Starting phenix.real_space_refine on Mon Dec 30 11:00:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hpm_34933/12_2024/8hpm_34933.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hpm_34933/12_2024/8hpm_34933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hpm_34933/12_2024/8hpm_34933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hpm_34933/12_2024/8hpm_34933.map" model { file = "/net/cci-nas-00/data/ceres_data/8hpm_34933/12_2024/8hpm_34933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hpm_34933/12_2024/8hpm_34933.cif" } resolution = 3.82 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 29 5.16 5 C 8181 2.51 5 N 2157 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12803 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2115 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 267} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2007 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 254} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2657 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 176 Chain: "D" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2658 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 165 Chain: "E" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3281 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 31, 'TRANS': 405} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} 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 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.79, per 1000 atoms: 0.69 Number of scatterers: 12803 At special positions: 0 Unit cell: (83.64, 93.48, 165.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 6 15.00 O 2430 8.00 N 2157 7.00 C 8181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ALPHA1-1 " GLC G 1 " - " GLC G 2 " Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 15 sheets defined 52.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.620A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 76 through 111 removed outlier: 3.715A pdb=" N TRP A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.691A pdb=" N ILE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.784A pdb=" N TRP A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 161 through 190 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 203 removed outlier: 4.050A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.838A pdb=" N LYS A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 236 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.456A pdb=" N LEU A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 removed outlier: 4.460A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 291 removed outlier: 3.530A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 37 Proline residue: B 27 - end of helix removed outlier: 4.344A pdb=" N ILE B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 64 through 98 removed outlier: 4.129A pdb=" N SER B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.087A pdb=" N LEU B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.528A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 138 through 164 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.587A pdb=" N LYS B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 206 removed outlier: 5.273A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Proline residue: B 189 - end of helix Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'B' and resid 241 through 263 Proline residue: B 255 - end of helix removed outlier: 3.789A pdb=" N ILE B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.525A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 Processing helix chain 'C' and resid 170 through 189 Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.649A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 266 through 275 removed outlier: 5.312A pdb=" N LEU C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 140 through 154 removed outlier: 5.124A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 173 through 189 Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 274 removed outlier: 4.015A pdb=" N LEU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 374 through 377 Processing helix chain 'E' and resid 40 through 55 Processing helix chain 'E' and resid 71 through 83 removed outlier: 3.920A pdb=" N LEU E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.816A pdb=" N PHE E 101 " --> pdb=" O TRP E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 4.150A pdb=" N ASP E 113 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 4.388A pdb=" N ALA E 120 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 134 removed outlier: 3.742A pdb=" N LEU E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 134 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.554A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 Processing helix chain 'E' and resid 254 through 264 removed outlier: 3.546A pdb=" N