Starting phenix.real_space_refine on Mon May 12 00:28:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihh_35444/05_2025/8ihh_35444.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihh_35444/05_2025/8ihh_35444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihh_35444/05_2025/8ihh_35444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihh_35444/05_2025/8ihh_35444.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihh_35444/05_2025/8ihh_35444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihh_35444/05_2025/8ihh_35444.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.075 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 58 5.16 5 C 5545 2.51 5 N 1473 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2381 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 281} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1698 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2480 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 376 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "S" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'P8A': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.00, per 1000 atoms: 0.58 Number of scatterers: 8670 At special positions: 0 Unit cell: (88.11, 117.81, 136.62, 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 58 16.00 O 1594 8.00 N 1473 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 601 " - " ASN R 17 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 990.8 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.9% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'R' and resid 23 through 27 Processing helix chain 'R' and resid 29 through 55 removed outlier: 3.602A pdb=" N PHE R 54 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 79 removed outlier: 3.742A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 Processing helix chain 'R' and resid 97 through 130 removed outlier: 4.939A pdb=" N VAL R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.836A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 removed outlier: 3.627A pdb=" N THR R 159 " --> pdb=" O THR R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 187 through 196 removed outlier: 3.734A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 218 removed outlier: 3.519A pdb=" N GLY R 202 " --> pdb=" O PHE R 198 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 261 removed outlier: 3.657A pdb=" N THR R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 246 - end of helix removed outlier: 3.584A pdb=" N HIS R 259 " --> pdb=" O PHE R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.647A pdb=" N LEU R 274 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 284 No H-bonds generated for 'chain 'R' and resid 282 through 284' Processing helix chain 'R' and resid 285 through 290 Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.547A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.583A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.296A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.843A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.694A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.609A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.647A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.972A pdb=" N ILE R 182 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 169 through 171 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.547A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.484A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.567A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.858A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.732A 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: 3.564A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.446A 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: 7.000A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.593A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.093A 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: 3.644A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.718A pdb=" N SER S 7 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 Processing sheet with id=AB4, first strand: chain 'S' and resid 45 through 46 removed outlier: 3.503A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.372A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1095 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: 2.48 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2795 1.35 - 1.48: 2326 1.48 - 1.60: 3663 1.60 - 1.73: 0 1.73 - 1.86: 81 Bond restraints: 8865 Sorted by residual: bond pdb=" O P8A R 602 " pdb=" C7 P8A R 602 " ideal model delta sigma weight residual 1.256 1.307 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C7 P8A R 602 " pdb=" O1 P8A R 602 " ideal model delta sigma weight residual 1.259 1.222 0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C6 P8A R 602 " pdb=" C7 P8A R 602 " ideal model delta sigma weight residual 1.513 1.477 0.036 2.00e-02 2.50e+03 3.30e+00 bond pdb=" CA PHE R 255 " pdb=" C PHE R 255 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.35e-02 5.49e+03 3.26e+00 bond pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " ideal model delta sigma weight residual 1.808 1.860 -0.052 3.30e-02 9.18e+02 2.44e+00 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11897 2.02 - 4.04: 119 4.04 - 6.06: 18 6.06 - 8.08: 4 8.08 - 10.10: 1 Bond angle restraints: 12039 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.10 108.53 4.57 9.70e-01 1.06e+00 2.22e+01 angle pdb=" CA CYS R 183 " pdb=" CB CYS R 183 " pdb=" SG CYS R 183 " ideal model delta sigma weight residual 114.40 122.34 -7.94 2.30e+00 1.89e-01 1.19e+01 angle pdb=" CB MET R 285 " pdb=" CG MET R 285 " pdb=" SD MET R 285 " ideal model delta sigma weight residual 112.70 122.80 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N CYS R 183 " pdb=" CA CYS R 183 " pdb=" C CYS R 183 " ideal model delta sigma weight residual 108.79 113.54 -4.75 1.53e+00 4.27e-01 9.62e+00 angle pdb=" N MET R 167 " pdb=" CA MET R 167 " pdb=" C MET R 167 " ideal model delta sigma weight residual 109.81 116.23 -6.42 2.21e+00 2.05e-01 8.44e+00 ... (remaining 12034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.66: 4995 32.66 - 65.31: 192 65.31 - 97.97: 11 97.97 - 130.63: 0 130.63 - 163.29: 1 Dihedral angle restraints: 5199 sinusoidal: 1923 harmonic: 3276 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual -86.00 -146.12 60.12 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N LEU R 118 " pdb=" CA LEU R 118 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 51.47 41.53 1 1.00e+01 1.00e-02 2.41e+01 ... (remaining 5196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 938 0.035 - 0.070: 315 0.070 - 0.105: 87 0.105 - 0.140: 35 0.140 - 0.175: 2 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA CYS R 183 " pdb=" N CYS R 183 " pdb=" C CYS R 183 " pdb=" CB CYS R 183 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.32e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1374 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 31 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO R 32 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 32 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 32 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C THR B 87 " -0.032 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO S 236 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 285 2.71 - 3.26: 8403 3.26 - 3.81: 13570 3.81 - 4.35: 17725 4.35 - 4.90: 30656 Nonbonded interactions: 70639 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.233 3.040 nonbonded pdb=" OG SER R 62 " pdb=" OD2 ASP R 124 " model vdw 2.233 3.040 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.248 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.253 3.040 ... (remaining 70634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.410 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 0.052 8869 Z= 0.127 Angle : 0.535 10.103 12048 Z= 0.292 Chirality : 0.040 0.175 1377 Planarity : 0.004 0.063 1523 Dihedral : 16.534 163.285 3072 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.22 % Allowed : 24.44 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1115 helix: 0.06 (0.27), residues: 355 sheet: -0.01 (0.32), residues: 271 loop : -1.06 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.001 0.000 HIS B 183 PHE 0.010 0.001 PHE B 151 TYR 0.019 0.001 TYR S 235 ARG 0.005 0.000 ARG B 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 2.51348 ( 3) hydrogen bonds : bond 0.25134 ( 390) hydrogen bonds : angle 8.09708 ( 1095) SS BOND : bond 0.00779 ( 3) SS BOND : angle 2.50129 ( 6) covalent geometry : bond 0.00257 ( 8865) covalent geometry : angle 0.53108 (12039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.898 Fit side-chains REVERT: R 50 TRP cc_start: 0.5776 (t60) cc_final: 0.5245 (t-100) REVERT: R 106 MET cc_start: 0.7405 (tpt) cc_final: 0.7200 (tpp) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2255 time to fit residues: 39.6468 Evaluate side-chains 120 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 110 ASN A 306 GLN B 88 ASN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120873 restraints weight = 11054.657| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.71 r_work: 0.3357 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8869 Z= 0.203 Angle : 0.597 7.891 12048 Z= 0.317 Chirality : 0.044 0.236 1377 Planarity : 0.005 0.054 1523 Dihedral : 6.823 150.098 1241 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.22 % Allowed : 23.33 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1115 helix: 0.82 (0.27), residues: 370 sheet: -0.12 (0.31), residues: 274 loop : -1.07 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.005 0.001 HIS B 225 PHE 0.012 0.002 PHE B 151 TYR 0.033 0.002 TYR S 235 ARG 0.004 0.000 ARG R 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 1) link_NAG-ASN : angle 2.61762 ( 3) hydrogen bonds : bond 0.05291 ( 390) hydrogen bonds : angle 5.19152 ( 1095) SS BOND : bond 0.00645 ( 3) SS BOND : angle 1.72271 ( 6) covalent geometry : bond 0.00475 ( 8865) covalent geometry : angle 0.59408 (12039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.995 Fit side-chains REVERT: R 192 MET cc_start: 0.8010 (ttp) cc_final: 0.7731 (ttm) REVERT: R 219 GLN cc_start: 0.7465 (mp10) cc_final: 0.7170 (mp10) REVERT: B 35 ASN cc_start: 0.7722 (t0) cc_final: 0.7239 (p0) REVERT: S 6 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: S 38 ARG cc_start: 0.8713 (ptt180) cc_final: 0.8487 (ptt180) outliers start: 29 outliers final: 17 residues processed: 151 average time/residue: 0.2171 time to fit residues: 45.0996 Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 237 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 189 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123441 restraints weight = 11159.704| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.46 r_work: 0.3398 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8869 Z= 0.146 Angle : 0.540 8.346 12048 Z= 0.284 Chirality : 0.042 0.225 1377 Planarity : 0.004 0.045 1523 Dihedral : 6.365 144.015 1239 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.56 % Allowed : 23.22 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1115 helix: 1.17 (0.27), residues: 372 sheet: -0.14 (0.31), residues: 271 loop : -1.05 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 151 TYR 0.032 0.001 TYR S 235 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 2.68617 ( 3) hydrogen bonds : bond 0.04446 ( 390) hydrogen bonds : angle 4.68433 ( 1095) SS BOND : bond 0.00480 ( 3) SS BOND : angle 1.29638 ( 6) covalent geometry : bond 0.00338 ( 8865) covalent geometry : angle 0.53737 (12039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.023 Fit side-chains REVERT: R 33 VAL cc_start: 0.7658 (t) cc_final: 0.7268 (p) REVERT: R 192 MET cc_start: 0.8102 (ttp) cc_final: 0.7841 (ttm) REVERT: R 219 GLN cc_start: 0.7555 (mp10) cc_final: 0.7189 (mp10) REVERT: B 35 ASN cc_start: 0.7664 (t0) cc_final: 0.7215 (p0) REVERT: S 6 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: S 93 MET cc_start: 0.8762 (ttt) cc_final: 0.8489 (ttm) REVERT: S 244 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7996 (ttmm) outliers start: 32 outliers final: 18 residues processed: 150 average time/residue: 0.2226 time to fit residues: 45.3520 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121540 restraints weight = 11114.026| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.68 r_work: 0.3403 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8869 Z= 0.206 Angle : 0.589 9.650 12048 Z= 0.308 Chirality : 0.044 0.253 1377 Planarity : 0.004 0.044 1523 Dihedral : 6.562 147.269 1239 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.33 % Allowed : 23.44 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.24), residues: 1115 helix: 1.18 (0.27), residues: 372 sheet: -0.24 (0.30), residues: 271 loop : -1.14 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.006 0.001 HIS B 225 PHE 0.011 0.002 PHE R 277 TYR 0.033 0.002 TYR S 235 ARG 0.003 0.000 ARG S 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 2.34582 ( 3) hydrogen bonds : bond 0.04521 ( 390) hydrogen bonds : angle 4.66575 ( 1095) SS BOND : bond 0.00745 ( 3) SS BOND : angle 1.82426 ( 6) covalent geometry : bond 0.00495 ( 8865) covalent geometry : angle 0.58684 (12039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.929 Fit side-chains REVERT: R 33 VAL cc_start: 0.7495 (t) cc_final: 0.7184 (p) REVERT: R 219 GLN cc_start: 0.7688 (mp10) cc_final: 0.7341 (mp10) REVERT: A 20 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: B 34 THR cc_start: 0.8893 (p) cc_final: 0.8674 (t) REVERT: B 35 ASN cc_start: 0.7694 (t0) cc_final: 0.7187 (p0) REVERT: B 205 ASP cc_start: 0.8267 (p0) cc_final: 0.8054 (p0) REVERT: S 6 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: S 38 ARG cc_start: 0.8797 (ptt180) cc_final: 0.8515 (ptt180) REVERT: S 93 MET cc_start: 0.8738 (ttt) cc_final: 0.8499 (ttm) REVERT: S 202 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7819 (mtm110) REVERT: S 235 TYR cc_start: 0.7292 (OUTLIER) cc_final: 0.6903 (t80) REVERT: S 244 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8106 (ttmm) outliers start: 39 outliers final: 28 residues processed: 157 average