Starting phenix.real_space_refine on Mon Mar 11 18:22:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/03_2024/6kpg_0745_updated.pdb" } resolution = 3.0 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= 0.004 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 67 5.16 5 C 5623 2.51 5 N 1500 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 258": "OE1" <-> "OE2" Residue "S ASP 189": "OD1" <-> "OD2" 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: 8805 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1771 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2592 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2223 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1755 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'8D0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.61 Number of scatterers: 8805 At special positions: 0 Unit cell: (105.04, 118.56, 105.04, 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 67 16.00 O 1615 8.00 N 1500 7.00 C 5623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 14 sheets defined 29.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 7 through 23 removed outlier: 3.502A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.535A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.777A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.693A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'B' and resid 4 through 23 removed outlier: 3.779A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.753A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 37 through 47 removed outlier: 3.573A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 138 removed outlier: 3.523A pdb=" N ILE R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL R 131 " --> pdb=" O GLY R 127 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 143 No H-bonds generated for 'chain 'R' and resid 140 through 143' Processing helix chain 'R' and resid 151 through 162 removed outlier: 3.663A pdb=" N ILE R 156 " --> pdb=" O TYR R 153 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU R 159 " --> pdb=" O ILE R 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL R 161 " --> pdb=" O SER R 158 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA R 162 " --> pdb=" O LEU R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 175 removed outlier: 3.704A pdb=" N TYR R 172 " --> pdb=" O VAL R 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 219 removed outlier: 3.515A pdb=" N THR R 201 " --> pdb=" O THR R 197 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL R 204 " --> pdb=" O PHE R 200 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 227 removed outlier: 3.669A pdb=" N TYR R 224 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS R 225 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 245 removed outlier: 3.776A pdb=" N VAL R 234 " --> pdb=" O ARG R 230 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU R 239 " --> pdb=" O VAL R 235 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP R 241 " --> pdb=" O PHE R 237 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 253 No H-bonds generated for 'chain 'R' and resid 250 through 253' Processing helix chain 'R' and resid 279 through 300 removed outlier: 5.206A pdb=" N LEU R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 289 " --> pdb=" O VAL R 285 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET R 295 " --> pdb=" O VAL R 291 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 305 No H-bonds generated for 'chain 'R' and resid 302 through 305' Processing helix chain 'R' and resid 307 through 310 No H-bonds generated for 'chain 'R' and resid 307 through 310' Processing helix chain 'R' and resid 337 through 349 removed outlier: 3.677A pdb=" N LEU R 341 " --> pdb=" O MET R 337 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS R 343 " --> pdb=" O ILE R 339 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR R 344 " --> pdb=" O GLU R 340 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 354 No H-bonds generated for 'chain 'R' and resid 351 through 354' Processing helix chain 'R' and resid 356 through 366 removed outlier: 3.538A pdb=" N MET R 363 " --> pdb=" O LEU R 359 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR R 365 " --> pdb=" O ALA R 361 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP R 366 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 373 through 380 removed outlier: 3.819A pdb=" N ALA R 380 " --> pdb=" O LYS R 376 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 393 removed