Starting phenix.real_space_refine on Thu Mar 14 15:32:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/03_2024/8jis_36326.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/03_2024/8jis_36326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/03_2024/8jis_36326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/03_2024/8jis_36326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/03_2024/8jis_36326.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jis_36326/03_2024/8jis_36326.pdb" } resolution = 2.46 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= 0.020 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 57 5.16 5 C 5828 2.51 5 N 1574 2.21 5 O 1699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R GLU 292": "OE1" <-> "OE2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R GLU 387": "OE1" <-> "OE2" 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: 9158 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1856 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2572 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 238 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 427 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3104 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Time building chain proxies: 4.94, per 1000 atoms: 0.54 Number of scatterers: 9158 At special positions: 0 Unit cell: (86.751, 95.319, 173.502, 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 57 16.00 O 1699 8.00 N 1574 7.00 C 5828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 40.5% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.643A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.723A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.648A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.796A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 4.051A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.074A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.655A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 31 through 49 Processing helix chain 'R' and resid 89 through 93 Processing helix chain 'R' and resid 139 through 169 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.683A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 211 Processing helix chain 'R' and resid 216 through 221 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.584A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 292 Proline residue: R 277 - end of helix removed outlier: 3.963A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.830A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.587A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 354 removed outlier: 4.145A pdb=" N CYS R 347 " --> pdb=" O THR R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 361 Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 377 through 404 removed outlier: 3.762A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 removed outlier: 3.814A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.630A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.502A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.763A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.742A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.978A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.734A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.980A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.516A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 112 through 114 removed outlier: 4.646A pdb=" N ASP R 114 " --> pdb=" O LEU R 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU R 118 " --> pdb=" O ASP R 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 443 hydrogen bonds defined for protein. 