time/residue: 0.2024 time to fit residues: 43.7656 Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 107 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** S 169 ASN ** 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 = 0.3972 r_free = 0.3972 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120361 restraints weight = 11004.367| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.32 r_work: 0.3404 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8869 Z= 0.214 Angle : 0.589 7.700 12048 Z= 0.309 Chirality : 0.044 0.261 1377 Planarity : 0.004 0.064 1523 Dihedral : 6.580 147.300 1239 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.89 % Allowed : 22.67 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1115 helix: 1.10 (0.27), residues: 378 sheet: -0.31 (0.30), residues: 270 loop : -1.23 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.006 0.001 HIS B 225 PHE 0.011 0.002 PHE B 151 TYR 0.037 0.002 TYR S 235 ARG 0.004 0.000 ARG S 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 1) link_NAG-ASN : angle 2.25493 ( 3) hydrogen bonds : bond 0.04439 ( 390) hydrogen bonds : angle 4.60287 ( 1095) SS BOND : bond 0.00710 ( 3) SS BOND : angle 1.84513 ( 6) covalent geometry : bond 0.00513 ( 8865) covalent geometry : angle 0.58687 (12039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.899 Fit side-chains REVERT: R 33 VAL cc_start: 0.7355 (t) cc_final: 0.7057 (p) REVERT: R 219 GLN cc_start: 0.7706 (mp10) cc_final: 0.7332 (mp10) REVERT: A 20 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: B 34 THR cc_start: 0.8950 (p) cc_final: 0.8748 (t) REVERT: B 35 ASN cc_start: 0.7692 (t0) cc_final: 0.7218 (p0) REVERT: S 6 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: S 38 ARG cc_start: 0.8800 (ptt180) cc_final: 0.8595 (ptt180) REVERT: S 93 MET cc_start: 0.8714 (ttt) cc_final: 0.8483 (ttm) REVERT: S 202 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7806 (mtm180) REVERT: S 244 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8027 (ttmm) outliers start: 53 outliers final: 35 residues processed: 166 average time/residue: 0.2119 time to fit residues: 48.5123 Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 CYS Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 167 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 220 GLN S 13 GLN ** S 169 ASN ** 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 = 0.4021 r_free = 0.4021 target = 0.160474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125290 restraints weight = 10879.536| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.31 r_work: 0.3468 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8869 Z= 0.107 Angle : 0.513 11.551 12048 Z= 0.267 Chirality : 0.041 0.145 1377 Planarity : 0.004 0.050 1523 Dihedral : 6.097 140.411 1239 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.11 % Allowed : 24.33 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1115 helix: 1.65 (0.27), residues: 372 sheet: -0.15 (0.31), residues: 271 loop : -1.06 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 54 TYR 0.028 0.001 TYR S 235 ARG 0.003 0.000 ARG S 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 1) link_NAG-ASN : angle 2.35017 ( 3) hydrogen bonds : bond 0.03600 ( 390) hydrogen bonds : angle 4.23318 ( 1095) SS BOND : bond 0.00695 ( 3) SS BOND : angle 1.58229 ( 6) covalent geometry : bond 0.00237 ( 8865) covalent geometry : angle 0.51079 (12039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.031 Fit side-chains REVERT: R 33 VAL cc_start: 0.7303 (t) cc_final: 0.6923 (p) REVERT: R 219 GLN cc_start: 0.7514 (mp10) cc_final: 0.7131 (mp10) REVERT: A 20 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: B 34 THR cc_start: 0.8887 (p) cc_final: 0.8676 (t) REVERT: B 35 ASN cc_start: 0.7662 (t0) cc_final: 0.7198 (p0) REVERT: B 55 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8627 (mp) REVERT: S 13 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7100 (pp30) REVERT: S 38 ARG cc_start: 0.8769 (ptt180) cc_final: 0.8492 (ptt180) REVERT: S 93 MET cc_start: 0.8701 (ttt) cc_final: 0.8431 (ttm) REVERT: S 202 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7776 (mtm180) REVERT: S 244 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7908 (ttmm) outliers start: 37 outliers final: 19 residues processed: 149 average time/residue: 0.2157 time to fit residues: 44.0786 Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 0.0060 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** S 169 ASN ** 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 = 0.3768 r_free = 0.3768 target = 0.148127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114615 restraints weight = 11416.439| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.31 r_work: 0.3207 