_start: 0.7579 (m-80) cc_final: 0.7125 (m-10) REVERT: N 73 ASP cc_start: 0.7896 (t0) cc_final: 0.7455 (p0) REVERT: N 76 LYS cc_start: 0.9234 (ttmm) cc_final: 0.8957 (tttp) REVERT: B 57 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8118 (mtmm) REVERT: B 78 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7592 (ptpp) REVERT: B 262 MET cc_start: 0.7616 (tpp) cc_final: 0.7186 (tpp) REVERT: A 10 LYS cc_start: 0.8284 (mttp) cc_final: 0.7702 (mttm) REVERT: A 14 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7795 (mp0) REVERT: A 21 LYS cc_start: 0.7150 (tttm) cc_final: 0.6711 (ttpp) REVERT: A 25 GLU cc_start: 0.7543 (mp0) cc_final: 0.7169 (mp0) REVERT: A 98 GLN cc_start: 0.8400 (pm20) cc_final: 0.8144 (pm20) REVERT: A 131 ASN cc_start: 0.8186 (t0) cc_final: 0.7914 (t0) REVERT: A 192 PHE cc_start: 0.8411 (t80) cc_final: 0.7929 (t80) REVERT: A 199 ASP cc_start: 0.9328 (p0) cc_final: 0.8836 (p0) REVERT: A 230 ASP cc_start: 0.8604 (m-30) cc_final: 0.8373 (m-30) REVERT: S 218 MET cc_start: 0.5623 (ttp) cc_final: 0.5375 (ttp) outliers start: 26 outliers final: 12 residues processed: 241 average time/residue: 0.2373 time to fit residues: 78.1809 Evaluate side-chains 224 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 236 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 47 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.118957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.096050 restraints weight = 26257.667| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 4.24 r_work: 0.3526 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10272 Z= 0.159 Angle : 0.624 6.495 13954 Z= 0.328 Chirality : 0.044 0.190 1596 Planarity : 0.004 0.048 1766 Dihedral : 4.206 22.563 1417 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.78 % Allowed : 18.47 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.54 (0.24), residues: 1294 helix: 1.67 (0.26), residues: 423 sheet: 0.09 (0.29), residues: 319 loop : -0.45 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.021 0.002 PHE R 314 TYR 0.015 0.001 TYR N 95 ARG 0.005 0.001 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 518) hydrogen bonds : angle 4.92302 ( 1452) SS BOND : bond 0.01070 ( 6) SS BOND : angle 2.09488 ( 12) covalent geometry : bond 0.00365 (10265) covalent geometry : angle 0.62158 (13942) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.8993 (m-80) cc_final: 0.8551 (m-80) REVERT: R 15 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9327 (mm) REVERT: R 34 LEU cc_start: 0.8822 (tp) cc_final: 0.8600 (mm) REVERT: R 120 MET cc_start: 0.8512 (tmm) cc_final: 0.8180 (tmm) REVERT: R 228 MET cc_start: 0.8027 (ppp) cc_final: 0.7794 (tmm) REVERT: R 312 MET cc_start: 0.8753 (tpp) cc_final: 0.8502 (tpt) REVERT: N 27 PHE cc_start: 0.6411 (p90) cc_final: 0.5750 (p90) REVERT: N 32 TYR cc_start: 0.8054 (m-80) cc_final: 0.6870 (m-80) REVERT: N 53 GLN cc_start: 0.7045 (mp10) cc_final: 0.6670 (mp10) REVERT: N 61 THR cc_start: 0.8652 (t) cc_final: 0.7905 (m) REVERT: N 73 ASP cc_start: 0.7968 (t0) cc_final: 0.7513 (p0) REVERT: N 76 LYS cc_start: 0.9317 (ttmm) cc_final: 0.8952 (tttp) REVERT: N 80 TYR cc_start: 0.7997 (m-80) cc_final: 0.7352 (m-10) REVERT: B 57 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8215 (mtmm) REVERT: B 61 MET cc_start: 0.8920 (ppp) cc_final: 0.8672 (ppp) REVERT: B 78 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7832 (ptpp) REVERT: B 262 MET cc_start: 0.7788 (tpp) cc_final: 