1275 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: 2.11 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1496 1.31 - 1.44: 2689 1.44 - 1.56: 5100 1.56 - 1.69: 1 1.69 - 1.82: 78 Bond restraints: 9364 Sorted by residual: bond pdb=" C ASP R 53 " pdb=" N PRO R 54 " ideal model delta sigma weight residual 1.331 1.385 -0.054 8.70e-03 1.32e+04 3.87e+01 bond pdb=" C GLU A 311 " pdb=" O GLU A 311 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.26e-02 6.30e+03 2.01e+01 bond pdb=" CA ALA R 368 " pdb=" C ALA R 368 " ideal model delta sigma weight residual 1.523 1.487 0.036 8.20e-03 1.49e+04 1.97e+01 bond pdb=" CA ALA B 328 " pdb=" C ALA B 328 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.18e-02 7.18e+03 1.90e+01 bond pdb=" CA SER B 191 " pdb=" C SER B 191 " ideal model delta sigma weight residual 1.520 1.472 0.048 1.12e-02 7.97e+03 1.83e+01 ... (remaining 9359 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.64: 285 106.64 - 114.16: 5225 114.16 - 121.68: 5239 121.68 - 129.19: 1885 129.19 - 136.71: 90 Bond angle restraints: 12724 Sorted by residual: angle pdb=" N HIS R 374 " pdb=" CA HIS R 374 " pdb=" C HIS R 374 " ideal model delta sigma weight residual 114.12 99.29 14.83 1.39e+00 5.18e-01 1.14e+02 angle pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" C ASP R 344 " ideal model delta sigma weight residual 113.19 101.25 11.94 1.19e+00 7.06e-01 1.01e+02 angle pdb=" N GLU A 281 " pdb=" CA GLU A 281 " pdb=" C GLU A 281 " ideal model delta sigma weight residual 112.34 101.39 10.95 1.30e+00 5.92e-01 7.09e+01 angle pdb=" N ILE R 345 " pdb=" CA ILE R 345 " pdb=" C ILE R 345 " ideal model delta sigma weight residual 110.42 102.95 7.47 9.60e-01 1.09e+00 6.06e+01 angle pdb=" N SER R 93 " pdb=" CA SER R 93 " pdb=" C SER R 93 " ideal model delta sigma weight residual 112.23 103.05 9.18 1.26e+00 6.30e-01 5.31e+01 ... (remaining 12719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4676 17.50 - 35.01: 523 35.01 - 52.51: 231 52.51 - 70.02: 75 70.02 - 87.52: 20 Dihedral angle restraints: 5525 sinusoidal: 2097 harmonic: 3428 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 -179.90 -87.10 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -127.73 41.73 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA CYS R 46 " pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " ideal model delta sinusoidal sigma weight residual -73.00 -6.57 -66.43 1 2.00e+01 2.50e-03 1.44e+01 ... (remaining 5522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1140 0.081 - 0.161: 214 0.161 - 0.242: 52 0.242 - 0.322: 18 0.322 - 0.402: 7 Chirality restraints: 1431 Sorted by residual: chirality pdb=" CA THR N 111 " pdb=" N THR N 111 " pdb=" C THR N 111 " pdb=" CB THR N 111 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA SER B 136 " pdb=" N SER B 136 " pdb=" C SER B 136 " pdb=" CB SER B 136 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 1428 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 90 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C PRO R 90 " 0.067 2.00e-02 2.50e+03 pdb=" O PRO R 90 " -0.024 2.00e-02 2.50e+03 pdb=" N TRP R 91 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 280 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C PRO A 280 " -0.052 2.00e-02 2.50e+03 pdb=" O PRO A 280 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 281 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 42 " 0.014 2.00e-02 2.50e+03 2.98e-02 8.90e+00 pdb=" C GLU G 42 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU G 42 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA G 43 " 0.018 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2581 2.79 - 3.32: 8268 3.32 - 3.85: 15774 3.85 - 4.37: 18580 4.37 - 4.90: 30732 Nonbonded interactions: 75935 Sorted by model distance: nonbonded pdb=" OD2 ASP A 26 " pdb=" NZ LYS B 78 " model vdw 2.266 2.520 nonbonded pdb=" O SER A 44 " pdb=" OG SER A 44 " model vdw 2.294 2.440 nonbonded pdb=" O LEU R 349 " pdb=" OG1 THR R 353 " model vdw 2.303 2.440 nonbonded pdb=" N HIS R 374 " pdb=" N ALA R 375 " model vdw 2.320 2.560 nonbonded pdb=" OE2 GLU A 20 " pdb=" NZ LYS B 89 " model vdw 2.346 2.520 ... (remaining 75930 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 23.800 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.009 0.057 9364 Z= 0.611 Angle : 1.200 14.827 12724 Z= 0.787 Chirality : 0.077 0.402 1431 Planarity : 0.005 0.067 1619 Dihedral : 19.441 87.521 3292 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.91 % Favored : 92.23 % Rotamer: Outliers : 14.75 % Allowed : 17.86 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1158 helix: 0.00 (0.25), residues: 418 sheet: -0.37 (0.33), residues: 215 loop : -1.64 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 211 HIS 0.006 0.001 HIS A 324 PHE 0.024 