Starting phenix.real_space_refine on Thu Feb 15 11:30:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oit_20081/02_2024/6oit_20081.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oit_20081/02_2024/6oit_20081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oit_20081/02_2024/6oit_20081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oit_20081/02_2024/6oit_20081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oit_20081/02_2024/6oit_20081.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oit_20081/02_2024/6oit_20081.pdb" } resolution = 3.5 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 7643 2.51 5 N 2101 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "C ARG 55": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 404": "NH1" <-> "NH2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D ARG 234": "NH1" <-> "NH2" Residue "D PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 234": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 308": "NH1" <-> "NH2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 388": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "F PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ARG 308": "NH1" <-> "NH2" Residue "F ARG 347": "NH1" <-> "NH2" Residue "F ARG 388": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12085 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1010 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1034 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain: "C" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2619 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 325} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1722 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2634 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 327} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2678 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 332} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 388 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 6.60, per 1000 atoms: 0.55 Number of scatterers: 12085 At special positions: 0 Unit cell: (98.44, 110.21, 145.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 2270 8.00 N 2101 7.00 C 7643 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 2.3 seconds 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 13 sheets defined 54.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 39 through 57 removed outlier: 3.589A pdb=" N SER A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 89 through 104 removed outlier: 4.078A pdb=" N ASP A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.667A pdb=" N GLU A 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 110 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 138 through 148 removed outlier: 4.214A pdb=" N MET A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.550A pdb=" N SER A 154 " --> pdb=" O MET A 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 56 Processing helix chain 'B' and resid 72 through 84 Processing helix chain 'B' and resid 89 through 102 removed outlier: 3.557A pdb=" N ASN B 93 " --> pdb=" O HIS B 89 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.597A pdb=" N ILE B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.921A pdb=" N THR B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.996A pdb=" N SER B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 99 removed outlier: 4.123A pdb=" N SER C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 124 Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.877A pdb=" N VAL C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.511A pdb=" N VAL C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 165 through 182 removed outlier: 3.730A pdb=" N GLY C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR C 178 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.831A pdb=" N VAL C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 Processing helix chain 'C' and resid 277 through 280 removed outlier: 3.761A pdb=" N LEU C 280 " --> pdb=" O PRO C 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 280' Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.630A pdb=" N ASN C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 3.563A pdb=" N ALA C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 318 removed outlier: 3.629A pdb=" N ILE C 318 " --> pdb=" O LEU C 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 315 through 318' Processing helix chain 'C' and resid 356 through 407 removed outlier: 3.935A pdb=" N TYR C 360 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN C 394 " --> pdb=" O HIS C 390 