0.7074 (tpp) REVERT: A 14 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7816 (mp0) REVERT: A 21 LYS cc_start: 0.7396 (tttm) cc_final: 0.6909 (ttpp) REVERT: A 25 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: A 98 GLN cc_start: 0.8448 (pm20) cc_final: 0.8169 (pm20) REVERT: A 120 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8194 (mt-10) REVERT: A 131 ASN cc_start: 0.8269 (t0) cc_final: 0.7921 (t0) REVERT: A 192 PHE cc_start: 0.8482 (t80) cc_final: 0.8219 (t80) REVERT: A 199 ASP cc_start: 0.9403 (p0) cc_final: 0.8876 (p0) REVERT: A 230 ASP cc_start: 0.8778 (m-30) cc_final: 0.8559 (m-30) REVERT: Q 13 ASN cc_start: 0.8102 (t0) cc_final: 0.7072 (p0) outliers start: 29 outliers final: 14 residues processed: 233 average time/residue: 0.2688 time to fit residues: 85.1368 Evaluate side-chains 216 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 15 LEU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.116930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.093951 restraints weight = 26617.222| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.23 r_work: 0.3487 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10272 Z= 0.180 Angle : 0.649 7.726 13954 Z= 0.339 Chirality : 0.044 0.183 1596 Planarity : 0.004 0.051 1766 Dihedral : 4.260 23.592 1417 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.35 % Allowed : 19.14 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.56 (0.24), residues: 1294 helix: 1.74 (0.26), residues: 423 sheet: 0.02 (0.28), residues: 340 loop : -0.43 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.030 0.002 PHE A 192 TYR 0.021 0.001 TYR N 115 ARG 0.004 0.001 ARG R 32 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 518) hydrogen bonds : angle 4.91120 ( 1452) SS BOND : bond 0.01757 ( 6) SS BOND : angle 3.08605 ( 12) covalent geometry : bond 0.00417 (10265) covalent geometry : angle 0.64317 (13942) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.8946 (m-80) cc_final: 0.8553 (m-80) REVERT: R 120 MET cc_start: 0.8530 (tmm) cc_final: 0.8163 (tmm) REVERT: R 157 TYR cc_start: 0.7867 (t80) cc_final: 0.7561 (t80) REVERT: R 312 MET cc_start: 0.8888 (tpp) cc_final: 0.8653 (tpt) REVERT: N 32 TYR cc_start: 0.8127 (m-80) cc_final: 0.6795 (m-80) REVERT: N 53 GLN cc_start: 0.7108 (mp10) cc_final: 0.6727 (mp10) REVERT: N 61 THR cc_start: 0.8657 (t) cc_final: 0.7949 (m) REVERT: N 73 ASP cc_start: 0.8105 (t0) cc_final: 0.7644 (p0) REVERT: N 76 LYS cc_start: 0.9322 (ttmm) cc_final: 0.8990 (tttp) REVERT: N 115 TYR cc_start: 0.8024 (t80) cc_final: 0.7737 (t80) REVERT: B 57 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8353 (mtmm) REVERT: B 61 MET cc_start: 0.8981 (ppp) cc_final: 0.8724 (ppp) REVERT: B 220 GLN cc_start: 0.8611 (mp10) cc_final: 0.8148 (mp10) REVERT: B 262 MET cc_start: 0.7738 (tpp) cc_final: 0.6952 (tpp) REVERT: A 10 LYS cc_start: 0.8454 (mttp) cc_final: 0.7815 (mttm) REVERT: A 14 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7781 (mp0) REVERT: A 21 LYS cc_start: 0.7431 (tttm) cc_final: 0.6861 (ttpp) REVERT: A 25 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 75 GLN cc_start: 0.7349 (pp30) cc_final: 0.7120 (pp30) REVERT: A 83 MET cc_start: 0.8626 (ttm) cc_final: 0.8278 (ttm) REVERT: A 98 GLN cc_start: 0.8460 (pm20) cc_final: 0.8161 (pm20) REVERT: A 117 ARG cc_start: 0.9132 (mtp180) cc_final: 0.8764 (mmm-85) REVERT: A 120 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8271 (mm-30) REVERT: A 131 ASN cc_start: 0.8344 (t0) cc_final: 0.8020 (t0) REVERT: A 195 LYS cc_start: 0.9402 (tptp) cc_final: 0.8984 (tptp) REVERT: A 199 ASP cc_start: 0.9394 (p0) cc_final: 0.8923 (p0) REVERT: A 230 ASP cc_start: 0.8804 (m-30) cc_final: 0.8585 (m-30) REVERT: S 151 LYS cc_start: 0.8290 (pttt) cc_final: 0.8036 (pttm) outliers start: 35 outliers final: 24 residues processed: 238 average time/residue: 0.2514 time to fit residues: 82.4275 Evaluate side-chains 231 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 0.1980 chunk 117 optimal weight: 0.0070 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 0.0040 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 198 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.120260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.098233 restraints weight = 26419.107| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 4.14 r_work: 0.3554 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10272 Z= 0.124 Angle : 0.638 10.741 13954 Z= 0.328 Chirality : 0.043 0.195 1596 Planarity : 0.004 0.052 1766 Dihedral : 4.118 23.992 1417 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.58 % Allowed : 21.15 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.70 (0.24), residues: 1294 helix: 1.97 (0.26), residues: 414 sheet: -0.01 (0.29), residues: 330 loop : -0.32 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 181 HIS 0.005 0.001 HIS R 18 PHE 0.028 0.001 PHE R 339 TYR 0.018 0.001 TYR N 115 ARG 0.007 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 518) hydrogen bonds : angle 4.77121 ( 1452) SS BOND : bond 0.00875 ( 6) SS BOND : angle 2.17387 ( 12) covalent geometry : bond 0.00275 (10265) covalent geometry : angle 0.63510 (13942) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.8993 (m-80) cc_final: 0.8635 (m-80) REVERT: R 120 MET cc_start: 0.8547 (tmm) cc_final: 0.8326 (tmm) REVERT: R 149 HIS cc_start: 0.8352 (m90) cc_final: 0.8113 (m-70) REVERT: R 267 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8155 (mmmt) REVERT: R 291 VAL cc_start: 0.9185 (t) cc_final: 0.8980 (p) REVERT: R 334 PHE cc_start: 0.5055 (OUTLIER) cc_final: 0.4578 (t80) REVERT: N 53 GLN cc_start: 0.7043 (mp10) cc_final: 0.6694 (mp10) REVERT: N 61 THR cc_start: 0.8474 (t) cc_final: 0.7733 (m) REVERT: N 73 ASP cc_start: 0.8136 (t0) cc_final: 0.7673 (p0) REVERT: N 76 LYS cc_start: 0.9275 (ttmm) cc_final: 0.8945 (tttp) REVERT: B 57 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8380 (mtmm) REVERT: B 61 MET cc_start: 0.8891 (ppp) cc_final: 0.8608 (ppp) REVERT: B 145 TYR cc_start: 0.8969 (p90) cc_final: 0.8658 (p90) REVERT: B 146 LEU cc_start: 0.8721 (tp) cc_final: 0.8485 (tt) REVERT: B 220 GLN cc_start: 0.8567 (mp10) cc_final: 0.8188 (mp10) REVERT: B 262 MET cc_start: 0.7701 (tpp) cc_final: 0.7030 (tpp) REVERT: B 336 LEU cc_start: 0.8517 (tp) cc_final: 0.8008 (tp) REVERT: A 10 LYS cc_start: 0.8339 (mttp) cc_final: 0.7676 (mttm) REVERT: A 14 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7943 (mp0) REVERT: A 21 LYS cc_start: 0.7421 (tttm) cc_final: 0.6796 (ttpp) REVERT: A 25 GLU cc_start: 0.7722 (mp0) cc_final: 0.7254 (mp0) REVERT: A 75 GLN cc_start: 0.7400 (pp30) cc_final: 0.7179 (pp30) REVERT: A 83 MET cc_start: 0.8556 (ttm) cc_final: 0.8243 (ttm) REVERT: A 98 GLN cc_start: 0.8468 (pm20) cc_final: 0.8162 (pm20) REVERT: A 120 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8265 (mm-30) REVERT: A 131 ASN cc_start: 0.8337 (t0) cc_final: 0.7998 (t0) REVERT: A 195 LYS cc_start: 0.9400 (tptp) cc_final: 0.8969 (tptp) REVERT: A 199 ASP cc_start: 0.9372 (p0) cc_final: 0.8865 (p0) REVERT: A 230 ASP cc_start: 0.8857 (m-30) cc_final: 0.8594 (m-30) REVERT: S 67 ARG cc_start: 0.8194 (ptt-90) cc_final: 0.6519 (ptt-90) REVERT: Q 13 ASN cc_start: 0.7811 (m-40) cc_final: 0.7027 (p0) outliers start: 27 outliers final: 17 residues processed: 239 average time/residue: 0.2489 time to fit residues: 80.5639 Evaluate side-chains 222 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 334 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 125 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 82 optimal weight: 0.0270 chunk 127 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.116775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.095074 restraints weight = 26830.138| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 4.05 r_work: 0.3501 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10272 Z= 0.166 Angle : 0.677 12.837 13954 Z= 0.346 Chirality : 0.043 0.187 1596 Planarity : 0.004 0.057 1766 Dihedral : 4.204 23.011 1417 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.54 % Allowed : 21.34 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.69 (0.24), residues: 1294 helix: 1.98 (0.26), residues: 415 sheet: -0.06 (0.27), residues: 358 loop : -0.33 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.023 0.002 PHE R 339 TYR 0.029 0.002 TYR N 115 ARG 0.005 0.001 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 518) hydrogen bonds : angle 4.80607 ( 1452) SS BOND : bond 0.01004 ( 6) SS BOND : angle 2.31804 ( 12) covalent geometry : bond 0.00387 (10265) covalent geometry : angle 0.67342 (13942) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.9059 (m-80) cc_final: 0.8653 (m-80) REVERT: R 15 LEU cc_start: 0.9525 (mp) cc_final: 0.9218 (tp) REVERT: R 16 ARG cc_start: 0.9016 (mmm160) cc_final: 0.8805 (mmm160) REVERT: R 157 TYR cc_start: 0.8036 (t80) cc_final: 0.7775 (t80) REVERT: R 267 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8236 (mmmt) REVERT: R 334 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.5090 (t80) REVERT: N 53 GLN cc_start: 0.7287 (mp10) cc_final: 0.6898 (mp10) REVERT: N 73 ASP cc_start: 0.8215 (t0) cc_final: 0.7675 (p0) REVERT: N 76 LYS cc_start: 0.9282 (ttmm) cc_final: 0.9036 (ttmm) REVERT: N 80 TYR cc_start: 0.8054 (m-80) cc_final: 0.7640 (m-10) REVERT: B 57 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8569 (mtmm) REVERT: B 61 MET cc_start: 0.8898 (ppp) cc_final: 0.8628 (ppp) REVERT: B 146 LEU cc_start: 0.8714 (tp) cc_final: 0.8506 (tt) REVERT: B 220 GLN cc_start: 0.8608 (mp10) cc_final: 0.8262 (mp10) REVERT: B 262 MET cc_start: 0.7742 (tpp) cc_final: 0.6974 (tpp) REVERT: A 14 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7886 (mp0) REVERT: A 21 LYS cc_start: 0.7477 (tttm) cc_final: 0.6839 (ttpp) REVERT: A 25 GLU cc_start: 0.7846 (mp0) cc_final: 0.7464 (mp0) REVERT: A 75 GLN cc_start: 0.7603 (pp30) cc_final: 0.7317 (pp30) REVERT: A 83 MET cc_start: 0.8551 (ttm) cc_final: 0.8151 (ttm) REVERT: A 120 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8394 (mm-30) REVERT: A 131 ASN cc_start: 0.8406 (t0) cc_final: 0.8042 (t0) REVERT: A 195 LYS cc_start: 0.9412 (tptp) cc_final: 0.8888 (tptp) REVERT: A 199 ASP cc_start: 0.9397 (p0) cc_final: 0.8819 (p0) REVERT: S 87 ARG cc_start: 0.7684 (mpp80) cc_final: 0.7418 (mtm-85) REVERT: S 88 SER cc_start: 