0.002 PHE B 199 TYR 0.027 0.002 TYR R 148 ARG 0.008 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 171 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8569 (m) REVERT: A 324 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8622 (p-80) REVERT: A 359 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: B 175 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7625 (mp10) REVERT: B 186 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7015 (m-30) REVERT: B 228 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: B 292 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8551 (m-10) REVERT: P 21 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8520 (tm-30) REVERT: G 21 MET cc_start: 0.6642 (ppp) cc_final: 0.6419 (ppp) REVERT: G 46 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8699 (tppt) REVERT: G 50 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7350 (mm) REVERT: N 34 MET cc_start: 0.8307 (mmm) cc_final: 0.8043 (mmm) REVERT: N 46 GLU cc_start: 0.8158 (pt0) cc_final: 0.7764 (mm-30) REVERT: N 53 GLN cc_start: 0.8153 (mp10) cc_final: 0.7910 (mp10) REVERT: R 31 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8264 (p) REVERT: R 42 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: R 107 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.4978 (pm20) REVERT: R 261 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.6972 (t) REVERT: R 346 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5609 (mmtt) REVERT: R 351 LYS cc_start: 0.8762 (tmtp) cc_final: 0.8389 (tptp) REVERT: R 369 PHE cc_start: 0.8034 (m-80) cc_final: 0.7719 (m-80) outliers start: 142 outliers final: 20 residues processed: 272 average time/residue: 1.1415 time to fit residues: 330.9636 Evaluate side-chains 173 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 190 GLN B 230 ASN G 44 HIS R 63 ASN R 180 HIS R 406 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9364 Z= 0.207 Angle : 0.621 10.636 12724 Z= 0.330 Chirality : 0.042 0.181 1431 Planarity : 0.005 0.052 1619 Dihedral : 8.268 84.965 1332 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 6.13 % Allowed : 23.99 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1158 helix: 1.37 (0.25), residues: 444 sheet: 0.16 (0.34), residues: 211 loop : -1.39 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 110 HIS 0.004 0.001 HIS A 197 PHE 0.018 0.001 PHE A 307 TYR 0.024 0.001 TYR R 148 ARG 0.014 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 159 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.8577 (mt0) cc_final: 0.8241 (mt0) REVERT: A 201 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8504 (t) REVERT: A 209 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.6967 (ptp-170) REVERT: A 281 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8005 (mm-30) REVERT: B 59 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: B 186 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: B 217 MET cc_start: 0.8612 (pmt) cc_final: 0.8292 (pmm) REVERT: P 21 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8502 (tm-30) REVERT: G 21 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6715 (ppp) REVERT: G 46 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8584 (tppt) REVERT: N 34 MET cc_start: 0.8075 (mmm) cc_final: 0.7860 (mmm) REVERT: N 122 THR cc_start: 0.7441 (m) cc_final: 0.7073 (p) REVERT: R 31 SER cc_start: 0.9060 (m) cc_final: 0.8853 (p) REVERT: R 42 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: R 107 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5901 (pm20) REVERT: R 112 GLN cc_start: 0.7142 (mm110) cc_final: 0.6675 (mm110) REVERT: R 261 SER cc_start: 0.6962 (OUTLIER) cc_final: 0.6706 (t) REVERT: R 346 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5258 (mmtt) REVERT: R 351 LYS cc_start: 0.8862 (tmtp) cc_final: 0.8657 (tptm) REVERT: R 370 VAL cc_start: 0.5463 (OUTLIER) cc_final: 0.5179 (t) REVERT: R 371 MET cc_start: 0.8419 (mpp) cc_final: 0.7964 (mpp) outliers start: 59 outliers final: 19 residues processed: 203 average time/residue: 1.1024 time to fit residues: 239.5568 Evaluate side-chains 172 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 209 ARG Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 40.0000 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 