Starting phenix.real_space_refine on Fri Nov 15 07:54:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/11_2024/8ihh_35444.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/11_2024/8ihh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/11_2024/8ihh_35444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/11_2024/8ihh_35444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/11_2024/8ihh_35444.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihh_35444/11_2024/8ihh_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-5513/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: 5.33, per 1000 atoms: 0.61 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.11 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: 2.66 Time building geometry restraints manager: 2.50 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: 0.230 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- 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 8865 Z= 0.170 Angle : 0.531 10.103 12039 Z= 0.290 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 *********************** 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 : 0.963 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: 0.2450 time to fit residues: 42.9737 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 : 0.960 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 8865 Z= 0.306 Angle : 0.594 7.891 12039 Z= 0.316 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 *********************** 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 : 0.979 Fit side-chains REVERT: R 192 MET cc_start: 0.8085 (ttp) cc_final: 0.7805 (ttm) REVERT: R 219 GLN cc_start: 0.7410 (mp10) cc_final: 0.7137 (mp10) REVERT: B 35 ASN cc_start: 0.7718 (t0) cc_final: 0.7277 (p0) REVERT: S 6 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8285 (pt0) REVERT: S 38 ARG cc_start: 0.8658 (ptt180) cc_final: 0.8381 (ptt180) REVERT: S 144 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6756 (m) outliers start: 29 outliers final: 17 residues processed: 151 average time/residue: 0.2249 time to fit residues: 46.3574 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 144 THR 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 55 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8865 Z= 0.205 Angle : 0.527 8.242 12039 Z= 0.278 Chirality : 0.042 0.219 1377 Planarity : 0.004 0.046 1523 Dihedral : 6.297 143.181 1239 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.67 % Allowed : 23.44 % Favored : 72.89 % 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: -0.10 (0.25), residues: 1115 helix: 1.22 (0.27), residues: 371 sheet: -0.12 (0.31), residues: 271 loop : -1.02 (0.27), residues: 473 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 0.031 0.001 TYR S 235 ARG 0.002 0.000 ARG A 32 *********************** 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 164 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.142 Fit side-chains REVERT: R 33 VAL cc_start: 0.7714 (t) cc_final: 0.7378 (p) REVERT: R 192 MET cc_start: 0.8087 (ttp) cc_final: 0.7851 (ttm) REVERT: R 219 GLN cc_start: 0.7376 (mp10) cc_final: 0.7035 (mp10) REVERT: B 35 ASN cc_start: 0.7675 (t0) cc_final: 0.7310 (p0) REVERT: S 38 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8383 (ptt180) REVERT: S 93 MET cc_start: 0.8661 (ttt) cc_final: 0.8377 (ttm) REVERT: S 235 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6788 (t80) REVERT: S 244 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7889 (ttmm) outliers start: 33 outliers final: 19 residues processed: 154 average time/residue: 0.2268 time to fit residues: 47.2596 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 R residue 235 VAL 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 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 235 TYR 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 98 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8865 Z= 0.363 Angle : 0.610 9.766 12039 Z= 0.319 Chirality : 0.045 0.260 1377 Planarity : 0.004 0.045 1523 Dihedral : 6.664 149.033 1239 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.00 % Allowed : 22.78 % 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: -0.32 (0.24), residues: 1115 helix: 1.04 (0.27), residues: 377 sheet: -0.26 (0.30), residues: 271 loop : -1.19 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.007 0.001 HIS B 225 PHE 0.013 0.002 PHE R 277 TYR 0.036 0.002 TYR S 235 ARG 0.003 0.000 ARG S 98 *********************** 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 172 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 0.976 Fit side-chains REVERT: R 33 VAL cc_start: 0.7550 (t) cc_final: 0.7285 (p) REVERT: R 219 GLN cc_start: 0.7500 (mp10) cc_final: 0.7171 (mp10) REVERT: A 20 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: B 35 ASN cc_start: 0.7685 (t0) cc_final: 0.7296 (p0) REVERT: S 38 ARG cc_start: 0.8737 (ptt180) cc_final: 0.8502 (ptt180) REVERT: S 93 MET cc_start: 0.8652 (ttt) cc_final: 0.8374 (ttm) REVERT: S 202 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7963 (mtm110) REVERT: S 235 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7058 (t80) REVERT: S 244 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7964 (ttmm) outliers start: 45 outliers final: 31 residues processed: 163 average time/residue: 0.2196 time to fit residues: 49.6196 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain R residue 71 VAL 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 88 optimal weight: 9.9990 chunk 60 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8865 Z= 0.147 Angle : 0.492 7.418 12039 Z= 0.259 Chirality : 0.041 0.178 1377 Planarity : 0.004 0.067 1523 Dihedral : 6.021 139.169 1239 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.67 % Allowed : 23.89 % 