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8869 Z= 0.198 Angle : 0.585 9.747 12048 Z= 0.303 Chirality : 0.044 0.232 1377 Planarity : 0.004 0.044 1523 Dihedral : 6.481 145.562 1239 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.33 % Allowed : 23.67 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1115 helix: 1.48 (0.27), residues: 371 sheet: -0.20 (0.30), residues: 268 loop : -1.16 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.002 PHE A 334 TYR 0.034 0.002 TYR S 235 ARG 0.002 0.000 ARG S 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 1) link_NAG-ASN : angle 0.87220 ( 3) hydrogen bonds : bond 0.04149 ( 390) hydrogen bonds : angle 4.43450 ( 1095) SS BOND : bond 0.00706 ( 3) SS BOND : angle 2.23481 ( 6) covalent geometry : bond 0.00474 ( 8865) covalent geometry : angle 0.58293 (12039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.949 Fit side-chains REVERT: R 219 GLN cc_start: 0.7642 (mp10) cc_final: 0.7241 (mp10) REVERT: A 20 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8371 (m-30) REVERT: B 35 ASN cc_start: 0.7692 (t0) cc_final: 0.7254 (p0) REVERT: B 55 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8596 (mp) REVERT: S 6 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: S 13 GLN cc_start: 0.7679 (pm20) cc_final: 0.6979 (pp30) REVERT: S 93 MET cc_start: 0.8802 (ttt) cc_final: 0.8571 (ttm) REVERT: S 202 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7868 (mtm180) REVERT: S 244 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8127 (ttmm) outliers start: 39 outliers final: 29 residues processed: 148 average time/residue: 0.2061 time to fit residues: 42.0233 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 136 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** S 169 ASN ** 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 = 0.3778 r_free = 0.3778 target = 0.149414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115764 restraints weight = 11464.623| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.25 r_work: 0.3226 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8869 Z= 0.126 Angle : 0.527 8.050 12048 Z= 0.273 Chirality : 0.042 0.192 1377 Planarity : 0.004 0.043 1523 Dihedral : 6.210 141.838 1239 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.89 % Allowed : 24.11 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1115 helix: 1.70 (0.27), residues: 371 sheet: -0.20 (0.30), residues: 274 loop : -1.11 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 151 TYR 0.030 0.001 TYR S 235 ARG 0.002 0.000 ARG S 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.31661 ( 3) hydrogen bonds : bond 0.03679 ( 390) hydrogen bonds : angle 4.24233 ( 1095) SS BOND : bond 0.00669 ( 3) SS BOND : angle 1.94510 ( 6) covalent geometry : bond 0.00291 ( 8865) covalent geometry : angle 0.52489 (12039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.049 Fit side-chains REVERT: R 33 VAL cc_start: 0.7734 (p) cc_final: 0.7517 (t) REVERT: R 84 MET cc_start: 0.6940 (ttt) cc_final: 0.6691 (tpp) REVERT: R 219 GLN cc_start: 0.7568 (mp10) cc_final: 0.7160 (mp10) REVERT: A 20 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: B 32 GLN cc_start: 0.8765 (tt0) cc_final: 0.8405 (tt0) REVERT: B 35 ASN cc_start: 0.7630 (t0) cc_final: 0.7220 (p0) REVERT: B 55 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8587 (mp) REVERT: S 6 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: S 13 GLN cc_start: 0.7530 (pm20) cc_final: 0.7017 (pp30) REVERT: S 93 MET cc_start: 0.8798 (ttt) cc_final: 0.8570 (ttm) REVERT: S 202 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7800 (mtm180) REVERT: S 244 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8095 (ttmm) outliers start: 35 outliers final: 27 residues processed: 146 average time/residue: 0.2117 time to fit residues: 42.5839 Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 50.0000 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 99 optimal weight: 0.0570 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** S 169 ASN ** 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 = 0.3743 r_free = 0.3743 target = 0.146304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112154 restraints weight = 11412.628| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.29 r_work: 0.3178 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8869 Z= 0.218 Angle : 0.596 8.538 12048 Z= 0.309 Chirality : 0.044 0.238 1377 Planarity : 0.004 0.059 1523 Dihedral : 6.565 147.445 1239 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.33 % Allowed : 23.33 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1115 helix: 1.46 (0.27), residues: 371 sheet: -0.29 (0.30), residues: 275 loop : -1.24 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.017 0.002 PHE A 334 TYR 0.035 