230 ASN R 180 HIS R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9364 Z= 0.204 Angle : 0.568 8.241 12724 Z= 0.302 Chirality : 0.040 0.162 1431 Planarity : 0.004 0.047 1619 Dihedral : 6.812 83.800 1306 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 5.09 % Allowed : 25.86 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1158 helix: 1.84 (0.25), residues: 440 sheet: 0.33 (0.35), residues: 211 loop : -1.23 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.002 0.000 HIS A 197 PHE 0.016 0.001 PHE A 307 TYR 0.024 0.001 TYR R 148 ARG 0.008 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 153 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.6788 (OUTLIER) cc_final: 0.6404 (t) REVERT: A 190 GLN cc_start: 0.8638 (mt0) cc_final: 0.8287 (mt0) REVERT: A 281 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: B 37 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.6652 (pp) REVERT: B 59 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: B 217 MET cc_start: 0.8660 (pmt) cc_final: 0.8330 (pmm) REVERT: B 336 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8790 (mp) REVERT: P 17 GLN cc_start: 0.8475 (tt0) cc_final: 0.8235 (tp40) REVERT: P 21 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8480 (tm-30) REVERT: G 38 MET cc_start: 0.7698 (mtp) cc_final: 0.7425 (mtm) REVERT: G 46 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8649 (tppt) REVERT: N 122 THR cc_start: 0.7316 (m) cc_final: 0.7003 (p) REVERT: R 42 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: R 107 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: R 112 GLN cc_start: 0.7520 (mm110) cc_final: 0.7087 (mm110) REVERT: R 221 GLN cc_start: 0.7754 (mm110) cc_final: 0.7520 (mm110) REVERT: R 351 LYS cc_start: 0.8735 (tmtp) cc_final: 0.8533 (tmtp) REVERT: R 371 MET cc_start: 0.8510 (mpp) cc_final: 0.8013 (mpp) outliers start: 49 outliers final: 13 residues processed: 190 average time/residue: 1.1692 time to fit residues: 237.1048 Evaluate side-chains 158 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 343 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 230 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9364 Z= 0.201 Angle : 0.553 8.223 12724 Z= 0.294 Chirality : 0.040 0.152 1431 Planarity : 0.004 0.050 1619 Dihedral : 5.766 83.042 1289 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 4.88 % Allowed : 26.17 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1158 helix: 2.26 (0.25), residues: 430 sheet: 0.51 (0.35), residues: 210 loop : -1.17 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.001 0.000 HIS A 197 PHE 0.013 0.001 PHE A 189 TYR 0.023 0.001 TYR R 148 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8323 (tp30) cc_final: 0.8005 (mm-30) REVERT: A 190 GLN cc_start: 0.8642 (mt0) cc_final: 0.8280 (mt0) REVERT: A 239 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8018 (t0) REVERT: B 59 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: B 186 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7105 (m-30) REVERT: B 217 MET cc_start: 0.8723 (pmt) cc_final: 0.8370 (pmm) REVERT: B 228 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: B 280 LYS cc_start: 0.8585 (tppp) cc_final: 0.8273 (tptp) REVERT: B 336 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8792 (mp) REVERT: P 16 GLU cc_start: 0.8455 (tp30) cc_final: 0.8006 (mm-30) REVERT: P 17 GLN cc_start: 0.8441 (tt0) cc_final: 0.8216 (tp40) REVERT: P 21 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8387 (tm-30) REVERT: G 38 MET cc_start: 0.7772 (mtp) cc_final: 0.7509 (mtm) REVERT: N 53 GLN cc_start: 0.8046 (mp10) cc_final: 0.7737 (mp10) REVERT: N 122 THR cc_start: 0.7245 (m) cc_final: 0.7024 (p) REVERT: R 37 GLN cc_start: 0.9152 (pp30) cc_final: 0.8931 (pp30) REVERT: R 42 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: R 107 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6826 (pm20) REVERT: R 112 GLN cc_start: 0.7233 (mm110) cc_final: 0.6851 (mm110) outliers start: 47 outliers final: 21 residues processed: 185 average time/residue: 1.1922 time to fit residues: 235.6475 Evaluate side-chains 165 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 0.0270 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9364 Z= 