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 (0.25), residues: 1115 helix: 1.61 (0.27), residues: 371 sheet: -0.13 (0.31), residues: 271 loop : -1.00 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.011 0.001 PHE S 27 TYR 0.028 0.001 TYR S 235 ARG 0.003 0.000 ARG S 98 *********************** 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 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.942 Fit side-chains REVERT: R 219 GLN cc_start: 0.7297 (mp10) cc_final: 0.6953 (mp10) REVERT: A 20 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: B 35 ASN cc_start: 0.7632 (t0) cc_final: 0.7284 (p0) REVERT: S 6 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: S 13 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7202 (pp30) REVERT: S 38 ARG cc_start: 0.8715 (ptt180) cc_final: 0.8449 (ptt180) REVERT: S 202 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7910 (mtm180) REVERT: S 235 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6669 (t80) REVERT: S 244 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7782 (ttmm) outliers start: 33 outliers final: 16 residues processed: 156 average time/residue: 0.2289 time to fit residues: 48.3272 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 195 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 13 GLN 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 178 LEU Chi-restraints excluded: chain S residue 193 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN B 220 GLN ** S 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8865 Z= 0.292 Angle : 0.564 8.810 12039 Z= 0.293 Chirality : 0.043 0.221 1377 Planarity : 0.004 0.052 1523 Dihedral : 6.414 145.583 1239 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.11 % Allowed : 22.78 % 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: 0.00 (0.25), residues: 1115 helix: 1.51 (0.27), residues: 370 sheet: -0.20 (0.30), residues: 271 loop : -1.06 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS B 225 PHE 0.011 0.002 PHE B 151 TYR 0.034 0.001 TYR S 235 ARG 0.003 0.000 ARG S 98 *********************** 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 163 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.971 Fit side-chains REVERT: R 33 VAL cc_start: 0.7658 (p) cc_final: 0.7451 (t) REVERT: R 219 GLN cc_start: 0.7471 (mp10) cc_final: 0.7105 (mp10) REVERT: A 20 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8121 (m-30) REVERT: B 35 ASN cc_start: 0.7650 (t0) cc_final: 0.7244 (p0) REVERT: S 13 GLN cc_start: 0.7580 (pm20) cc_final: 0.7033 (pp30) REVERT: S 202 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7966 (mtm110) REVERT: S 235 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6856 (t80) REVERT: S 244 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8007 (ttmm) outliers start: 46 outliers final: 31 residues processed: 153 average time/residue: 0.2132 time to fit residues: 45.1652 Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 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 263 SER Chi-restraints excluded: chain A residue 351 CYS 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 270 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 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 235 TYR 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 11 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8865 Z= 0.148 Angle : 0.500 7.927 12039 Z= 0.260 Chirality : 0.041 0.174 1377 Planarity : 0.004 0.043 1523 Dihedral : 6.029 139.666 1239 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.67 % Allowed : 24.11 % 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: 0.22 (0.25), residues: 1115 helix: 1.84 (0.27), residues: 369 sheet: -0.12 (0.31), residues: 271 loop : -1.04 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.012 0.001 PHE A 334 TYR 0.027 0.001 TYR S 235 ARG 0.003 0.000 ARG S 67 *********************** 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 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.999 Fit side-chains REVERT: R 219 GLN cc_start: 0.7258 (mp10) cc_final: 0.6889 (mp10) REVERT: A 20 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: B 35 ASN cc_start: 0.7550 (t0) cc_final: 0.7142 (p0) REVERT: B 55 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8520 (mp) REVERT: B 259 GLN cc_start: 0.8599 (pt0) cc_final: 0.8396 (pt0) REVERT: S 6 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: S 13 GLN cc_start: 0.7333 (pm20) cc_final: 0.6918 (pp30) REVERT: S 202 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7940 (mtm180) REVERT: S 235 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6586 (t80) REVERT: S 244 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7960 (ttmm) outliers start: 33 outliers final: 20 residues processed: 141 average time/residue: 0.2180 time to fit residues: 42.4553 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 PHE 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 195 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain A residue 20 ASP 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 B residue 270 ILE 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 178 LEU Chi-restraints excluded: chain S residue 193 SER 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 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 63 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8865 Z= 0.280 Angle : 0.560 7.698 12039 Z= 0.291 Chirality : 0.043 0.221 1377 Planarity : 0.004 0.047 1523 Dihedral : 6.376 146.335 1239 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.11 % Allowed : 23.78 % 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: 0.07 (0.25), residues: 1115 helix: 1.66 (0.27), residues: 371 sheet: -0.16 (0.30), residues: 274 loop : -1.13 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.011 0.001 PHE R 277 TYR 0.033 0.002 