0.8855 (t) cc_final: 0.8583 (p) outliers start: 37 outliers final: 23 residues processed: 236 average time/residue: 0.2545 time to fit residues: 80.9169 Evaluate side-chains 219 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 334 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.118546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096837 restraints weight = 26740.700| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 4.10 r_work: 0.3530 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10272 Z= 0.133 Angle : 0.680 13.878 13954 Z= 0.344 Chirality : 0.043 0.185 1596 Planarity : 0.004 0.052 1766 Dihedral : 4.119 22.078 1417 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.30 % Allowed : 22.87 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.66 (0.24), residues: 1294 helix: 1.88 (0.26), residues: 418 sheet: 0.00 (0.28), residues: 346 loop : -0.35 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 111 HIS 0.005 0.001 HIS A 209 PHE 0.026 0.002 PHE N 68 TYR 0.026 0.001 TYR N 115 ARG 0.009 0.001 ARG S 179 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 518) hydrogen bonds : angle 4.76059 ( 1452) SS BOND : bond 0.00929 ( 6) SS BOND : angle 2.02065 ( 12) covalent geometry : bond 0.00307 (10265) covalent geometry : angle 0.67721 (13942) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.8961 (m-80) cc_final: 0.8611 (m-80) REVERT: R 15 LEU cc_start: 0.9540 (mp) cc_final: 0.9269 (tp) REVERT: R 16 ARG cc_start: 0.9066 (mmm160) cc_final: 0.8859 (mmm160) REVERT: R 34 LEU cc_start: 0.8604 (tp) cc_final: 0.8249 (mm) REVERT: R 267 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8160 (mmmt) REVERT: R 334 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.5177 (t80) REVERT: N 53 GLN cc_start: 0.7181 (mp10) cc_final: 0.6835 (mp10) REVERT: N 73 ASP cc_start: 0.8263 (t0) cc_final: 0.7790 (p0) REVERT: N 76 LYS cc_start: 0.9282 (ttmm) cc_final: 0.9036 (ttmm) REVERT: N 80 TYR cc_start: 0.7951 (m-80) cc_final: 0.7632 (m-10) REVERT: B 57 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8505 (mtmm) REVERT: B 145 TYR cc_start: 0.9003 (p90) cc_final: 0.8664 (p90) REVERT: B 220 GLN cc_start: 0.8563 (mp10) cc_final: 0.8335 (mp10) REVERT: B 262 MET cc_start: 0.7768 (tpp) cc_final: 0.6983 (tpp) REVERT: B 336 LEU cc_start: 0.8416 (tp) cc_final: 0.7986 (tp) REVERT: A 14 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7862 (mp0) REVERT: A 21 LYS cc_start: 0.7281 (tttm) cc_final: 0.6730 (ttpp) REVERT: A 25 GLU cc_start: 0.7854 (mp0) cc_final: 0.7370 (mp0) REVERT: A 75 GLN cc_start: 0.7617 (pp30) cc_final: 0.7316 (pp30) REVERT: A 83 MET cc_start: 0.8534 (ttm) cc_final: 0.8177 (ttm) REVERT: A 131 ASN cc_start: 0.8387 (t0) cc_final: 0.8026 (t0) REVERT: A 195 LYS cc_start: 0.9425 (tptp) cc_final: 0.8960 (tptp) REVERT: A 199 ASP cc_start: 0.9428 (p0) cc_final: 0.8854 (p0) REVERT: A 231 CYS cc_start: 0.9206 (m) cc_final: 0.8896 (m) REVERT: S 88 SER cc_start: 0.8943 (t) cc_final: 0.8686 (p) outliers start: 24 outliers final: 14 residues processed: 223 average time/residue: 0.2990 time to fit residues: 90.1232 Evaluate side-chains 212 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 105 GLN Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 334 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain S residue 100 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.118457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.096755 restraints weight = 