Starting phenix.real_space_refine on Fri Mar 15 00:59:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyx_26197/03_2024/7tyx_26197.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyx_26197/03_2024/7tyx_26197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyx_26197/03_2024/7tyx_26197.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyx_26197/03_2024/7tyx_26197.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyx_26197/03_2024/7tyx_26197.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyx_26197/03_2024/7tyx_26197.pdb" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.098 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 6565 2.51 5 N 1739 2.21 5 O 1844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 97": "NH1" <-> "NH2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R GLU 210": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10219 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 804 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "P" Number of atoms: 285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Conformer: "B" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 266 Chain: "R" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2962 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1909 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 256 Unusual residues: {'NAG': 3, 'PLM': 8, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG P 18 " occ=0.50 Time building chain proxies: 5.96, per 1000 atoms: 0.58 Number of scatterers: 10219 At special positions: 0 Unit cell: (125.33, 107.07, 141.93, 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 1844 8.00 N 1739 7.00 C 6565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 125 " " NAG R 502 " - " ASN R 130 " " NAG R 503 " - " ASN R 73 " Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 45.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.583A pdb=" N ALA E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.342A pdb=" N CYS E 84 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 107 removed outlier: 5.670A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Proline residue: E 92 - end of helix Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.784A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 167 removed outlier: 3.791A pdb=" N ALA E 148 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Proline residue: E 153 - end of helix removed outlier: 3.580A pdb=" N LEU E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Proline residue: E 158 - end of helix Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'R' and resid 40 through 61 Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.245A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.931A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.553A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.851A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 4.063A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.510A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.652A pdb=" N LEU R 291 " --> pdb=" O ASN R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 331 Proline residue: R 304 - end of helix removed outlier: 3.600A pdb=" N ASN R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.569A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.576A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.502A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.899A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.573A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.273A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.536A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.785A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.667A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.581A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.540A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.676A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.713A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 removed outlier: 3.769A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.818A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.237A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.522A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.663A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.907A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.584A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.567A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.544A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.861A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1486 