0.189 Angle : 0.540 9.526 12724 Z= 0.285 Chirality : 0.039 0.147 1431 Planarity : 0.004 0.050 1619 Dihedral : 5.537 83.254 1284 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 4.67 % Allowed : 26.38 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1158 helix: 2.43 (0.25), residues: 427 sheet: 0.60 (0.35), residues: 208 loop : -1.02 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.001 0.000 HIS B 183 PHE 0.013 0.001 PHE A 189 TYR 0.022 0.001 TYR R 148 ARG 0.007 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8315 (tp30) cc_final: 0.7999 (mm-30) REVERT: A 239 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7996 (t0) REVERT: B 37 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.6838 (pt) REVERT: B 59 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: B 186 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7076 (m-30) REVERT: B 217 MET cc_start: 0.8745 (pmt) cc_final: 0.8327 (pmm) REVERT: B 228 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8428 (m-30) REVERT: B 280 LYS cc_start: 0.8599 (tppp) cc_final: 0.8287 (tptp) REVERT: B 336 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8793 (mp) REVERT: P 16 GLU cc_start: 0.8455 (tp30) cc_final: 0.8104 (mm-30) REVERT: P 21 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8457 (tm-30) REVERT: G 21 MET cc_start: 0.7335 (tmm) cc_final: 0.6942 (ttm) REVERT: G 38 MET cc_start: 0.7775 (mtp) cc_final: 0.7532 (mtm) REVERT: R 37 GLN cc_start: 0.9205 (pp30) cc_final: 0.8995 (pp30) REVERT: R 42 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: R 112 GLN cc_start: 0.7405 (mm110) cc_final: 0.7025 (mm110) outliers start: 45 outliers final: 26 residues processed: 182 average time/residue: 1.1847 time to fit residues: 230.3574 Evaluate side-chains 166 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 133 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN N 31 ASN R 37 GLN R 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9364 Z= 0.310 Angle : 0.590 7.373 12724 Z= 0.313 Chirality : 0.041 0.154 1431 Planarity : 0.004 0.051 1619 Dihedral : 5.405 81.970 1281 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 5.09 % Allowed : 27.10 % Favored : 67.81 % 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: 0.88 (0.26), residues: 1158 helix: 2.31 (0.25), residues: 431 sheet: 0.47 (0.34), residues: 229 loop : -0.95 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 243 HIS 0.002 0.001 HIS B 225 PHE 0.021 0.002 PHE N 108 TYR 0.025 0.002 TYR R 148 ARG 0.008 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8308 (tp30) cc_final: 0.7989 (mm-30) REVERT: B 37 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.6962 (pt) REVERT: B 59 TYR cc_start: 0.9076 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: B 127 LYS cc_start: 0.8670 (mptt) cc_final: 0.8457 (tppp) REVERT: B 186 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.6991 (m-30) REVERT: B 217 MET cc_start: 0.8735 (pmt) cc_final: 0.8356 (pmm) REVERT: B 336 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8832 (mp) REVERT: P 16 GLU cc_start: 0.8511 (tp30) cc_final: 0.8146 (mm-30) REVERT: P 21 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8444 (tm-30) REVERT: G 21 MET cc_start: 0.7365 (tmm) cc_final: 0.7044 (ttm) REVERT: G 38 MET cc_start: 0.7740 (mtp) cc_final: 0.7499 (mtm) REVERT: N 65 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8929 (ttpp) REVERT: N 120 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8272 (mm-40) REVERT: R 42 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: R 112 GLN cc_start: 0.7053 (mm110) cc_final: 0.6695 (mm110) REVERT: R 371 MET cc_start: 0.8407 (mpp) cc_final: 0.7803 (mpp) outliers start: 49 outliers final: 28 residues processed: 175 average time/residue: 1.1858 time to fit residues: 221.1522 Evaluate side-chains 165 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 422 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9364 Z= 0.264 Angle : 0.571 7.539 12724 Z= 0.304 Chirality : 0.041 0.151 1431 Planarity : 0.004 0.052 1619 Dihedral : 5.361 81.119 1281 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 4.78 % Allowed : 27.62 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1158 helix: 2.34 (0.25), residues: 431 sheet: 0.59 (0.34), residues: 