ALA E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 286 removed outlier: 4.298A pdb=" N SER E 279 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Proline residue: E 298 - end of helix Processing helix chain 'E' and resid 313 through 325 Processing helix chain 'E' and resid 360 through 371 Processing helix chain 'E' and resid 374 through 382 removed outlier: 3.979A pdb=" N TYR E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR E 379 " --> pdb=" O ASN E 375 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 404 through 412 removed outlier: 3.628A pdb=" N ILE E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 435 Processing helix chain 'E' and resid 442 through 459 removed outlier: 3.509A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 31 removed outlier: 5.320A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 159 through 161 removed outlier: 6.644A pdb=" N PHE C 160 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N VAL C 195 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 245 through 250 Processing sheet with id=AA5, first strand: chain 'C' and resid 292 through 293 removed outlier: 4.041A pdb=" N GLU C 366 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 315 through 316 Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.599A pdb=" N ILE D 67 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 192 through 196 removed outlier: 6.599A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL D 40 " --> pdb=" O MET D 212 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU D 213 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 84 removed outlier: 6.928A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 245 through 249 removed outlier: 3.785A pdb=" N SER D 378 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 256 through 258 Processing sheet with id=AB3, first strand: chain 'D' and resid 291 through 293 removed outlier: 4.062A pdb=" N GLU D 366 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 315 through 316 Processing sheet with id=AB5, first strand: chain 'E' and resid 60 through 66 removed outlier: 10.554A pdb=" N ASP E 94 " --> pdb=" O PRO E 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY E 347 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR E 147 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 269 through 270 653 hydrogen bonds defined for protein. 1857 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: 3.96 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2432 1.32 - 1.45: 2961 1.45 - 1.57: 7600 1.57 - 1.70: 10 1.70 - 1.82: 54 Bond restraints: 13057 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 GLC G 1 " pdb=" O5 GLC G 1 " ideal model delta sigma weight residual 1.415 1.549 -0.134 2.00e-02 2.50e+03 4.50e+01 ... (remaining 13052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 17270 3.91 - 7.83: 597 7.83 - 11.74: 13 11.74 - 15.65: 2 15.65 - 19.57: 4 Bond angle restraints: 17886 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.30 19.57 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.33 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.39 16.44 1.00e+00 1.00e+00 2.70e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.68e+01 ... (remaining 17881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7249 17.61 - 35.23: 458 35.23 - 52.84: 90 52.84 - 70.46: 23 70.46 - 88.07: 4 Dihedral angle restraints: 7824 sinusoidal: 2776 harmonic: 5048 Sorted by residual: dihedral pdb=" CA ASP C 321 " pdb=" C ASP C 321 " pdb=" N LYS C 322 " pdb=" CA LYS C 322 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LEU A 151 " pdb=" C LEU A 151 " pdb=" N LEU A 152 " pdb=" CA LEU A 152 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER D 156 " pdb=" C SER D 156 " pdb=" N PRO D 157 " pdb=" CA PRO D 157 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 7821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1836 0.130 - 0.260: 310 0.260 - 0.390: 20 0.390 - 0.520: 4 0.520 - 0.650: 1 Chirality restraints: 2171 Sorted by residual: chirality pdb=" C1 GLC G 1 " pdb=" C2 GLC G 1 " pdb=" O5 GLC G 1 " pdb=" O1 GLC G 2 " both_signs ideal model delta sigma weight residual False 2.40 2.29 0.11 2.00e-02 2.50e+03 3.03e+01 chirality pdb=" C5 GLC G 2 " pdb=" C4 GLC G 2 " pdb=" C6 GLC G 2 " pdb=" O5 GLC G 2 " both_signs ideal model delta sigma weight residual False -2.50 -1.85 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA LYS C 109 " pdb=" N LYS C 109 " pdb=" C LYS C 109 " pdb=" CB LYS C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 2168 not shown) Planarity restraints: 2300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 106 " -0.118 2.00e-02 2.50e+03 6.65e-02 1.11e+02 pdb=" CG TRP E 106 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP E 106 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP E 106 " 0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP E 106 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP E 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 106 " 0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 106 " -0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 106 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP E 106 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 333 " -0.120 2.00e-02 2.50e+03 6.73e-02 9.06e+01 pdb=" CG TYR E 333 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 333 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR E 333 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR E 333 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR E 333 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR E 333 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 333 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 80 " 0.100 2.00e-02 2.50e+03 5.74e-02 8.24e+01 pdb=" CG TRP A 80 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 80 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 80 " -0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP A 80 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP A 80 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A 80 " -0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 80 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 80 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 80 " 0.074 2.00e-02 2.50e+03 ... (remaining 2297 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 779 2.76 - 3.29: 14479 3.29 - 3.83: 20019 3.83 - 4.36: 25123 4.36 - 4.90: 40654 Nonbonded interactions: 101054 Sorted by model distance: nonbonded pdb=" O ALA D 23 " pdb=" C VAL D 24 " model vdw 2.225 3.270 nonbonded pdb=" O ALA C 90 " pdb=" NH1 ARG C 151 " model vdw 2.249 3.120 nonbonded pdb=" O ALA D 23 " pdb=" O VAL D 24 " model vdw 2.261 3.040 nonbonded pdb=" CG PRO E 37 " pdb=" NE2 GLN E 73 " model vdw 2.282 3.520 nonbonded pdb=" N LYS D 11 " pdb=" O VAL D 24 " model vdw 2.302 3.120 ... (remaining 101049 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 or (resid 75 through 76 and (n \ ame N or name CA or name C or name O or name CB )) or resid 77 through 79 or (re \ sid 80 through 81 and (name N or name CA or name C or name O or name CB )) or re \ sid 82 through 95 or (resid 96 and (name N or name CA or name C or name O or nam \ e CB )) or resid 97 through 126 or (resid 127 and (name N or name CA or name C o \ r name O or name CB )) or resid 128 through 143 or (resid 144 and (name N or nam \ e CA or name C or name O or name CB )) or resid 145 through 165 or (resid 166 an \ d (name N or name CA or name C or name O or name CB )) or resid 167 through 168 \ or (resid 169 through 172 and (name N or name CA or name C or name O or name CB \ )) or resid 173 through 176 or (resid 177 through 179 and (name N or name CA or \ name C or name O or name CB )) or resid 180 through 204 or (resid 205 and (name \ N or name CA or name C or name O or name CB )) or resid 206 through 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 231 or (resid 232 through 233 and (name N or name CA or name C or name O or \ name CB )) or resid 234 through 244 or (resid 245 and (name N or name CA or name \ C or name O or name CB )) or resid 246 through 286 or (resid 287 and (name N or \ name CA or name C or name O or name CB )) or resid 288 through 316 or (resid 31 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) or re \ sid 341 through 367 or (resid 368 through 369 and (name N or name CA or name C o \ r name O or name CB )) or resid 370 through 391 or resid 501)) selection = (chain 'D' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 14 or (resid 21 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 131 or (res \ id 132 and (name N or name CA or name C or name O or name CB )) or resid 133 thr \ ough 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) \ or resid 173 through 177 or (resid 178 through 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 180 through 190 or (resid 191 through 192 a \ nd (name N or name CA or name C or name O or name CB )) or resid 193 or (resid 1 \ 94 through 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 226 or (resid 227 and (name N or name CA or name C or name O or nam \ e CB )) or resid 228 or (resid 229 and (name N or name CA or name C or name O or \ name CB )) or resid 230 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 289 or (resid 290 and (name N o \ r name CA or name C or name O or name CB )) or resid 291 through 292 or (resid 2 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 294 through \ 325 or (resid 326 and (name N or name CA or name C or name O or name CB )) or r \ esid 327 through 365 or (resid 366 and (name N or name CA or name C or name O or \ name CB )) or resid 367 through 391 or resid 501)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.220 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.290 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.012 