outlier: 3.731A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 402 through 410 removed outlier: 4.536A pdb=" N ALA R 407 " --> pdb=" O ASP R 403 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.660A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 removed outlier: 6.894A pdb=" N ALA A 220 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.000A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.088A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.620A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 252 removed outlier: 3.654A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.877A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.557A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.828A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.261A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 4 through 6 removed outlier: 3.614A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.760A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.780A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER S 196 " --> pdb=" O ALA S 199 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.506A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2090 1.33 - 1.45: 2119 1.45 - 1.58: 4678 1.58 - 1.70: 3 1.70 - 1.82: 96 Bond restraints: 8986 Sorted by residual: bond pdb=" C26 8D0 R 501 " pdb=" N1 8D0 R 501 " ideal model delta sigma weight residual 1.512 1.202 0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C6 8D0 R 501 " pdb=" O1 8D0 R 501 " ideal model delta sigma weight residual 1.594 1.371 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C9 8D0 R 501 " pdb=" O1 8D0 R 501 " ideal model delta sigma weight residual 1.617 1.412 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C26 8D0 R 501 " pdb=" S1 8D0 R 501 " ideal model delta sigma weight residual 1.787 1.583 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C23 8D0 R 501 " pdb=" C24 8D0 R 501 " ideal model delta sigma weight residual 1.346 1.538 -0.192 2.00e-02 2.50e+03 9.18e+01 ... (remaining 8981 not shown) Histogram of bond angle deviations from ideal: 98.39 - 114.53: 5497 114.53 - 130.68: 6626 130.68 - 146.82: 49 146.82 - 162.96: 0 162.96 - 179.10: 1 Bond angle restraints: 12173 Sorted by residual: angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 109.81 123.06 -13.25 2.21e+00 2.05e-01 3.59e+01 angle pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " pdb=" CG TYR S 223 " ideal model delta sigma weight residual 113.90 104.72 9.18 1.80e+00 3.09e-01 2.60e+01 angle pdb=" N VAL R 249 " pdb=" CA VAL R 249 " pdb=" C VAL R 249 " ideal model delta sigma weight residual 112.29 107.67 4.62 9.40e-01 1.13e+00 2.41e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C ILE A 285 " pdb=" CA ILE A 285 " pdb=" CB ILE A 285 " ideal model delta sigma weight residual 111.81 106.61 5.20 1.25e+00 6.40e-01 1.73e+01 ... (remaining 12168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.69: 4978 22.69 - 45.38: 323 45.38 - 68.07: 22 68.07 - 90.77: 6 90.77 - 113.46: 2 Dihedral angle restraints: 5331 sinusoidal: 2039 harmonic: 3292 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 148.40 31.60 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA THR B 86 " pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta harmonic sigma weight residual -180.00 -149.90 -30.10 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA LEU R 276 " pdb=" C LEU R 276 " pdb=" N MET R 277 " pdb=" CA MET R 277 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 5328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1219 0.093 - 0.186: 166 0.186 - 0.280: 13 0.280 - 0.373: 0 0.373 - 0.466: 1 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1396 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 230 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO R 231 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR S 223 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C TYR S 223 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR S 223 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO S 224 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 140 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.10e+00 pdb=" C ALA B 140 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA B 140 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY B 141 " 0.016 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1704 2.76 - 3.29: 7974 3.29 - 3.83: 14872 3.83 - 4.36: 18267 4.36 - 4.90: 31354 Nonbonded interactions: 74171 Sorted by model distance: nonbonded pdb=" O