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: 3.12 Time building geometry restraints manager: 4.24 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: 1637 1.32 - 1.44: 2929 1.44 - 1.57: 5793 1.57 - 1.69: 0 1.69 - 1.82: 99 Bond restraints: 10458 Sorted by residual: bond pdb=" N GLY P 33 " pdb=" CA GLY P 33 " ideal model delta sigma weight residual 1.446 1.476 -0.030 1.06e-02 8.90e+03 8.03e+00 bond pdb=" N VAL P 32 " pdb=" CA VAL P 32 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N ASN P 35 " pdb=" CA ASN P 35 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.40e+00 bond pdb=" N SER P 34 " pdb=" CA SER P 34 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.86e+00 ... (remaining 10453 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.23: 259 106.23 - 113.18: 5593 113.18 - 120.12: 3771 120.12 - 127.07: 4409 127.07 - 134.01: 138 Bond angle restraints: 14170 Sorted by residual: angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 122.28 118.37 3.91 1.00e+00 1.00e+00 1.52e+01 angle pdb=" CA THR P 36 " pdb=" C THR P 36 " pdb=" O THR P 36 " ideal model delta sigma weight residual 121.55 117.78 3.77 1.06e+00 8.90e-01 1.27e+01 angle pdb=" C GLU R 255 " pdb=" N LYS R 256 " pdb=" CA LYS R 256 " ideal model delta sigma weight residual 121.87 127.54 -5.67 2.24e+00 1.99e-01 6.42e+00 angle pdb=" C ASN R 124 " pdb=" N ASN R 125 " pdb=" CA ASN R 125 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.40e+00 angle pdb=" CA ASN P 35 " pdb=" C ASN P 35 " pdb=" O ASN P 35 " ideal model delta sigma weight residual 120.55 117.99 2.56 1.06e+00 8.90e-01 5.82e+00 ... (remaining 14165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5854 17.83 - 35.67: 386 35.67 - 53.50: 87 53.50 - 71.33: 27 71.33 - 89.16: 9 Dihedral angle restraints: 6363 sinusoidal: 2648 harmonic: 3715 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 177.67 -84.67 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -48.61 -37.39 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 6360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1438 0.069 - 0.137: 128 0.137 - 0.206: 4 0.206 - 0.274: 1 0.274 - 0.343: 1 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 125 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA VAL P 32 " pdb=" N VAL P 32 " pdb=" C VAL P 32 " pdb=" CB VAL P 32 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1569 not shown) Planarity restraints: 1789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 304 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 91 " -0.021 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 92 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 92 " -0.018 5.00e-02 4.00e+02 ... (remaining 1786 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1833 2.76 - 3.30: 9357 3.30 - 3.83: 16551 3.83 - 4.37: 21526 4.37 - 4.90: 35885 Nonbonded interactions: 85152 Sorted by model distance: nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.231 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.261 2.440 nonbonded pdb=" O ILE R 347 " pdb=" OH TYR R 391 " model vdw 2.267 2.440 nonbonded pdb=" O GLU R 397 " pdb=" OG1 THR R 401 " model vdw 2.268 2.440 nonbonded pdb=" O LEU R 62 " pdb=" NH2 ARG R 74 " model vdw 2.269 2.520 ... (remaining 85147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.500 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.610 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.004 0.037 10458 Z= 0.237 Angle : 0.518 5.992 14170 Z= 0.298 Chirality : 0.041 0.343 1572 Planarity : 0.003 0.039 1786 Dihedral : 13.246 89.163 3932 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.62 % Allowed : 11.62 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -3.16 (0.19), residues: 1252 helix: -3.28 (0.13), residues: 518 sheet: -0.41 (0.31), residues: 229 loop : -1.30 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.009 0.001 TYR R 391 ARG 0.002 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.133 Fit side-chains REVERT: R 101 ASP cc_start: 0.5997 (m-30) cc_final: 0.5636 (m-30) REVERT: R 143 LYS cc_start: 0.7668 (tttt) cc_final: 0.7401 (ttpp) REVERT: A 311 TYR cc_start: 0.2458 (m-80) cc_final: 0.2257 (m-80) REVERT: A 368 ASP cc_start: 0.7438 (m-30) cc_final: 0.6859 (m-30) REVERT: A 386 MET cc_start: 0.6756 (ttm) cc_final: 0.6375 (mtt) REVERT: A 389 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7355 (ttm110) REVERT: A 390 GLN cc_start: 0.7358 (mt0) cc_final: 