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 125 removed outlier: 3.950A pdb=" N HIS D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 139 removed outlier: 3.867A pdb=" N VAL D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 160 No H-bonds generated for 'chain 'D' and resid 157 through 160' Processing helix chain 'D' and resid 165 through 177 Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 188 through 196 removed outlier: 3.881A pdb=" N VAL D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 270 through 273 removed outlier: 3.857A pdb=" N ILE D 273 " --> pdb=" O VAL D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 270 through 273' Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'E' and resid 47 through 98 removed outlier: 3.942A pdb=" N LEU E 98 " --> pdb=" O HIS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.553A pdb=" N GLN E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 138 removed outlier: 3.858A pdb=" N VAL E 132 " --> pdb=" O SER E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 177 removed outlier: 3.814A pdb=" N LEU E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 196 removed outlier: 3.805A pdb=" N GLU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.912A pdb=" N CYS E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'E' and resid 307 through 313 Processing helix chain 'E' and resid 314 through 318 removed outlier: 3.575A pdb=" N ILE E 318 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 405 removed outlier: 3.723A pdb=" N HIS E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 92 Processing helix chain 'F' and resid 118 through 125 removed outlier: 4.180A pdb=" N HIS F 125 " --> pdb=" O GLN F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 138 removed outlier: 3.846A pdb=" N VAL F 132 " --> pdb=" O SER F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 removed outlier: 3.593A pdb=" N VAL F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 161 removed outlier: 4.032A pdb=" N GLY F 161 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 177 removed outlier: 3.668A pdb=" N GLY F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 196 removed outlier: 3.552A pdb=" N VAL F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 218 removed outlier: 4.548A pdb=" N LEU F 213 " --> pdb=" O GLY F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 273 removed outlier: 4.111A pdb=" N ILE F 273 " --> pdb=" O VAL F 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 270 through 273' Processing helix chain 'F' and resid 289 through 294 Processing helix chain 'F' and resid 295 through 298 removed outlier: 3.531A pdb=" N LEU F 298 " --> pdb=" O PHE F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 295 through 298' Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 358 through 408 Processing helix chain 'G' and resid 47 through 57 removed outlier: 3.587A pdb=" N ALA G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 87 through 92 Processing sheet with id=AA1, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AA2, first strand: chain 'C' and resid 184 through 186 removed outlier: 4.037A pdb=" N PHE C 225 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 227 " --> pdb=" O PHE D 336 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 336 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 268 removed outlier: 3.940A pdb=" N GLY C 267 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 335 through 339 removed outlier: 6.656A pdb=" N VAL D 184 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL D 185 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 161 through 162 removed outlier: 3.681A pdb=" N LYS D 162 " --> pdb=" O GLN D 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 267 through 268 removed outlier: 3.742A pdb=" N GLY D 267 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 removed outlier: 7.044A pdb=" N VAL E 185 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AA9, first strand: chain 'E' and resid 225 through 228 Processing sheet with id=AB1, first strand: chain 'E' and resid 265 through 268 removed outlier: 6.315A pdb=" N VAL E 304 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 338 through 339 removed outlier: 3.738A pdb=" N PHE F 225 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 184 through 186 removed outlier: 3.606A pdb=" N ILE F 228 " --> pdb=" O VAL F 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.148A pdb=" N VAL F 304 " --> pdb=" O LEU F 266 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1698 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: 3.15 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2892 