ILE R 247 " pdb=" OH TYR R 275 " model vdw 2.219 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.221 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.249 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 2.440 ... (remaining 74166 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.000 Extract box with map and model: 3.000 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.220 Find NCS groups from input model: 0.250 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.014 0.310 8986 Z= 0.940 Angle : 1.090 13.246 12173 Z= 0.580 Chirality : 0.063 0.466 1399 Planarity : 0.007 0.078 1522 Dihedral : 14.619 113.457 3199 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.49 % Rotamer: Outliers : 0.74 % Allowed : 8.60 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.19), residues: 1119 helix: -4.49 (0.12), residues: 372 sheet: -3.37 (0.25), residues: 243 loop : -2.33 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 99 HIS 0.010 0.002 HIS A 195 PHE 0.029 0.004 PHE S 108 TYR 0.033 0.003 TYR S 223 ARG 0.006 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 ASN cc_start: 0.7593 (t0) cc_final: 0.7381 (t0) REVERT: A 271 LYS cc_start: 0.7549 (pttp) cc_final: 0.7320 (ptmt) REVERT: A 287 TYR cc_start: 0.8310 (m-80) cc_final: 0.7691 (m-80) REVERT: A 296 TYR cc_start: 0.7782 (t80) cc_final: 0.7461 (t80) REVERT: A 318 GLU cc_start: 0.6836 (tp30) cc_final: 0.6220 (mm-30) REVERT: A 333 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8076 (mm-40) REVERT: B 290 ASP cc_start: 0.6977 (m-30) cc_final: 0.6645 (m-30) REVERT: R 109 MET cc_start: 0.5139 (pmm) cc_final: 0.4466 (pp-130) REVERT: R 278 PHE cc_start: 0.7378 (t80) cc_final: 0.7111 (t80) outliers start: 7 outliers final: 3 residues processed: 207 average time/residue: 1.1099 time to fit residues: 245.8833 Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain R residue 222 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.2980 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 195 HIS A 213 HIS A 269 ASN A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 62 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 119 ASN B 175 GLN B 259 GLN B 340 ASN C 24 ASN R 270 HIS S 82 GLN S 113 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8986 Z= 0.226 Angle : 0.617 8.882 12173 Z= 0.319 Chirality : 0.042 0.293 1399 Planarity : 0.004 0.059 1522 Dihedral : 7.824 102.514 1245 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.35 % Allowed : 17.83 % Favored : 77.81 % 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: -3.94 (0.21), residues: 1119 helix: -2.98 (0.20), residues: 378 sheet: -3.11 (0.25), residues: 257 loop : -1.74 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 108 TYR 0.021 0.002 TYR S 223 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 185 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 247 MET cc_start: 0.7429 (mtp) cc_final: 0.6963 (mtp) REVERT: A 287 TYR cc_start: 0.7997 (m-80) cc_final: 0.7653 (m-80) REVERT: A 305 CYS cc_start: 0.8394 (p) cc_final: 0.8065 (p) REVERT: A 333 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8210 (mm-40) REVERT: B 59 TYR cc_start: 0.8219 (m-10) cc_final: 0.7951 (m-10) REVERT: B 258 ASP cc_start: 0.7563 (t0) cc_final: 0.7122 (t0) REVERT: B 290 ASP cc_start: 0.6703 (m-30) cc_final: 0.6420 (m-30) REVERT: C 29 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7269 (mmtm) REVERT: R 109 MET cc_start: 0.5527 (pmm) cc_final: 0.4886 (ppp) REVERT: R 133 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6213 (tp30) REVERT: R 134 ASN cc_start: 0.7086 (t0) cc_final: 0.6878 (t0) REVERT: S 86 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8716 (pp) outliers start: 41 outliers final: 18 residues processed: 205 average time/residue: 1.0474 time to fit residues: 230.5001 Evaluate side-chains 175 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.0870 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8986 Z= 0.260 Angle : 0.607 8.632 12173 Z= 0.309 Chirality : 0.043 0.284 1399 Planarity : 0.004 0.044 1522 Dihedral : 7.391 98.982 1244 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 6.69 % Allowed : 20.06 % Favored : 73.25 % 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: -3.30 (0.23), residues: 1119 helix: -2.04 (0.24), residues: 389 sheet: -3.05 (0.25), residues: 253 loop : -1.55 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS R 154 PHE 0.017 0.001 PHE R 129 TYR 0.023 0.002 TYR S 223 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 163 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 