TYR S 235 ARG 0.002 0.000 ARG S 98 *********************** 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: 37 poor density : 117 time to evaluate : 0.996 Fit side-chains REVERT: R 219 GLN cc_start: 0.7385 (mp10) cc_final: 0.6993 (mp10) REVERT: A 20 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: B 35 ASN cc_start: 0.7593 (t0) cc_final: 0.7235 (p0) REVERT: B 55 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8541 (mp) REVERT: S 13 GLN cc_start: 0.7454 (pm20) cc_final: 0.7031 (pp30) REVERT: S 235 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6751 (t80) REVERT: S 244 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8131 (ttmm) outliers start: 37 outliers final: 32 residues processed: 145 average time/residue: 0.2219 time to fit residues: 44.2657 Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 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 263 SER 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 245 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 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 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 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 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 104 optimal weight: 0.3980 chunk 63 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8865 Z= 0.132 Angle : 0.494 7.854 12039 Z= 0.256 Chirality : 0.040 0.162 1377 Planarity : 0.004 0.044 1523 Dihedral : 5.965 139.922 1239 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.56 % Allowed : 24.22 % 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: 0.27 (0.25), residues: 1115 helix: 1.95 (0.27), residues: 370 sheet: -0.20 (0.30), residues: 283 loop : -1.02 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.014 0.001 PHE A 334 TYR 0.026 0.001 TYR S 235 ARG 0.003 0.000 ARG A 208 *********************** 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 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.870 Fit side-chains REVERT: R 30 LEU cc_start: 0.7970 (mp) cc_final: 0.7600 (mp) REVERT: R 219 GLN cc_start: 0.7283 (mp10) cc_final: 0.6944 (mp10) REVERT: B 32 GLN cc_start: 0.8549 (tt0) cc_final: 0.8224 (tt0) REVERT: B 35 ASN cc_start: 0.7455 (t0) cc_final: 0.7191 (p0) REVERT: B 55 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8511 (mp) REVERT: S 6 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: S 13 GLN cc_start: 0.7421 (pm20) cc_final: 0.7026 (pp30) REVERT: S 235 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6483 (t80) REVERT: S 244 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7988 (ttmm) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.2290 time to fit residues: 44.7728 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 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 245 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 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 235 TYR 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 49 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8865 Z= 0.204 Angle : 0.531 8.224 12039 Z= 0.274 Chirality : 0.042 0.185 1377 Planarity : 0.004 0.058 1523 Dihedral : 6.099 142.711 1239 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.22 % Allowed : 24.33 % 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: 0.19 (0.25), residues: 1115 helix: 1.76 (0.27), residues: 371 sheet: -0.10 (0.30), residues: 274 loop : -1.05 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.041 0.001 PHE A 334 TYR 0.029 0.001 TYR S 235 ARG 0.002 0.000 ARG A 208 ********************** 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 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.020 Fit side-chains REVERT: R 33 VAL cc_start: 0.7706 (t) cc_final: 0.7359 (p) REVERT: R 219 GLN cc_start: 0.7313 (mp10) cc_final: 0.6867 (mp10) REVERT: A 9 ASP cc_start: 0.7651 (t0) cc_final: 0.7438 (m-30) REVERT: B 32 GLN cc_start: 0.8555 (tt0) cc_final: 0.8234 (tt0) REVERT: B 35 ASN cc_start: 0.7573 (t0) cc_final: 0.7212 (p0) REVERT: B 55 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 101 MET cc_start: 0.8875 (mtp) cc_final: 0.8621 (mtm) REVERT: S 6 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: S 13 GLN cc_start: 0.7423 (pm20) cc_final: 0.7037 (pp30) REVERT: S 38 ARG cc_start: 0.8597 (ptt180) cc_final: 0.8317 (ptt180) REVERT: S 235 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6603 (t80) REVERT: S 244 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7973 (ttmm) outliers start: 29 outliers final: 24 residues processed: 138 average time/residue: 0.2154 time to fit residues: 41.1632 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 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 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 57 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 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 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 80 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.150423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117053 restraints weight = 11276.759| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.21 r_work: 0.3243 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8865 Z= 0.193 Angle : 0.525 8.281 12039 Z= 0.270 Chirality : 0.042 0.188 1377 Planarity : 0.004 0.053 1523 Dihedral : 6.043 140.673 1239 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.11 % Allowed : 24.56 % 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: 0.20 (0.25), residues: 1115 helix: 1.78 (0.27), residues: 371 sheet: -0.11 (0.30), residues: 274 loop : -1.05 (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 0.036 0.001 PHE A 334 TYR 0.030 0.001 TYR S 235 ARG 0.002 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.07 seconds wall clock time: 40 minutes 19.31 seconds (2419.31 seconds total)