0.7065 (mp10) REVERT: B 17 GLN cc_start: 0.6387 (tt0) cc_final: 0.6143 (tm-30) outliers start: 17 outliers final: 2 residues processed: 212 average time/residue: 1.0498 time to fit residues: 241.2602 Evaluate side-chains 138 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain A residue 349 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 ASN P 22 ASN P 35 ASN R 52 GLN R 184 HIS R 186 ASN R 227 GLN R 399 GLN A 14 ASN A 292 ASN B 17 GLN B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 82 GLN N 120 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10458 Z= 0.188 Angle : 0.547 7.394 14170 Z= 0.288 Chirality : 0.042 0.298 1572 Planarity : 0.004 0.048 1786 Dihedral : 6.419 59.382 1701 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.14 % Allowed : 15.81 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.63 (0.22), residues: 1252 helix: -0.04 (0.21), residues: 514 sheet: -0.09 (0.31), residues: 246 loop : -0.84 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 339 HIS 0.004 0.001 HIS R 331 PHE 0.016 0.002 PHE A 212 TYR 0.021 0.001 TYR N 60 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: E 167 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6544 (ttm110) REVERT: R 101 ASP cc_start: 0.5755 (m-30) cc_final: 0.5453 (m-30) REVERT: R 140 GLU cc_start: 0.6978 (tp30) cc_final: 0.6637 (tp30) REVERT: R 174 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7357 (mtt180) REVERT: A 311 TYR cc_start: 0.2658 (m-80) cc_final: 0.2317 (m-80) REVERT: A 389 ARG cc_start: 0.7868 (ttt90) cc_final: 0.7295 (ttm110) REVERT: B 17 GLN cc_start: 0.6433 (tt0) cc_final: 0.6102 (tm-30) REVERT: B 59 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7601 (t80) REVERT: B 173 THR cc_start: 0.7670 (m) cc_final: 0.7466 (p) REVERT: N 25 SER cc_start: 0.6831 (OUTLIER) cc_final: 0.6303 (t) REVERT: N 83 MET cc_start: 0.5052 (mtm) cc_final: 0.4798 (mtp) outliers start: 33 outliers final: 12 residues processed: 170 average time/residue: 1.1002 time to fit residues: 202.6473 Evaluate side-chains 147 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN B 175 GLN B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10458 Z= 0.247 Angle : 0.550 7.291 14170 Z= 0.290 Chirality : 0.043 0.295 1572 Planarity : 0.004 0.052 1786 Dihedral : 6.220 59.580 1699 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.00 % Allowed : 16.38 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1252 helix: 0.95 (0.23), residues: 513 sheet: -0.15 (0.31), residues: 251 loop : -0.66 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 362 PHE 0.016 0.002 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.006 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: E 167 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6599 (ttm110) REVERT: R 101 ASP cc_start: 0.5776 (m-30) cc_final: 0.5487 (m-30) REVERT: R 174 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7466 (mtt180) REVERT: R 288 ASN cc_start: 0.7415 (m-40) cc_final: 0.6910 (m-40) REVERT: R 367 MET cc_start: 0.4928 (OUTLIER) cc_final: 0.4633 (ttt) REVERT: R 405 GLN cc_start: 0.7264 (mp10) cc_final: 0.7046 (mp10) REVERT: A 60 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.5961 (mpp) REVERT: A 311 TYR cc_start: 0.2864 (m-80) cc_final: 0.2373 (m-80) REVERT: A 386 MET cc_start: 0.6749 (mtp) cc_final: 0.6395 (mtt) REVERT: A 389 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7332 (ttm110) REVERT: B 13 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6922 (mm-40) REVERT: B 17 GLN cc_start: 0.6445 (tt0) cc_final: 0.6172 (tm-30) REVERT: B 59 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7509 (t80) REVERT: B 130 GLU cc_start: 0.5158 (OUTLIER) cc_final: 0.4923 (pp20) REVERT: N 25 SER cc_start: 0.6868 (OUTLIER) cc_final: 0.6422 (t) outliers start: 42 outliers final: 16 residues processed: 160 average time/residue: 1.1297 time to fit residues: 195.4852 Evaluate side-chains 147 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 102 HIS R 121 HIS ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 175 GLN B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10458 Z= 0.304 Angle : 0.592 9.311 14170 Z= 0.311 Chirality : 0.045 0.295 1572 Planarity : 0.004 0.056 1786 Dihedral : 6.529 59.847 1699 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.38 % Allowed : 16.38 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.23), residues: 1252 helix: 1.20 (0.23), residues: 513 sheet: -0.25 (0.32), residues: 247 loop : -0.68 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.018 