1.33 - 1.45: 2311 1.45 - 1.57: 6970 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12288 Sorted by residual: bond pdb=" N VAL F 283 " pdb=" CA VAL F 283 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.01e+01 bond pdb=" N ILE C 241 " pdb=" CA ILE C 241 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.25e-02 6.40e+03 8.26e+00 bond pdb=" N GLY F 289 " pdb=" CA GLY F 289 " ideal model delta sigma weight residual 1.445 1.473 -0.028 1.01e-02 9.80e+03 7.88e+00 bond pdb=" N VAL D 237 " pdb=" CA VAL D 237 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.52e+00 bond pdb=" N CYS F 282 " pdb=" CA CYS F 282 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.35e-02 5.49e+03 7.01e+00 ... (remaining 12283 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.60: 240 105.60 - 112.93: 6445 112.93 - 120.26: 5046 120.26 - 127.59: 4747 127.59 - 134.92: 92 Bond angle restraints: 16570 Sorted by residual: angle pdb=" C LEU F 252 " pdb=" N LYS F 253 " pdb=" CA LYS F 253 " ideal model delta sigma weight residual 120.94 130.86 -9.92 1.90e+00 2.77e-01 2.73e+01 angle pdb=" N THR A 136 " pdb=" CA THR A 136 " pdb=" C THR A 136 " ideal model delta sigma weight residual 109.81 120.39 -10.58 2.21e+00 2.05e-01 2.29e+01 angle pdb=" N THR B 136 " pdb=" CA THR B 136 " pdb=" C THR B 136 " ideal model delta sigma weight residual 109.81 119.89 -10.08 2.21e+00 2.05e-01 2.08e+01 angle pdb=" N GLU E 220 " pdb=" CA GLU E 220 " pdb=" C GLU E 220 " ideal model delta sigma weight residual 110.91 116.01 -5.10 1.17e+00 7.31e-01 1.90e+01 angle pdb=" CA GLY C 238 " pdb=" C GLY C 238 " pdb=" O GLY C 238 " ideal model delta sigma weight residual 121.47 117.63 3.84 9.00e-01 1.23e+00 1.82e+01 ... (remaining 16565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 6948 15.41 - 30.83: 399 30.83 - 46.24: 120 46.24 - 61.66: 13 61.66 - 77.07: 9 Dihedral angle restraints: 7489 sinusoidal: 3050 harmonic: 4439 Sorted by residual: dihedral pdb=" CA ILE D 318 " pdb=" C ILE D 318 " pdb=" N SER D 319 " pdb=" CA SER D 319 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA PRO D 262 " pdb=" C PRO D 262 " pdb=" N PRO D 263 " pdb=" CA PRO D 263 " ideal model delta harmonic sigma weight residual -180.00 -157.07 -22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA LEU E 256 " pdb=" C LEU E 256 " pdb=" N PRO E 257 " pdb=" CA PRO E 257 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1576 0.075 - 0.151: 249 0.151 - 0.226: 29 0.226 - 0.302: 10 0.302 - 0.377: 2 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CB ILE D 330 " pdb=" CA ILE D 330 " pdb=" CG1 ILE D 330 " pdb=" CG2 ILE D 330 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CB ILE F 228 " pdb=" CA ILE F 228 " pdb=" CG1 ILE F 228 " pdb=" CG2 ILE F 228 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CG LEU B 128 " pdb=" CB LEU B 128 " pdb=" CD1 LEU B 128 " pdb=" CD2 LEU B 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1863 not shown) Planarity restraints: 2139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 234 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ARG D 234 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG D 234 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO D 235 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 234 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ARG F 234 " 0.063 2.00e-02 2.50e+03 pdb=" O ARG F 234 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO F 235 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 386 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C VAL C 386 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL C 386 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU C 387 " -0.019 2.00e-02 2.50e+03 ... (remaining 2136 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1991 2.77 - 3.30: 11162 3.30 - 3.83: 18808 3.83 - 4.37: 21700 4.37 - 4.90: 37580 Nonbonded interactions: 91241 Sorted by model distance: nonbonded pdb=" O ILE F 273 " pdb=" NH2 ARG F 291 " model vdw 2.233 2.520 nonbonded pdb=" O GLN C 239 " pdb=" CB ASP C 250 " model vdw 2.247 3.440 nonbonded pdb=" O GLU E 166 " pdb=" OG SER E 169 " model vdw 2.308 2.440 nonbonded pdb=" O ILE A 132 " pdb=" OG1 THR A 136 " model vdw 2.321 2.440 nonbonded pdb=" O ARG E 301 " pdb=" OG SER E 319 " model vdw 2.327 2.440 ... (remaining 91236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 39 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 161)) } ncs_group { reference = (chain 'C' and (resid 52 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 or resid 117 through 219 or ( \ resid 220 and (name N or name CA or name C or name O or name CB )) or resid 221 \ through 352 or resid 357 through 405)) selection = (chain 'E' and (resid 52 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 or resid 117 through 352 or r \ esid 357 through 405)) selection = (chain 'F' and (resid 52 through 98 or resid 117 through 218 or (resid 219 throu \ gh 220 and (name N or name CA or name C or name O or name CB )) or resid 221 thr \ ough 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.560 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: 3.640 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.500 Find NCS groups from input model: 0.800 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: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.006 0.066 12288 Z= 0.422 Angle : 1.020 10.583 16570 Z= 0.557 Chirality : 0.059 0.377 1866 Planarity : 0.008 0.071 2139 Dihedral : 11.442 77.069 4621 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.45 % Allowed : 7.18 % Favored : 92.37 % 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: -2.34 (0.18), residues: 1506 helix: -1.22 (0.16), residues: 732 sheet: -3.06 (0.83), residues: 30 loop : -1.78 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 127 HIS 0.018 0.003 HIS A 118 PHE 0.042 0.003 PHE A 104 TYR 0.022 0.002 TYR E 198 ARG 0.013 0.001 ARG F 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 301 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8769 (tp30) cc_final: 0.8557 (tp30) REVERT: C 245 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8258 (mt) REVERT: C 357 MET cc_start: 0.7360 (ptp) cc_final: 0.7100 (ptm) REVERT: C 367 MET cc_start: 0.7778 (tpp) cc_final: 0.7271 (tpp) REVERT: G 74 MET cc_start: 0.7038 (tpt) cc_final: 0.6695 (tpp) outliers start: 6 outliers final: 2 residues processed: 307 average time/residue: 0.2833 time to fit residues: 119.4194 Evaluate side-chains 180 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain E residue 237 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 0.0370 chunk 45 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS B 63 ASN B 111 GLN B 118 HIS C 92 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN D 201 HIS D 232 ASN D 246 GLN D 297 ASN E 65 ASN E 232 ASN E 297 ASN E 303 GLN F 52 ASN F 167 ASN F 297 ASN ** F 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12288 Z= 0.191 Angle : 0.584 8.020 16570 Z= 0.299 Chirality : 0.041 0.173 1866 Planarity : 0.005 0.057 2139 Dihedral : 5.189 56.818 1656 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.25 % Allowed : 11.40 % Favored : 85.35 % 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: -0.41 (0.20), residues: 1506 helix: 0.82 (0.19), residues: 751 sheet: -2.88 (0.86), residues: 30 loop : -1.34 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 82 HIS 0.006 0.001 HIS A 118 PHE 0.022 0.002 PHE E 393 TYR 0.018 0.001 TYR D 286 ARG 0.006 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: C 245 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 357 MET cc_start: 0.7346 (ptp) cc_final: 0.6922 (ptm) REVERT: E 63 MET cc_start: 0.7962 (mtt) cc_final: 0.7731 (mtm) REVERT: E 369 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7566 (tm-30) REVERT: F 213 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6162 (pt) REVERT: F 387 LEU cc_start: 0.8975 (tt) cc_final: 0.8757 (mp) outliers start: 43 outliers final: 18 residues processed: 222 average time/residue: 0.2426 time to fit residues: 77.5441 Evaluate side-chains 188 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 342 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS C 340 ASN D 232 ASN D 246 GLN F 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12288 Z= 0.296 Angle : 0.614 7.549 16570 Z= 0.312 Chirality : 0.044 0.162 1866 Planarity : 0.005 0.058 2139 Dihedral : 4.951 55.733 1653 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.08 % Allowed : 12.16 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1506 helix: 1.48 (0.19), residues: 754 sheet: -2.55 (0.87), residues: 30 loop : -1.22 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 127 HIS 0.009 0.001 HIS A 141 PHE 0.023 0.002 PHE E 299 TYR 0.016 0.002 TYR C 296 ARG 0.005 0.001 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 175 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: C 74 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8363 (mt) REVERT: C 170 GLN cc_start: 0.8069 (tp40) cc_final: 0.7601 (tp-100) REVERT: C 245 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8151 (mt) REVERT: C 281 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8690 (tp) REVERT: C 348 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7361 (t80) REVERT: D 133 