CYS cc_start: 0.8418 (p) cc_final: 0.8093 (p) REVERT: A 306 GLN cc_start: 0.8387 (tp40) cc_final: 0.8173 (mm110) REVERT: B 59 TYR cc_start: 0.8221 (m-10) cc_final: 0.7990 (m-10) REVERT: B 258 ASP cc_start: 0.7821 (t0) cc_final: 0.7421 (t0) REVERT: B 290 ASP cc_start: 0.6730 (m-30) cc_final: 0.6456 (m-30) REVERT: C 29 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7299 (mmtm) REVERT: R 109 MET cc_start: 0.5197 (pmm) cc_final: 0.4639 (ppp) REVERT: R 292 TYR cc_start: 0.7293 (t80) cc_final: 0.6717 (t80) REVERT: S 86 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8743 (pp) outliers start: 63 outliers final: 26 residues processed: 199 average time/residue: 0.9711 time to fit residues: 208.7539 Evaluate side-chains 181 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8986 Z= 0.265 Angle : 0.598 8.421 12173 Z= 0.305 Chirality : 0.042 0.278 1399 Planarity : 0.004 0.045 1522 Dihedral : 7.101 96.926 1244 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.26 % Allowed : 22.29 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.24), residues: 1119 helix: -1.55 (0.25), residues: 391 sheet: -2.86 (0.27), residues: 245 loop : -1.57 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS S 35 PHE 0.026 0.001 PHE S 68 TYR 0.021 0.001 TYR S 223 ARG 0.009 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 164 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 HIS cc_start: 0.7754 (m-70) cc_final: 0.7523 (m-70) REVERT: A 305 CYS cc_start: 0.8407 (p) cc_final: 0.8061 (p) REVERT: B 258 ASP cc_start: 0.7864 (t0) cc_final: 0.7463 (t0) REVERT: B 290 ASP cc_start: 0.6731 (m-30) cc_final: 0.6469 (m-30) REVERT: C 29 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7300 (mmtm) REVERT: R 109 MET cc_start: 0.5250 (pmm) cc_final: 0.4667 (ppp) REVERT: R 292 TYR cc_start: 0.7259 (t80) cc_final: 0.6687 (t80) REVERT: S 86 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8737 (pp) outliers start: 59 outliers final: 36 residues processed: 201 average time/residue: 0.9434 time to fit residues: 205.0552 Evaluate side-chains 191 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 74 ASP Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8986 Z= 0.230 Angle : 0.586 9.737 12173 Z= 0.296 Chirality : 0.042 0.303 1399 Planarity : 0.004 0.040 1522 Dihedral : 6.795 96.778 1242 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 6.05 % Allowed : 23.57 % Favored : 70.38 % 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: -2.55 (0.24), residues: 1119 helix: -1.13 (0.26), residues: 388 sheet: -2.63 (0.26), residues: 274 loop : -1.31 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS S 35 PHE 0.023 0.001 PHE S 68 TYR 0.018 0.001 TYR S 223 ARG 0.011 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 171 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 HIS cc_start: 0.7754 (m-70) cc_final: 0.7515 (m-70) REVERT: A 305 CYS cc_start: 0.8356 (p) cc_final: 0.8004 (p) REVERT: B 59 TYR cc_start: 0.8165 (m-10) cc_final: 0.7895 (m-80) REVERT: B 96 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7635 (mtp180) REVERT: B 290 ASP cc_start: 0.6667 (m-30) cc_final: 0.6430 (m-30) REVERT: C 29 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7315 (mmtm) REVERT: R 109 MET cc_start: 0.5057 (pmm) cc_final: 0.4499 (ppp) REVERT: R 186 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5379 (tmt90) REVERT: R 228 VAL cc_start: 0.7908 (t) cc_final: 0.7695 (m) REVERT: R 292 TYR cc_start: 0.7285 (t80) cc_final: 0.6710 (t80) REVERT: S 86 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8703 (pp) outliers start: 57 outliers final: 40 residues processed: 202 average time/residue: 0.9937 time to fit residues: 217.1195 Evaluate side-chains 191 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 186 ARG Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 406 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 241 ASN A 256 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN S 113 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8986 Z= 0.194 Angle : 0.573 9.844 12173 Z= 0.291 Chirality : 0.042 0.286 1399 Planarity : 0.004 0.057 1522 Dihedral : 6.584 96.504 1242 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 6.26 % Allowed : 25.05 % Favored : 68.68 % 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: -2.22 (0.25), residues: 1119 helix: -0.73 (0.27), residues: 383 sheet: -2.40 (0.28), residues: 260 loop : -1.35 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.010 0.001 HIS R 304 PHE 0.033 0.001 PHE R 189 TYR 0.015 0.001 TYR S 223 