0.002 TYR S 235 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 1.31827 ( 3) hydrogen bonds : bond 0.04276 ( 390) hydrogen bonds : angle 4.44872 ( 1095) SS BOND : bond 0.00723 ( 3) SS BOND : angle 1.96522 ( 6) covalent geometry : bond 0.00527 ( 8865) covalent geometry : angle 0.59432 (12039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 1.009 Fit side-chains REVERT: R 219 GLN cc_start: 0.7656 (mp10) cc_final: 0.7226 (mp10) REVERT: A 20 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: B 32 GLN cc_start: 0.8820 (tt0) cc_final: 0.8475 (tt0) REVERT: B 35 ASN cc_start: 0.7645 (t0) cc_final: 0.7236 (p0) REVERT: B 55 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8610 (mp) REVERT: S 6 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8308 (pt0) REVERT: S 13 GLN cc_start: 0.7630 (pm20) cc_final: 0.7131 (pp30) REVERT: S 93 MET cc_start: 0.8818 (ttt) cc_final: 0.8574 (ttm) REVERT: S 202 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7830 (mtm180) REVERT: S 244 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8244 (ttmm) outliers start: 39 outliers final: 30 residues processed: 144 average time/residue: 0.2160 time to fit residues: 42.6996 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 136 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 43 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** S 169 ASN ** 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 = 0.3781 r_free = 0.3781 target = 0.149645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116249 restraints weight = 11430.716| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.22 r_work: 0.3230 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8869 Z= 0.121 Angle : 0.524 7.996 12048 Z= 0.271 Chirality : 0.041 0.194 1377 Planarity : 0.004 0.053 1523 Dihedral : 6.193 141.507 1239 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.78 % Allowed : 24.11 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1115 helix: 1.69 (0.27), residues: 371 sheet: -0.23 (0.30), residues: 275 loop : -1.19 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE A 334 TYR 0.029 0.001 TYR S 235 ARG 0.003 0.000 ARG S 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00036 ( 1) link_NAG-ASN : angle 1.42720 ( 3) hydrogen bonds : bond 0.03629 ( 390) hydrogen bonds : angle 4.21787 ( 1095) SS BOND : bond 0.00620 ( 3) SS BOND : angle 1.53794 ( 6) covalent geometry : bond 0.00279 ( 8865) covalent geometry : angle 0.52219 (12039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 1.050 Fit side-chains REVERT: R 84 MET cc_start: 0.6981 (ttt) cc_final: 0.6740 (tpp) REVERT: R 219 GLN cc_start: 0.7511 (mp10) cc_final: 0.7098 (mp10) REVERT: A 20 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: B 32 GLN cc_start: 0.8749 (tt0) cc_final: 0.8421 (tt0) REVERT: B 35 ASN cc_start: 0.7636 (t0) cc_final: 0.7302 (p0) REVERT: B 55 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8595 (mp) REVERT: S 6 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: S 13 GLN cc_start: 0.7577 (pm20) cc_final: 0.7138 (pp30) REVERT: S 202 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7797 (mtm180) REVERT: S 244 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8155 (ttmm) outliers start: 34 outliers final: 27 residues processed: 141 average time/residue: 0.2151 time to fit residues: 41.3687 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 136 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 237 LEU Chi-restraints excluded: chain S residue 244 LYS Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** S 169 ASN ** 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 = 0.3747 r_free = 0.3747 target = 0.146589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112484 restraints weight = 11418.027| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.28 r_work: 0.3185 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8869 Z= 0.203 Angle : 0.585 8.279 12048 Z= 0.303 Chirality : 0.044 0.228 1377 Planarity : 0.004 0.049 1523 Dihedral : 6.510 146.863 1239 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.44 % Allowed : 24.11 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1115 helix: 1.51 (0.27), residues: 372 sheet: -0.28 (0.30), residues: 275 loop : -1.23 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.015 0.002 PHE A 334 TYR 0.035 0.002 TYR S 235 ARG 0.002 0.000 ARG R 253 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.41158 ( 3) hydrogen bonds : bond 0.04153 ( 390) hydrogen bonds : angle 4.38622 ( 1095) SS BOND : bond 0.00650 ( 3) SS BOND : angle 1.72301 ( 6) covalent geometry : bond 0.00489 ( 8865) covalent geometry : angle 0.58384 (12039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5063.36 seconds wall clock time: 88 minutes 8.01 seconds (5288.01 seconds total)