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5944 (tp) REVERT: D 329 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7607 (pt) REVERT: E 63 MET cc_start: 0.7965 (mtt) cc_final: 0.7725 (mtm) REVERT: E 369 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7572 (tm-30) REVERT: F 387 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8753 (mp) outliers start: 54 outliers final: 29 residues processed: 217 average time/residue: 0.2308 time to fit residues: 72.8224 Evaluate side-chains 193 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 402 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 240 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12288 Z= 0.183 Angle : 0.527 8.522 16570 Z= 0.265 Chirality : 0.041 0.167 1866 Planarity : 0.004 0.049 2139 Dihedral : 4.530 51.150 1653 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.78 % Allowed : 13.29 % Favored : 82.93 % 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: 0.83 (0.22), residues: 1506 helix: 2.09 (0.19), residues: 747 sheet: -2.51 (0.89), residues: 30 loop : -1.01 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.005 0.001 HIS B 141 PHE 0.026 0.002 PHE F 76 TYR 0.010 0.001 TYR C 296 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 178 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7515 (ttm170) REVERT: C 74 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8360 (mt) REVERT: C 170 GLN cc_start: 0.7998 (tp40) cc_final: 0.7749 (tp40) REVERT: C 245 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8029 (mt) REVERT: C 311 MET cc_start: 0.8274 (ttp) cc_final: 0.7906 (ttm) REVERT: C 348 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7239 (t80) REVERT: C 381 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8035 (mt) REVERT: D 133 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5928 (tp) REVERT: E 63 MET cc_start: 0.7962 (mtt) cc_final: 0.7751 (mtm) REVERT: E 71 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: E 369 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7525 (tm-30) REVERT: E 385 GLN cc_start: 0.7042 (mt0) cc_final: 0.6824 (mt0) REVERT: F 387 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8714 (mp) outliers start: 50 outliers final: 27 residues processed: 216 average time/residue: 0.2414 time to fit residues: 74.7023 Evaluate side-chains 197 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 402 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12288 Z= 0.193 Angle : 0.521 7.541 16570 Z= 0.262 Chirality : 0.041 0.201 1866 Planarity : 0.004 0.050 2139 Dihedral : 4.356 47.190 1653 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.85 % Allowed : 14.05 % Favored : 82.10 % 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: 1.16 (0.22), residues: 1506 helix: 2.42 (0.19), residues: 746 sheet: -2.47 (0.91), residues: 30 loop : -0.89 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.007 0.001 HIS B 141 PHE 0.027 0.002 PHE F 76 TYR 0.013 0.001 TYR C 296 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7470 (ttm170) REVERT: C 74 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8380 (mt) REVERT: C 170 GLN cc_start: 0.7991 (tp40) cc_final: 0.7357 (tp40) REVERT: C 245 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8025 (mt) REVERT: C 311 MET cc_start: 0.8277 (ttp) cc_final: 0.8047 (ttm) REVERT: C 348 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7270 (t80) REVERT: C 381 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8119 (mt) REVERT: D 133 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5903 (tp) REVERT: E 63 MET cc_start: 0.7958 (mtt) cc_final: 0.7702 (mtm) REVERT: E 369 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7416 (tm-30) REVERT: E 385 GLN cc_start: 0.7028 (mt0) cc_final: 0.6809 (mt0) outliers start: 51 outliers final: 33 residues processed: 216 average time/residue: 0.2278 time to fit residues: 71.6288 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 402 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 76 optimal weight: 0.3980 chunk 139 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12288 Z= 0.231 Angle : 0.555 8.840 16570 Z= 0.276 Chirality : 0.042 0.262 1866 Planarity : 0.004 0.049 2139 Dihedral : 4.349 44.918 1653 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.00 % Allowed : 14.12 % Favored : 81.87 % 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: 1.22 (0.22), residues: 1506 helix: 2.45 (0.19), residues: 752 sheet: -2.43 (0.92), residues: 30 loop : -0.88 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 127 HIS 0.009 0.001 HIS B 141 PHE 0.029 0.002 PHE F 76 TYR 0.014 0.001 TYR C 296 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7722 (ttm170) REVERT: A 139 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6944 (m-70) REVERT: C 65 ASN cc_start: 0.7956 (m110) cc_final: 0.7723 (m-40) REVERT: C 74 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8391 (mt) REVERT: C 170 GLN cc_start: 0.7999 (tp40) cc_final: 0.7761 (tp40) REVERT: C 245 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8031 (mt) REVERT: C 311 MET cc_start: 0.8297 (ttp) cc_final: 0.8062 (ttm) REVERT: C 348 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7315 (t80) REVERT: C 381 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8125 (mt) REVERT: D 133 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5907 (tp) REVERT: E 63 MET cc_start: 0.7922 (mtt) cc_final: 0.7666 (mtm) REVERT: E 369 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7447 (tm-30) outliers start: 53 outliers final: 42 residues processed: 209 average time/residue: 0.2321 time to fit residues: 70.2966 Evaluate side-chains 210 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 162 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 402 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 66 optimal weight: 0.0010 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12288 Z= 0.169 Angle : 0.523 10.304 16570 Z= 0.258 Chirality : 0.040 0.300 1866 Planarity : 0.004 0.047 2139 Dihedral : 4.129 40.401 1653 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.85 % Allowed : 15.26 % Favored : 80.89 % 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: 1.50 (0.22), residues: 1506 helix: 2.72 (0.19), residues: 748 sheet: -2.34 (0.93), residues: 30 loop : -0.76 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 372 HIS 0.007 0.001 HIS B 141 PHE 0.033 0.001 PHE F 76 TYR 0.011 0.001 TYR C 296 ARG 0.005 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7687 (ttm170) REVERT: A 139 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6949 (m-70) REVERT: C 65 ASN cc_start: 0.8009 (m110) cc_final: 0.7793 (m-40) REVERT: C 66 LYS cc_start: 0.7226 (ttpt) cc_final: 0.7002 (tttp) REVERT: C 74 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8373 (mt) REVERT: C 170 GLN cc_start: 0.7983 (tp40) cc_final: 0.7777 (tp40) REVERT: C 245 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8048 (mt) REVERT: C 311 MET cc_start: 0.8237 (ttp) cc_final: 0.7857 (ttm) REVERT: C 348 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7244 (t80) REVERT: C 381 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8113 (mt) REVERT: D 133 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5905 (tp) REVERT: D 272 MET cc_start: 0.6797 (mpt) cc_final: 0.6578 (mpt) REVERT: E 63 MET cc_start: 0.7896 (mtt) cc_final: 0.7685 (mtm) REVERT: F 387 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8722 (mp) outliers start: 51 outliers final: 39 residues processed: 218 average time/residue: 0.2457 time to fit residues: 76.3644 Evaluate side-chains 212 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 92 GLN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.0470 chunk 138 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 232 ASN F 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12288 Z= 0.165 Angle : 0.533 11.499 16570 Z= 0.261 Chirality : 0.040 0.321 1866 Planarity : 0.004 0.047 2139 Dihedral : 4.046 37.651 1653 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.70 % Allowed : 16.01 % Favored : 80.29 % 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: 1.64 (0.22), residues: 1506 helix: 2.85 (0.19), residues: 748 sheet: -2.31 (0.92), residues: 30 loop : -0.71 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.011 0.001 HIS B 141 PHE 0.037 0.001 PHE F 76 TYR 0.013 0.001 TYR C 296 ARG 0.011 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 172 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7685 (ttm170) REVERT: A 139 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.6953 (m-70) REVERT: C 65 ASN cc_start: 0.7997 (m110) cc_final: 0.7794 (m-40) REVERT: C 74 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8374 (mt) REVERT: C 170 GLN cc_start: 0.7979 (tp40) cc_final: 0.7755 (tp40) REVERT: C 245 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8030 (mt) REVERT: C 311 MET cc_start: 0.8213 (ttp) cc_final: 0.7984 (ttm) REVERT: C 381 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8109 (mt) REVERT: D 133 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5961 (tp) REVERT: D 272 MET cc_start: 0.6781 (mpt) cc_final: 0.6523 (mpt) outliers start: 49 outliers final: 37 residues processed: 210 average time/residue: 0.2678 time to fit residues: 81.5872 Evaluate side-chains 