26481.133| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 4.02 r_work: 0.3548 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10272 Z= 0.135 Angle : 0.697 15.372 13954 Z= 0.347 Chirality : 0.043 0.208 1596 Planarity : 0.004 0.051 1766 Dihedral : 4.135 21.302 1417 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.39 % Allowed : 22.49 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.65 (0.24), residues: 1294 helix: 1.83 (0.26), residues: 420 sheet: 0.02 (0.28), residues: 353 loop : -0.35 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.023 0.001 PHE N 68 TYR 0.027 0.001 TYR N 115 ARG 0.013 0.001 ARG R 32 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 518) hydrogen bonds : angle 4.76799 ( 1452) SS BOND : bond 0.00876 ( 6) SS BOND : angle 1.90031 ( 12) covalent geometry : bond 0.00313 (10265) covalent geometry : angle 0.69473 (13942) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.9037 (m-80) cc_final: 0.8661 (m-80) REVERT: R 15 LEU cc_start: 0.9526 (mp) cc_final: 0.9259 (tp) REVERT: R 157 TYR cc_start: 0.8156 (t80) cc_final: 0.7945 (t80) REVERT: R 267 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8186 (mmmt) REVERT: R 334 PHE cc_start: 0.5602 (OUTLIER) cc_final: 0.5101 (t80) REVERT: N 53 GLN cc_start: 0.7202 (mp10) cc_final: 0.6869 (mp10) REVERT: N 73 ASP cc_start: 0.8271 (t0) cc_final: 0.7805 (p0) REVERT: N 76 LYS cc_start: 0.9226 (ttmm) cc_final: 0.8983 (ttmm) REVERT: N 80 TYR cc_start: 0.7942 (m-80) cc_final: 0.7648 (m-10) REVERT: B 57 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8384 (mtmm) REVERT: B 145 TYR cc_start: 0.8991 (p90) cc_final: 0.8669 (p90) REVERT: B 220 GLN cc_start: 0.8592 (mp10) cc_final: 0.8302 (mp10) REVERT: B 262 MET cc_start: 0.7756 (tpp) cc_final: 0.6980 (tpp) REVERT: B 336 LEU cc_start: 0.8441 (tp) cc_final: 0.8010 (tp) REVERT: A 14 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7880 (mp0) REVERT: A 21 LYS cc_start: 0.7419 (tttm) cc_final: 0.6784 (ttpp) REVERT: A 25 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7441 (mp0) REVERT: A 83 MET cc_start: 0.8494 (ttm) cc_final: 0.8159 (ttm) REVERT: A 131 ASN cc_start: 0.8407 (t0) cc_final: 0.8046 (t0) REVERT: A 195 LYS cc_start: 0.9435 (tptp) cc_final: 0.8987 (tptp) REVERT: A 199 ASP cc_start: 0.9413 (p0) cc_final: 0.8824 (p0) REVERT: A 231 CYS cc_start: 0.9128 (m) cc_final: 0.8829 (m) REVERT: S 88 SER cc_start: 0.8966 (t) cc_final: 0.8695 (p) outliers start: 25 outliers final: 19 residues processed: 217 average time/residue: 0.2894 time to fit residues: 86.7969 Evaluate side-chains 214 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 105 GLN Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 334 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain S residue 100 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.119319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.097745 restraints weight = 26715.486| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 4.09 r_work: 0.3553 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10272 Z= 0.134 Angle : 0.705 15.061 13954 Z= 0.348 Chirality : 0.043 0.196 1596 Planarity : 0.004 0.050 1766 Dihedral : 4.100 22.942 1417 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.20 % Allowed : 23.06 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.72 (0.24), residues: 1294 helix: 1.85 (0.26), residues: 419 sheet: 0.17 (0.28), residues: 348 loop : -0.34 (0.29), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.030 