0.134 13057 Z= 0.821 Angle : 1.823 19.566 17886 Z= 1.236 Chirality : 0.095 0.650 2171 Planarity : 0.012 0.120 2300 Dihedral : 12.983 88.073 4564 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 0.65 % Allowed : 4.95 % Favored : 94.40 % Cbeta Deviations : 0.31 % 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: -2.52 (0.18), residues: 1744 helix: -1.59 (0.15), residues: 810 sheet: -1.15 (0.43), residues: 143 loop : -1.74 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.023 TRP E 106 HIS 0.013 0.003 HIS C 94 PHE 0.062 0.012 PHE D 238 TYR 0.120 0.015 TYR E 333 ARG 0.011 0.001 ARG E 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 361 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7553 (ttt180) cc_final: 0.7203 (tmm160) REVERT: A 186 LEU cc_start: 0.9459 (tp) cc_final: 0.9247 (tt) REVERT: A 203 ASP cc_start: 0.8131 (m-30) cc_final: 0.7925 (t0) REVERT: A 279 PHE cc_start: 0.8653 (t80) cc_final: 0.8356 (t80) REVERT: B 13 TRP cc_start: 0.8172 (m100) cc_final: 0.7916 (m100) REVERT: B 68 SER cc_start: 0.8177 (t) cc_final: 0.7429 (t) REVERT: C 91 LEU cc_start: 0.8082 (mt) cc_final: 0.7825 (mp) REVERT: C 149 MET cc_start: 0.8851 (mtp) cc_final: 0.8483 (mtp) REVERT: C 316 GLU cc_start: 0.8770 (pt0) cc_final: 0.8388 (tt0) REVERT: C 380 PHE cc_start: 0.7776 (m-80) cc_final: 0.7025 (m-80) REVERT: D 99 GLN cc_start: 0.8718 (mt0) cc_final: 0.8267 (mt0) REVERT: D 100 ASN cc_start: 0.8012 (m-40) cc_final: 0.7762 (m110) REVERT: D 101 ILE cc_start: 0.8197 (mt) cc_final: 0.7906 (mm) REVERT: D 269 MET cc_start: 0.4923 (mmp) cc_final: 0.4378 (mtt) REVERT: D 386 LEU cc_start: 0.8926 (mt) cc_final: 0.8705 (mm) REVERT: E 76 GLN cc_start: 0.7464 (mm-40) cc_final: 0.7257 (mm-40) REVERT: E 281 LEU cc_start: 0.9194 (mt) cc_final: 0.8807 (mm) outliers start: 8 outliers final: 1 residues processed: 368 average time/residue: 0.2805 time to fit residues: 143.6136 Evaluate side-chains 223 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 275 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 0.1980 chunk 136 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN B 127 ASN B 231 ASN C 87 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN E 39 ASN E 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13057 Z= 0.234 Angle : 0.778 8.284 17886 Z= 0.406 Chirality : 0.049 0.239 2171 Planarity : 0.005 0.075 2300 Dihedral : 8.295 85.383 1965 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.10 % Rotamer: Outliers : 3.08 % Allowed : 13.39 % Favored : 83.52 % 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: -1.33 (0.19), residues: 1744 helix: -0.25 (0.17), residues: 836 sheet: -1.35 (0.37), residues: 177 loop : -1.39 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 12 HIS 0.013 0.002 HIS C 325 PHE 0.035 0.002 PHE A 83 TYR 0.024 0.002 TYR D 194 ARG 0.008 0.001 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7199 (tmm160) REVERT: B 68 SER cc_start: 0.8137 (t) cc_final: 0.6827 (t) REVERT: B 127 ASN cc_start: 0.8827 (t0) cc_final: 0.8336 (t0) REVERT: B 128 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5596 (ttm) REVERT: C 66 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7274 (mmm160) REVERT: C 86 PHE cc_start: 0.7189 (m-80) cc_final: 0.6259 (m-80) REVERT: C 380 PHE cc_start: 0.7644 (m-80) cc_final: 0.6935 (m-80) REVERT: D 100 ASN cc_start: 0.8232 (m-40) cc_final: 0.7611 (t0) REVERT: D 269 MET cc_start: 0.5156 (mmp) cc_final: 0.4839 (mtt) REVERT: D 380 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: E 263 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7356 (pt0) REVERT: E 281 LEU cc_start: 0.9086 (mt) cc_final: 0.8869 (mm) outliers start: 38 outliers final: 14 residues processed: 288 average time/residue: 0.2555 time to fit residues: 106.5180 Evaluate side-chains 230 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 50.0000 chunk 49 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN C 87 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13057 Z= 0.197 Angle : 0.680 8.604 17886 Z= 0.352 Chirality : 0.046 0.209 2171 Planarity : 0.005 0.045 2300 Dihedral : 7.536 85.049 1963 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.08 % Allowed : 18.43 % Favored : 78.49 % 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: -1.05 (0.20), residues: 1744 helix: 0.20 (0.18), residues: 831 sheet: -1.43 (0.36), residues: 182 loop : -1.48 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 30 HIS 0.006 0.001 HIS C 325 PHE 0.023 0.002 PHE E 328 TYR 0.023 0.002 TYR E 34 ARG 0.004 0.001 ARG E 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7884 (ttt180) cc_final: 0.7231 (tmm160) REVERT: A 51 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8375 (pp) REVERT: B 127 ASN cc_start: 0.8842 (t0) cc_final: 0.8319 (t0) REVERT: B 173 LYS cc_start: 0.8527 (mtmm) cc_final: 0.7963 (mmtm) REVERT: B 256 ILE cc_start: 0.8742 (pt) cc_final: 0.8402 (mt) REVERT: C 