204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN F 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12288 Z= 0.201 Angle : 0.553 11.634 16570 Z= 0.271 Chirality : 0.041 0.316 1866 Planarity : 0.004 0.048 2139 Dihedral : 4.065 35.091 1653 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.70 % Allowed : 16.24 % Favored : 80.06 % 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: 1.67 (0.22), residues: 1506 helix: 2.84 (0.19), residues: 748 sheet: -1.99 (0.91), residues: 35 loop : -0.66 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 127 HIS 0.010 0.001 HIS B 141 PHE 0.016 0.001 PHE E 299 TYR 0.016 0.001 TYR C 296 ARG 0.010 0.000 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 169 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7705 (ttm170) REVERT: A 139 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.6992 (m-70) REVERT: C 65 ASN cc_start: 0.8036 (m110) cc_final: 0.7810 (m-40) REVERT: C 74 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8319 (mt) REVERT: C 170 GLN cc_start: 0.8027 (tp40) cc_final: 0.7359 (tp40) REVERT: C 245 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8053 (mt) REVERT: C 311 MET cc_start: 0.8240 (ttp) cc_final: 0.8003 (ttm) REVERT: C 348 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7238 (t80) REVERT: C 381 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8129 (mt) REVERT: D 133 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5948 (tp) REVERT: D 272 MET cc_start: 0.6886 (mpt) cc_final: 0.6618 (mpt) outliers start: 49 outliers final: 39 residues processed: 206 average time/residue: 0.2409 time to fit residues: 71.3459 Evaluate side-chains 208 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 342 ASP Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 137 optimal weight: 0.0980 chunk 118 optimal weight: 0.0040 chunk 12 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 36 optimal weight: 0.0770 overall best weight: 0.1750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.002 0.036 12288 Z= 0.130 Angle : 0.526 11.547 16570 Z= 0.255 Chirality : 0.039 0.302 1866 Planarity : 0.004 0.047 2139 Dihedral : 3.793 31.347 1653 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.79 % Allowed : 17.30 % Favored : 79.91 % 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: 1.95 (0.22), residues: 1506 helix: 3.12 (0.19), residues: 742 sheet: -1.85 (0.93), residues: 35 loop : -0.54 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 127 HIS 0.009 0.001 HIS B 141 PHE 0.037 0.001 PHE F 76 TYR 0.011 0.001 TYR C 296 ARG 0.009 0.000 ARG C 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: A 98 ARG cc_start: 0.7868 (ttp-110) cc_final: 0.7549 (ttm170) REVERT: C 65 ASN cc_start: 0.7980 (m110) cc_final: 0.7760 (m-40) REVERT: C 74 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8274 (mt) REVERT: C 170 GLN cc_start: 0.7925 (tp40) cc_final: 0.7279 (tp40) REVERT: C 245 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7988 (mt) REVERT: C 311 MET cc_start: 0.8182 (ttp) cc_final: 0.7924 (ttm) REVERT: C 348 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7080 (t80) REVERT: C 381 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8103 (mt) REVERT: D 133 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5968 (tp) REVERT: D 272 MET cc_start: 0.6850 (mpt) cc_final: 0.6587 (mpt) outliers start: 37 outliers final: 25 residues processed: 205 average time/residue: 0.2417 time to fit residues: 70.9997 Evaluate side-chains 198 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 275 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN F 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.188656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.159449 restraints weight = 13937.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158385 restraints weight = 18375.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.159056 restraints weight = 17058.515| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12288 Z= 0.182 Angle : 0.548 11.789 16570 Z= 0.266 Chirality : 0.041 0.323 1866 Planarity : 0.004 0.047 2139 Dihedral : 3.832 31.620 1653 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.64 % Allowed : 17.30 % Favored : 80.06 % 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: 1.94 (0.22), residues: 1506 helix: 3.07 (0.19), residues: 745 sheet: -1.81 (0.92), residues: 35 loop : -0.50 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 372 HIS 0.012 0.001 HIS B 141 PHE 0.037 0.002 PHE F 76 TYR 0.013 0.001 TYR C 296 ARG 0.008 0.000 ARG C 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2505.44 seconds wall clock time: 46 minutes 18.25 seconds (2778.25 seconds total)