ARG 0.012 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 165 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8211 (m-40) cc_final: 0.7932 (m-40) REVERT: A 188 HIS cc_start: 0.7738 (m-70) cc_final: 0.7519 (m-70) REVERT: A 305 CYS cc_start: 0.8333 (p) cc_final: 0.7970 (p) REVERT: B 52 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7252 (mtp85) REVERT: B 96 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7491 (mtp180) REVERT: B 127 LYS cc_start: 0.9078 (mttp) cc_final: 0.8851 (mtpp) REVERT: B 290 ASP cc_start: 0.6810 (m-30) cc_final: 0.6578 (m-30) REVERT: B 335 PHE cc_start: 0.8134 (m-80) cc_final: 0.7807 (m-80) REVERT: C 29 LYS cc_start: 0.7877 (mtmm) cc_final: 0.7364 (mmtm) REVERT: C 62 ARG cc_start: 0.6036 (ptp90) cc_final: 0.5796 (ptp90) REVERT: R 109 MET cc_start: 0.5189 (pmm) cc_final: 0.4544 (ppp) REVERT: R 292 TYR cc_start: 0.7163 (t80) cc_final: 0.6608 (t80) REVERT: S 86 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8680 (pp) outliers start: 59 outliers final: 34 residues processed: 202 average time/residue: 0.9284 time to fit residues: 203.4029 Evaluate side-chains 196 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 406 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN S 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8986 Z= 0.183 Angle : 0.574 8.966 12173 Z= 0.289 Chirality : 0.041 0.242 1399 Planarity : 0.004 0.053 1522 Dihedral : 6.396 95.993 1242 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.63 % Allowed : 25.90 % Favored : 68.47 % 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: -2.03 (0.25), residues: 1119 helix: -0.45 (0.28), residues: 383 sheet: -2.28 (0.28), residues: 263 loop : -1.35 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.009 0.001 HIS R 304 PHE 0.024 0.001 PHE R 129 TYR 0.016 0.001 TYR S 223 ARG 0.012 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 175 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8153 (m-40) cc_final: 0.7921 (m-40) REVERT: A 188 HIS cc_start: 0.7697 (m-70) cc_final: 0.7485 (m-70) REVERT: A 305 CYS cc_start: 0.8355 (p) cc_final: 0.7988 (p) REVERT: B 52 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7212 (mtp85) REVERT: B 127 LYS cc_start: 0.9069 (mttp) cc_final: 0.8862 (mtpp) REVERT: B 258 ASP cc_start: 0.7650 (t0) cc_final: 0.7272 (t0) REVERT: B 290 ASP cc_start: 0.6801 (m-30) cc_final: 0.6588 (m-30) REVERT: B 335 PHE cc_start: 0.8145 (m-80) cc_final: 0.7842 (m-80) REVERT: C 29 LYS cc_start: 0.7852 (mtmm) cc_final: 0.7384 (mmtm) REVERT: R 109 MET cc_start: 0.5096 (pmm) cc_final: 0.4499 (ppp) REVERT: R 277 MET cc_start: 0.4963 (tmm) cc_final: 0.3672 (mtp) REVERT: R 292 TYR cc_start: 0.7098 (t80) cc_final: 0.6574 (t80) REVERT: S 86 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8668 (pp) outliers start: 53 outliers final: 34 residues processed: 204 average time/residue: 0.9368 time to fit residues: 207.6622 Evaluate side-chains 194 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 406 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.0050 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN B 88 ASN B 237 ASN ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8986 Z= 0.194 Angle : 0.598 9.890 12173 Z= 0.295 Chirality : 0.042 0.258 1399 Planarity : 0.004 0.053 1522 Dihedral : 6.344 95.859 1242 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.52 % Allowed : 26.33 % Favored : 68.15 % 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: -1.89 (0.25), residues: 1119 helix: -0.30 (0.28), residues: 383 sheet: -2.21 (0.28), residues: 268 loop : -1.29 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.009 0.001 HIS R 304 PHE 0.032 0.001 PHE R 189 TYR 0.018 0.001 TYR R 296 ARG 0.013 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8078 (m-40) cc_final: 0.7799 (m-40) REVERT: A 305 CYS cc_start: 0.8349 (p) cc_final: 0.7991 (p) REVERT: B 127 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8861 (mtpp) REVERT: B 258 ASP cc_start: 0.7610 (t0) cc_final: 0.7276 (t0) REVERT: B 335 PHE cc_start: 0.8161 (m-80) cc_final: 0.7915 (m-80) REVERT: C 29 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7379 (mmtm) REVERT: R 109 MET cc_start: 0.5000 (pmm) cc_final: 0.4490 (ppp) REVERT: R 277 MET cc_start: 0.4830 (tmm) cc_final: 0.3689 (mtp) REVERT: R 292 TYR cc_start: 0.7089 (t80) cc_final: 0.6560 (t80) REVERT: R 363 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7271 (pmt) REVERT: S 86 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8626 (pp) outliers start: 52 outliers final: 38 residues processed: 