66 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7278 (mmm160) REVERT: C 164 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 380 PHE cc_start: 0.7657 (m-80) cc_final: 0.6886 (m-80) REVERT: D 100 ASN cc_start: 0.8149 (m-40) cc_final: 0.7587 (t0) REVERT: D 174 ARG cc_start: 0.9084 (mmm-85) cc_final: 0.8853 (mmm160) REVERT: D 265 LEU cc_start: 0.5777 (mt) cc_final: 0.5455 (mt) REVERT: D 269 MET cc_start: 0.5651 (mmp) cc_final: 0.4908 (mtt) REVERT: D 322 LYS cc_start: 0.7929 (mmtp) cc_final: 0.7680 (mmtm) REVERT: D 380 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: E 263 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7353 (pt0) outliers start: 38 outliers final: 17 residues processed: 254 average time/residue: 0.2605 time to fit residues: 94.7645 Evaluate side-chains 224 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0470 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 150 optimal weight: 0.0070 chunk 45 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13057 Z= 0.250 Angle : 0.669 8.575 17886 Z= 0.343 Chirality : 0.046 0.229 2171 Planarity : 0.005 0.043 2300 Dihedral : 7.153 82.082 1963 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.06 % Allowed : 19.64 % Favored : 76.30 % 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: -0.95 (0.20), residues: 1744 helix: 0.41 (0.18), residues: 828 sheet: -1.47 (0.36), residues: 179 loop : -1.58 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 141 HIS 0.005 0.001 HIS C 325 PHE 0.019 0.002 PHE C 234 TYR 0.021 0.002 TYR D 194 ARG 0.004 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7956 (ttt180) cc_final: 0.7271 (tmm160) REVERT: A 173 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: A 230 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7591 (mmm-85) REVERT: B 173 LYS cc_start: 0.8550 (mtmm) cc_final: 0.7982 (mmtm) REVERT: C 66 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7206 (mmm160) REVERT: C 103 PHE cc_start: 0.9206 (t80) cc_final: 0.8967 (t80) REVERT: C 164 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8291 (tm-30) REVERT: C 212 MET cc_start: 0.7803 (mmp) cc_final: 0.7354 (mmp) REVERT: C 380 PHE cc_start: 0.7663 (m-80) cc_final: 0.6879 (m-80) REVERT: D 99 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8501 (tm-30) REVERT: D 100 ASN cc_start: 0.8282 (m-40) cc_final: 0.8032 (t0) REVERT: D 265 LEU cc_start: 0.5764 (mt) cc_final: 0.5441 (mt) REVERT: D 269 MET cc_start: 0.5630 (mmp) cc_final: 0.5150 (mtt) REVERT: D 351 GLN cc_start: 0.7569 (mp10) cc_final: 0.7288 (pm20) REVERT: D 367 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8435 (tm-30) REVERT: D 380 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8597 (m-80) outliers start: 50 outliers final: 26 residues processed: 252 average time/residue: 0.2402 time to fit residues: 88.6298 Evaluate side-chains 227 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN C 87 GLN C 168 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13057 Z= 0.355 Angle : 0.734 7.906 17886 Z= 0.376 Chirality : 0.047 0.218 2171 Planarity : 0.005 0.040 2300 Dihedral : 6.999 80.675 1963 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.71 % Allowed : 20.05 % Favored : 75.24 % 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: -1.07 (0.20), residues: 1744 helix: 0.34 (0.18), residues: 822 sheet: -1.49 (0.37), residues: 179 loop : -1.66 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 141 HIS 0.005 0.001 HIS C 325 PHE 0.020 0.002 PHE D 326 TYR 0.029 0.002 TYR B 145 ARG 0.006 0.001 ARG E 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: A 257 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8166 (tt) REVERT: B 64 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.5866 (t70) REVERT: B 173 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8053 (mmtm) REVERT: C 66 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7311 (mmm160) REVERT: C 164 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8270 (tm-30) REVERT: C 212 MET cc_start: 0.7751 (mmp) cc_final: 0.7395 (mmp) REVERT: D 99 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8586 (tm-30) REVERT: D 188 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8673 (mm) REVERT: D 367 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8583 (tp-100) REVERT: D 380 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8814 (m-80) outliers start: 58 outliers final: 37 residues processed: 240 average time/residue: 0.2421 time to fit residues: 84.9292 Evaluate side-chains 229 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 13 optimal weight: 0.0370 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 162 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 52 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13057 Z= 0.192 Angle : 0.655 11.042 17886 Z= 0.333 Chirality : 0.045 0.218 2171 Planarity : 0.005 0.043 2300 Dihedral : 6.563 79.462 1963 