0.002 PHE A 212 TYR 0.019 0.002 TYR N 60 ARG 0.003 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 136 time to evaluate : 1.065 Fit side-chains REVERT: R 101 ASP cc_start: 0.6054 (m-30) cc_final: 0.5789 (m-30) REVERT: R 140 GLU cc_start: 0.7223 (tp30) cc_final: 0.6949 (tp30) REVERT: R 174 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7485 (mtt180) REVERT: R 210 GLU cc_start: 0.6461 (tm-30) cc_final: 0.6255 (tm-30) REVERT: R 257 GLN cc_start: 0.7904 (mt0) cc_final: 0.7578 (mt0) REVERT: R 288 ASN cc_start: 0.7345 (m-40) cc_final: 0.6962 (m-40) REVERT: R 366 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6897 (mmtp) REVERT: R 367 MET cc_start: 0.4906 (OUTLIER) cc_final: 0.4533 (ttt) REVERT: R 405 GLN cc_start: 0.7261 (mp10) cc_final: 0.7044 (mp10) REVERT: A 28 LYS cc_start: 0.7707 (pptt) cc_final: 0.7017 (ptpt) REVERT: A 389 ARG cc_start: 0.7904 (ttt90) cc_final: 0.7319 (ttm110) REVERT: A 390 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6039 (mp10) REVERT: B 13 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6651 (tm-30) REVERT: B 17 GLN cc_start: 0.6546 (tt0) cc_final: 0.6334 (tm-30) REVERT: B 59 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7629 (t80) REVERT: B 130 GLU cc_start: 0.5306 (OUTLIER) cc_final: 0.4973 (pp20) REVERT: N 25 SER cc_start: 0.7063 (OUTLIER) cc_final: 0.6658 (t) REVERT: N 60 TYR cc_start: 0.7573 (m-80) cc_final: 0.7345 (m-80) REVERT: N 108 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7718 (m-80) outliers start: 46 outliers final: 21 residues processed: 164 average time/residue: 1.1329 time to fit residues: 200.6010 Evaluate side-chains 157 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 305 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 366 LYS Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 0.0270 chunk 40 optimal weight: 3.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 357 HIS B 175 GLN B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10458 Z= 0.168 Angle : 0.500 7.461 14170 Z= 0.264 Chirality : 0.041 0.295 1572 Planarity : 0.003 0.057 1786 Dihedral : 6.166 59.536 1699 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.24 % Allowed : 17.81 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.60 (0.23), residues: 1252 helix: 1.64 (0.23), residues: 514 sheet: -0.05 (0.32), residues: 243 loop : -0.63 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 381 PHE 0.014 0.001 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 0.996 Fit side-chains REVERT: E 167 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6042 (ttm110) REVERT: R 101 ASP cc_start: 0.5965 (m-30) cc_final: 0.5742 (m-30) REVERT: R 174 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7520 (mtt180) REVERT: R 257 GLN cc_start: 0.7745 (mt0) cc_final: 0.7489 (mt0) REVERT: R 288 ASN cc_start: 0.7333 (m-40) cc_final: 0.7058 (m-40) REVERT: R 367 MET cc_start: 0.4791 (OUTLIER) cc_final: 0.4332 (ttt) REVERT: A 28 LYS cc_start: 0.7662 (pptt) cc_final: 0.7060 (ptpt) REVERT: A 386 MET cc_start: 0.6649 (mtp) cc_final: 0.5946 (mtt) REVERT: A 389 ARG cc_start: 0.7900 (ttt90) cc_final: 0.7328 (ttm110) REVERT: A 390 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.6063 (mp10) REVERT: B 13 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6716 (tm-30) REVERT: B 59 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7480 (t80) REVERT: B 130 GLU cc_start: 0.5385 (OUTLIER) cc_final: 0.5040 (pp20) REVERT: N 25 SER cc_start: 0.7050 (OUTLIER) cc_final: 0.6621 (t) outliers start: 34 outliers final: 16 residues processed: 163 average time/residue: 1.1812 time to fit residues: 207.2730 Evaluate side-chains 158 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.0030 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 175 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10458 Z= 0.140 Angle : 0.484 9.135 14170 Z= 0.254 Chirality : 0.041 0.295 1572 Planarity : 0.003 0.058 1786 Dihedral : 5.920 59.820 1699 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.43 % Allowed : 18.38 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.85 (0.24), residues: 1252 helix: 1.93 (0.23), residues: 517 sheet: -0.17 (0.32), residues: 250 loop : -0.48 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 381 PHE 0.012 0.001 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.007 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.168 Fit side-chains REVERT: E 167 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6002 (ttm110) REVERT: P 16 LEU cc_start: 0.7154 (mt) cc_final: 0.6939 (mm) REVERT: R 101 ASP cc_start: 0.5880 (m-30) cc_final: 0.5657 (m-30) REVERT: R 257 GLN cc_start: 0.7801 (mt0) cc_final: 0.7590 (mt0) REVERT: R 288 ASN cc_start: 0.7308 (m-40) cc_final: 0.7042 (m-40) REVERT: R 405 GLN cc_start: 0.7259 (mp10) cc_final: 0.7010 (mp10) REVERT: A 28 LYS cc_start: 0.7616 (pptt) cc_final: 0.7150 (ptpt) REVERT: A 389 ARG cc_start: 0.7889 (ttt90) cc_final: 0.7337 (ttm110) REVERT: A 390 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6076 (mp10) REVERT: B 13 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6810 (tm-30) REVERT: B 17 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: B 195 ASP cc_start: 0.8200 (p0) cc_final: 0.7946 (p0) REVERT: N 108 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7541 (m-80) outliers start: 36 outliers final: 19 residues processed: 168 average time/residue: 1.0513 time to fit residues: 191.7079 Evaluate side-chains 160 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 346 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.0670 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 50.0000 chunk 118 optimal weight: 0.2980 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10458 Z= 0.274 Angle : 0.564 10.165 14170 Z= 0.294 Chirality : 0.044 0.298 1572 Planarity : 0.004 0.059 1786 Dihedral : 6.314 59.785 1699 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.24 % Allowed : 18.95 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1252 helix: 1.78 (0.23), residues: 519 sheet: -0.22 (0.32), residues: 250 loop : -0.50 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.009 0.001 HIS E 124 PHE 0.017 0.002 PHE A 212 TYR 0.017 0.002 TYR N 60 ARG 0.007 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.098 Fit side-chains REVERT: E 167 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6041 (ttm110) REVERT: R 101 ASP cc_start: 0.5990 (m-30) cc_final: 0.5774 (m-30) REVERT: R 105 SER cc_start: 0.8139 (m) cc_final: 0.7927 (p) REVERT: R 174 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7586 (mtt180) REVERT: R 257 GLN cc_start: 0.7856 (mt0) cc_final: 0.7614 (mt0) REVERT: R 288 ASN cc_start: 0.7342 (m-40) cc_final: 0.7044 (m-40) REVERT: A 60 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6042 (mpp) REVERT: A 253 TYR cc_start: 0.6095 (p90) cc_final: 0.5835 (p90) REVERT: A 389 ARG cc_start: 0.7908 (ttt90) cc_final: 0.7334 (ttm110) REVERT: A 390 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6049 (mp10) REVERT: B 13 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6787 (tm-30) REVERT: B 59 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7635 (t80) REVERT: B 195 ASP cc_start: 0.8281 (p0) cc_final: 0.8015 (p0) REVERT: N 25 SER cc_start: 0.7121 (OUTLIER) cc_final: 0.6700 (t) REVERT: N 108 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7754 (m-80) outliers start: 34 outliers final: 19 residues processed: 159 average time/residue: 1.1225 time to fit residues: 192.9583 Evaluate side-chains 158 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10458 Z= 0.323 Angle : 0.605 10.158 14170 Z= 0.316 Chirality : 0.045 0.299 1572 Planarity : 0.004 0.060 1786 Dihedral : 6.800 58.585 1699 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.00 % Allowed : 18.00 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.53 (0.24), residues: 1252 helix: 1.61 (0.23), residues: 516 sheet: -0.33 (0.32), residues: 248 loop : -0.57 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 362 PHE 0.019 0.002 PHE A 212 TYR 0.016 0.002 TYR N 60 ARG 0.008 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 1.228 Fit side-chains REVERT: E 167 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6685 (ttm110) REVERT: R 174 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7515 (mtt180) REVERT: R 257 GLN cc_start: 0.7921 (mt0) cc_final: 0.7721 (mt0) REVERT: R 288 ASN cc_start: 0.7288 (m-40) cc_final: 0.7015 (m-40) REVERT: R 367 MET cc_start: 0.4921 (OUTLIER) cc_final: 0.4410 (ttt) REVERT: R 405 GLN cc_start: 0.7351 (mp10) cc_final: 0.7095 (mp10) REVERT: A 28 LYS cc_start: 0.7691 (pptt) cc_final: 0.6923 (ptpt) REVERT: A 253 TYR cc_start: 0.6041 (p90) cc_final: 0.5833 (p90) REVERT: A 389 ARG cc_start: 0.7917 (ttt90) cc_final: 0.7332 (ttm110) REVERT: A 390 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6047 (mp10) REVERT: B 13 GLN cc_start: 0.7262 (mm-40) cc_final: 0.6756 (tm-30) REVERT: B 59 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7604 (t80) REVERT: N 25 SER cc_start: 0.7117 (OUTLIER) cc_final: 0.6721 (t) REVERT: N 