196 average time/residue: 0.9090 time to fit residues: 193.1394 Evaluate side-chains 195 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 363 MET Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 406 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 256 ASN B 237 ASN ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8986 Z= 0.166 Angle : 0.584 8.721 12173 Z= 0.290 Chirality : 0.041 0.236 1399 Planarity : 0.004 0.052 1522 Dihedral : 6.238 94.648 1242 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.99 % Allowed : 27.28 % Favored : 67.73 % 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: -1.78 (0.25), residues: 1119 helix: -0.25 (0.28), residues: 390 sheet: -2.05 (0.29), residues: 260 loop : -1.28 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS R 304 PHE 0.023 0.001 PHE R 129 TYR 0.014 0.001 TYR S 223 ARG 0.014 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 169 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7976 (m-40) cc_final: 0.7730 (m-40) REVERT: A 305 CYS cc_start: 0.8374 (p) cc_final: 0.7982 (p) REVERT: B 127 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8865 (mtpp) REVERT: B 258 ASP cc_start: 0.7526 (t0) cc_final: 0.7177 (t0) REVERT: B 290 ASP cc_start: 0.6814 (m-30) cc_final: 0.6607 (m-30) REVERT: B 335 PHE cc_start: 0.8032 (m-80) cc_final: 0.7794 (m-80) REVERT: C 29 LYS cc_start: 0.7820 (mtmm) cc_final: 0.7375 (mmtm) REVERT: R 109 MET cc_start: 0.4961 (pmm) cc_final: 0.4490 (ppp) REVERT: R 277 MET cc_start: 0.4849 (tmm) cc_final: 0.3786 (mtp) REVERT: R 292 TYR cc_start: 0.7047 (t80) cc_final: 0.6577 (t80) REVERT: R 363 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7053 (pmt) outliers start: 47 outliers final: 34 residues processed: 191 average time/residue: 0.9170 time to fit residues: 190.4461 Evaluate side-chains 194 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 363 MET Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 406 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8986 Z= 0.178 Angle : 0.598 8.706 12173 Z= 0.295 Chirality : 0.042 0.233 1399 Planarity : 0.004 0.051 1522 Dihedral : 6.188 94.307 1242 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.14 % Allowed : 28.66 % Favored : 67.20 % 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: -1.69 (0.25), residues: 1119 helix: -0.14 (0.28), residues: 395 sheet: -2.01 (0.29), residues: 266 loop : -1.26 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.008 0.001 HIS R 304 PHE 0.034 0.001 PHE R 189 TYR 0.016 0.001 TYR C 40 ARG 0.014 0.001 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 CYS cc_start: 0.8334 (p) cc_final: 0.7955 (p) REVERT: B 258 ASP cc_start: 0.7543 (t0) cc_final: 0.7188 (t0) REVERT: B 335 PHE cc_start: 0.8038 (m-80) cc_final: 0.7805 (m-80) REVERT: C 29 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7377 (mmtm) REVERT: R 109 MET cc_start: 0.4932 (pmm) cc_final: 0.4491 (ppp) REVERT: R 277 MET cc_start: 0.4841 (tmm) cc_final: 0.3749 (mtp) REVERT: R 292 TYR cc_start: 0.7047 (t80) cc_final: 0.6570 (t80) REVERT: R 363 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7194 (pmt) outliers start: 39 outliers final: 32 residues processed: 183 average time/residue: 0.9281 time to fit residues: 184.9250 Evaluate side-chains 193 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 363 MET Chi-restraints excluded: chain R residue 364 VAL Chi-restraints excluded: chain R residue 377 THR Chi-restraints excluded: chain R residue 383 SER Chi-restraints excluded: chain R residue 406 HIS Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 73 ASP Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 132 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.178121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.131312 restraints weight = 11369.527| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.47 r_work: 0.3733 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8986 Z= 0.220 Angle : 0.618 8.810 12173 Z= 0.303 Chirality : 0.042 0.243 1399 Planarity : 0.004 0.051 1522 Dihedral : 6.242 95.268 1242 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.25 % Allowed : 28.24 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 1119 helix: -0.09 (0.27), residues: 390 sheet: -2.03 (0.29), residues: 262 loop : -1.20 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.009 0.001 HIS R 304 PHE 0.015 0.001 PHE S 68 TYR 0.015 0.001 TYR R 275 ARG 0.012 0.001 ARG S 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3955.49 seconds wall clock time: 70 minutes 55.62 seconds (4255.62 seconds total)