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.92 % Allowed : 22.97 % Favored : 74.11 % 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: -0.80 (0.20), residues: 1744 helix: 0.57 (0.18), residues: 826 sheet: -1.44 (0.37), residues: 173 loop : -1.54 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 141 HIS 0.004 0.001 HIS C 325 PHE 0.040 0.001 PHE A 83 TYR 0.023 0.002 TYR D 194 ARG 0.004 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 PHE cc_start: 0.8555 (t80) cc_final: 0.8223 (t80) REVERT: B 64 ASP cc_start: 0.6375 (OUTLIER) cc_final: 0.6128 (t70) REVERT: B 66 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7102 (t80) REVERT: B 68 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7689 (t) REVERT: B 173 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8074 (mmtm) REVERT: C 164 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 273 LEU cc_start: 0.8480 (tt) cc_final: 0.8158 (pp) REVERT: D 99 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8122 (tp-100) REVERT: D 100 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7981 (t0) REVERT: D 380 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: D 390 ARG cc_start: 0.7235 (mmt180) cc_final: 0.7034 (mmt-90) REVERT: E 310 PHE cc_start: 0.8784 (t80) cc_final: 0.8578 (t80) outliers start: 36 outliers final: 18 residues processed: 228 average time/residue: 0.2475 time to fit residues: 82.6560 Evaluate side-chains 217 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 122 optimal weight: 30.0000 chunk 141 optimal weight: 0.0070 chunk 94 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13057 Z= 0.211 Angle : 0.668 9.099 17886 Z= 0.337 Chirality : 0.045 0.208 2171 Planarity : 0.005 0.152 2300 Dihedral : 6.397 78.935 1963 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.41 % Allowed : 23.46 % Favored : 73.13 % 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 (0.20), residues: 1744 helix: 0.67 (0.18), residues: 826 sheet: -1.38 (0.37), residues: 173 loop : -1.52 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 137 HIS 0.004 0.001 HIS C 325 PHE 0.027 0.001 PHE C 234 TYR 0.014 0.001 TYR B 145 ARG 0.016 0.001 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 PHE cc_start: 0.8610 (t80) cc_final: 0.8266 (t80) REVERT: B 66 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7305 (t80) REVERT: B 68 SER cc_start: 0.8275 (m) cc_final: 0.7483 (t) REVERT: B 173 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8030 (mmmt) REVERT: C 164 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8243 (tm-30) REVERT: C 212 MET cc_start: 0.7433 (tpp) cc_final: 0.7054 (tpp) REVERT: C 216 GLU cc_start: 0.7762 (pt0) cc_final: 0.7280 (pm20) REVERT: C 269 MET cc_start: 0.8925 (tpt) cc_final: 0.8103 (mtt) REVERT: D 100 ASN cc_start: 0.8609 (m-40) cc_final: 0.8315 (t0) REVERT: D 188 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8609 (mm) REVERT: D 367 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8517 (tp40) REVERT: D 380 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8784 (m-80) REVERT: E 310 PHE cc_start: 0.8795 (t80) cc_final: 0.8590 (t80) outliers start: 42 outliers final: 26 residues processed: 236 average time/residue: 0.2365 time to fit residues: 82.2625 Evaluate side-chains 223 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 352 PHE Chi-restraints excluded: chain D residue 380 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 152 optimal weight: 0.3980 chunk 160 optimal weight: 0.0770 chunk 146 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN E 150 GLN E 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13057 Z= 0.180 Angle : 0.670 14.574 17886 Z= 0.335 Chirality : 0.045 0.219 2171 Planarity : 0.005 0.043 2300 Dihedral : 6.176 78.540 1963 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.17 % Allowed : 23.94 % 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: -0.69 (0.20), residues: 1744 helix: 0.71 (0.18), residues: 829 sheet: -1.56 (0.35), residues: 183 loop : -1.49 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 207 HIS 0.003 0.001 HIS C 325 PHE 0.027 0.001 PHE A 83 TYR 0.021 0.001 TYR D 194 ARG 0.004 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8100 (ptm) cc_final: 0.7751 (ttp) REVERT: A 230 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7262 (mmm-85) REVERT: A 279 PHE cc_start: 0.8576 (t80) cc_final: 0.8279 (t80) REVERT: B 68 SER cc_start: 0.7970 (OUTLIER) cc_final: 0.7532 (t) REVERT: B 169 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8575 (mp0) REVERT: B 173 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8023 (mmmt) REVERT: C 53 MET cc_start: 0.8318 (mtp) cc_final: 0.7951 (ptp) REVERT: C 109 LYS cc_start: 0.6151 (tptp) cc_final: 0.5324 (mtpt) REVERT: C 164 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8193 (tm-30) REVERT: D 188 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8595 (mm) REVERT: D 316 GLU cc_start: 0.8603 (pt0) cc_final: 0.8385 (pp20) REVERT: D 367 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8503 (tp-100) REVERT: E 150 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: E 310 PHE cc_start: 0.8748 (t80) cc_final: 0.8541 (t80) outliers start: 39 outliers final: 23 residues processed: 234 average time/residue: 0.2495 time to fit residues: 85.2388 Evaluate side-chains 224 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 141 optimal weight: 0.0370 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN E 188 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13057 Z= 0.205 Angle : 0.681 12.451 17886 Z= 0.344 Chirality : 0.045 0.259 2171 Planarity : 0.004 0.043 2300 Dihedral : 6.116 78.515 1963 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.76 % Allowed : 24.92 % Favored : 72.32 % 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: -0.58 (0.20), residues: 1744 helix: 0.78 (0.18), residues: 830 sheet: -1.43 (0.36), residues: 173 loop : -1.44 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.004 0.001 HIS C 325 PHE 0.021 0.002 PHE C 234 TYR 0.014 0.001 TYR B 145 ARG 0.010 0.001 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8484 (t80) cc_final: 0.8090 (t80) REVERT: A 279 PHE cc_start: 0.8585 (t80) cc_final: 0.8272 (t80) REVERT: B 68 SER cc_start: 0.8138 (OUTLIER) cc_final: 0.7706 (t) REVERT: B 169 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8569 (mp0) REVERT: B 173 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8079 (mmmt) REVERT: C 109 LYS cc_start: 0.6125 (tptp) cc_final: 0.5322 (mtpt) REVERT: C 164 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8230 (tm-30) REVERT: C 213 LEU cc_start: 0.8782 (tt) cc_final: 0.8398 (mp) REVERT: D 188 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8521 (mm) REVERT: D 367 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8551 (tp-100) outliers start: 34 outliers final: 28 residues processed: 226 average time/residue: 0.2456 time to fit residues: 82.0213 Evaluate side-chains 230 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 89 TYR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 159 optimal weight: 0.0030 chunk 138 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN E 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13057 Z= 0.243 Angle : 0.706 11.908 17886 Z= 0.353 Chirality : 0.045 0.256 2171 Planarity : 0.005 0.041 2300 Dihedral : 6.100 78.629 1963 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.76 % Allowed : 24.68 % Favored : 72.56 % 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: -0.59 (0.20), residues: 1744 helix: 0.79 (0.18), residues: 833 sheet: -1.48 (0.37), residues: 173 loop : -1.47 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS C 325 PHE 0.019 0.002 PHE C 103 TYR 0.019 0.002 TYR D 194 ARG 0.005 0.001 ARG D 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3488 Ramachandran restraints generated. 1744 Oldfield, 0 Emsley, 1744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8290 (tt) REVERT: A 279 PHE cc_start: 0.8610 (t80) cc_final: 0.8286 (t80) REVERT: B 68 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.7824 (t) REVERT: B 169 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8573 (mp0) REVERT: B 173 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8017 (mmmt) REVERT: C 109 LYS cc_start: 0.6169 (tptp) cc_final: 0.5357 (mtpt) REVERT: C 164 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8114 (tm-30) REVERT: C 212 MET cc_start: 0.7781 (tpp) cc_final: 0.7510 (tpp) REVERT: D 188 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8506 (mm) REVERT: D 367 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8625 (tp-100) outliers start: 34 outliers final: 27 residues processed: 226 average time/residue: 0.2482 time to fit residues: 82.3003 Evaluate side-chains 228 residues out of total 1410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 372 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.139242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100968 restraints weight = 33374.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104006 restraints weight = 17469.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.106064 restraints weight = 11234.509| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13057 Z= 0.194 Angle : 0.685 11.374 17886 Z= 0.343 Chirality : 0.044 0.235 2171 Planarity : 0.005 0.055 2300 Dihedral : 5.961 78.717 1963 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.44 % Allowed : 25.00 % Favored : 72.56 % 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: -0.56 (0.20), residues: 1744 helix: 0.85 (0.18), residues: 832 sheet: -1.45 (0.37), residues: 171 loop : -1.51 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.003 0.001 HIS C 325 PHE 0.030 0.001 PHE E 310 TYR 0.014 0.001 TYR B 145 ARG 0.005 0.000 ARG D 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.84 seconds wall clock time: 52 minutes 39.55 seconds (3159.55 seconds total)