43 LYS cc_start: 0.7416 (mtpt) cc_final: 0.7184 (mttt) REVERT: N 108 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7795 (m-80) outliers start: 42 outliers final: 29 residues processed: 159 average time/residue: 1.1412 time to fit residues: 196.5500 Evaluate side-chains 162 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 0.0170 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10458 Z= 0.157 Angle : 0.506 8.733 14170 Z= 0.265 Chirality : 0.041 0.298 1572 Planarity : 0.003 0.059 1786 Dihedral : 6.360 59.552 1699 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.86 % Allowed : 19.24 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.84 (0.24), residues: 1252 helix: 1.97 (0.23), residues: 517 sheet: -0.30 (0.32), residues: 246 loop : -0.47 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS R 381 PHE 0.017 0.001 PHE R 172 TYR 0.018 0.001 TYR N 60 ARG 0.007 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.107 Fit side-chains REVERT: E 167 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.5951 (ttm110) REVERT: R 288 ASN cc_start: 0.7310 (m-40) cc_final: 0.7028 (m-40) REVERT: R 367 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.4311 (ttt) REVERT: A 28 LYS cc_start: 0.7571 (pptt) cc_final: 0.6937 (ptpt) REVERT: A 253 TYR cc_start: 0.6072 (p90) cc_final: 0.5860 (p90) REVERT: A 389 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7379 (ttm110) REVERT: A 390 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6022 (mp10) REVERT: A 392 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7037 (mt-10) REVERT: B 13 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6789 (tm-30) REVERT: B 59 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7385 (t80) REVERT: B 217 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.6594 (pmt) REVERT: N 108 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7417 (m-80) outliers start: 30 outliers final: 21 residues processed: 157 average time/residue: 1.1635 time to fit residues: 196.5989 Evaluate side-chains 159 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10458 Z= 0.160 Angle : 0.515 8.677 14170 Z= 0.270 Chirality : 0.042 0.301 1572 Planarity : 0.004 0.060 1786 Dihedral : 6.261 59.444 1699 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.05 % Allowed : 19.62 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.93 (0.24), residues: 1252 helix: 2.07 (0.23), residues: 517 sheet: -0.28 (0.32), residues: 245 loop : -0.44 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 381 PHE 0.017 0.001 PHE R 172 TYR 0.015 0.001 TYR N 60 ARG 0.009 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.094 Fit side-chains REVERT: E 167 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.5897 (ttm110) REVERT: R 288 ASN cc_start: 0.7175 (m-40) cc_final: 0.6972 (m-40) REVERT: R 367 MET cc_start: 0.4817 (OUTLIER) cc_final: 0.4285 (ttt) REVERT: A 28 LYS cc_start: 0.7621 (pptt) cc_final: 0.6997 (ptpt) REVERT: A 389 ARG cc_start: 0.7918 (ttt90) cc_final: 0.7375 (ttm110) REVERT: A 390 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6100 (mp10) REVERT: A 392 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7020 (mt-10) REVERT: B 13 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6789 (tm-30) REVERT: B 59 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7489 (t80) REVERT: B 217 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6577 (pmt) REVERT: N 108 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7491 (m-80) outliers start: 32 outliers final: 24 residues processed: 155 average time/residue: 1.2081 time to fit residues: 201.3942 Evaluate side-chains 162 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.213778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153057 restraints weight = 20029.472| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.32 r_work: 0.3702 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10458 Z= 0.168 Angle : 0.514 8.684 14170 Z= 0.269 Chirality : 0.042 0.302 1572 Planarity : 0.004 0.060 1786 Dihedral : 6.228 58.973 1699 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.14 % Allowed : 19.62 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.93 (0.24), residues: 1252 helix: 2.04 (0.23), residues: 519 sheet: -0.27 (0.32), residues: 245 loop : -0.41 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS E 124 PHE 0.017 0.001 PHE R 172 TYR 0.016 0.001 TYR N 60 ARG 0.006 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.30 seconds wall clock time: 75 minutes 19.86 seconds (4519.86 seconds total)