0.001 PHE A 192 TYR 0.028 0.001 TYR N 115 ARG 0.006 0.001 ARG R 16 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 518) hydrogen bonds : angle 4.73864 ( 1452) SS BOND : bond 0.00920 ( 6) SS BOND : angle 1.93292 ( 12) covalent geometry : bond 0.00312 (10265) covalent geometry : angle 0.70299 (13942) Misc. bond : bond 0.00020 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 11 PHE cc_start: 0.9100 (m-80) cc_final: 0.8721 (m-80) REVERT: R 157 TYR cc_start: 0.8192 (t80) cc_final: 0.7983 (t80) REVERT: R 334 PHE cc_start: 0.5693 (OUTLIER) cc_final: 0.5444 (t80) REVERT: N 32 TYR cc_start: 0.7660 (m-80) cc_final: 0.6794 (m-80) REVERT: N 53 GLN cc_start: 0.7216 (mp10) cc_final: 0.6915 (mp10) REVERT: N 73 ASP cc_start: 0.8274 (t0) cc_final: 0.7793 (p0) REVERT: N 76 LYS cc_start: 0.9241 (ttmm) cc_final: 0.8991 (ttmm) REVERT: N 80 TYR cc_start: 0.7942 (m-80) cc_final: 0.7723 (m-10) REVERT: B 57 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8384 (mtmm) REVERT: B 145 TYR cc_start: 0.9013 (p90) cc_final: 0.8552 (p90) REVERT: B 220 GLN cc_start: 0.8587 (mp10) cc_final: 0.8286 (mp10) REVERT: B 262 MET cc_start: 0.7760 (tpp) cc_final: 0.6981 (tpp) REVERT: B 336 LEU cc_start: 0.8476 (tp) cc_final: 0.8052 (tp) REVERT: A 14 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7895 (mp0) REVERT: A 21 LYS cc_start: 0.7437 (tttm) cc_final: 0.6894 (tttm) REVERT: A 25 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7568 (mp0) REVERT: A 83 MET cc_start: 0.8450 (ttm) cc_final: 0.8113 (ttm) REVERT: A 131 ASN cc_start: 0.8337 (t0) cc_final: 0.7974 (t0) REVERT: A 195 LYS cc_start: 0.9441 (tptp) cc_final: 0.8992 (tptp) REVERT: A 199 ASP cc_start: 0.9409 (p0) cc_final: 0.8823 (p0) REVERT: A 231 CYS cc_start: 0.9187 (m) cc_final: 0.8889 (m) REVERT: S 88 SER cc_start: 0.9052 (t) cc_final: 0.8785 (p) REVERT: Q 13 ASN cc_start: 0.8651 (m-40) cc_final: 0.8315 (m110) outliers start: 23 outliers final: 19 residues processed: 225 average time/residue: 0.2858 time to fit residues: 87.1756 Evaluate side-chains 217 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 105 GLN Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 334 PHE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain S residue 100 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.119122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.097720 restraints weight = 26491.934| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.07 r_work: 0.3549 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10272 Z= 0.133 Angle : 0.686 14.341 13954 Z= 0.344 Chirality : 0.043 0.185 1596 Planarity : 0.004 0.050 1766 Dihedral : 4.108 22.634 1417 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.30 % Allowed : 23.35 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.79 (0.24), residues: 1294 helix: 1.99 (0.26), residues: 419 sheet: 0.21 (0.28), residues: 352 loop : -0.38 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 111 HIS 0.011 0.001 HIS B 91 PHE 0.041 0.002 PHE R 339 TYR 0.029 0.001 TYR N 115 ARG 0.008 0.001 ARG S 179 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 518) hydrogen bonds : angle 4.69986 ( 1452) SS BOND : bond 0.00872 ( 6) SS BOND : angle 1.75723 ( 12) covalent geometry : bond 0.00309 (10265) covalent geometry : angle 0.68465 (13942) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6652.93 seconds wall clock time: 117 minutes 32.23 seconds (7052.23 seconds total)