226 loop : -0.93 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.002 0.001 HIS B 183 PHE 0.012 0.001 PHE A 189 TYR 0.023 0.001 TYR R 148 ARG 0.009 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 140 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8326 (tp30) cc_final: 0.7996 (mm-30) REVERT: B 37 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.6999 (pt) REVERT: B 59 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: B 127 LYS cc_start: 0.8707 (mptt) cc_final: 0.8493 (tppp) REVERT: B 186 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: B 217 MET cc_start: 0.8770 (pmt) cc_final: 0.8394 (pmm) REVERT: B 228 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8442 (m-30) REVERT: B 336 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8834 (mt) REVERT: P 16 GLU cc_start: 0.8511 (tp30) cc_final: 0.8176 (mm-30) REVERT: P 17 GLN cc_start: 0.8449 (tp40) cc_final: 0.8081 (tt0) REVERT: P 21 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8439 (tm-30) REVERT: G 21 MET cc_start: 0.7350 (tmm) cc_final: 0.7110 (ttm) REVERT: G 38 MET cc_start: 0.7663 (mtp) cc_final: 0.7411 (mtm) REVERT: N 65 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8944 (ttpp) REVERT: N 120 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8247 (mm-40) REVERT: R 42 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: R 112 GLN cc_start: 0.7184 (mm110) cc_final: 0.6835 (mm110) outliers start: 46 outliers final: 31 residues processed: 179 average time/residue: 1.1776 time to fit residues: 225.4389 Evaluate side-chains 175 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 422 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN N 31 ASN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9364 Z= 0.228 Angle : 0.567 7.633 12724 Z= 0.301 Chirality : 0.041 0.148 1431 Planarity : 0.004 0.051 1619 Dihedral : 5.280 79.711 1281 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 5.09 % Allowed : 27.52 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1158 helix: 2.41 (0.25), residues: 431 sheet: 0.55 (0.34), residues: 226 loop : -0.90 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 243 HIS 0.001 0.000 HIS B 183 PHE 0.012 0.001 PHE A 189 TYR 0.021 0.001 TYR R 148 ARG 0.008 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8347 (tp30) cc_final: 0.8023 (mm-30) REVERT: A 281 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: B 37 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7021 (pt) REVERT: B 59 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: B 127 LYS cc_start: 0.8671 (mptt) cc_final: 0.8436 (tppp) REVERT: B 186 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: B 217 MET cc_start: 0.8782 (pmt) cc_final: 0.8442 (pmm) REVERT: B 228 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8412 (m-30) REVERT: B 280 LYS cc_start: 0.8671 (tppp) cc_final: 0.8348 (tptp) REVERT: B 336 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8818 (mt) REVERT: P 16 GLU cc_start: 0.8511 (tp30) cc_final: 0.8171 (mm-30) REVERT: P 21 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8488 (tm-30) REVERT: G 21 MET cc_start: 0.7468 (tmm) cc_final: 0.7251 (ttm) REVERT: G 38 MET cc_start: 0.7615 (mtp) cc_final: 0.7346 (mtm) REVERT: N 120 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8247 (mm-40) REVERT: R 42 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: R 112 GLN cc_start: 0.7360 (mm110) cc_final: 0.6989 (mm110) outliers start: 49 outliers final: 29 residues processed: 175 average time/residue: 1.2092 time to fit residues: 226.0432 Evaluate side-chains 173 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 50.0000 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 216 ASN B 230 ASN N 31 ASN R 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9364 Z= 0.266 Angle : 0.606 9.194 12724 Z= 0.323 Chirality : 0.042 0.309 1431 Planarity : 0.004 0.051 1619 Dihedral : 4.810 55.119 1278 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.36 % Allowed : 28.14 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1158 helix: 2.41 (0.25), residues: 429 sheet: 0.48 (0.34), residues: 228 loop : -0.94 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 72 HIS 0.001 0.000 HIS B 183 PHE 0.015 0.001 PHE A 189 TYR 0.022 0.001 TYR R 148 ARG 0.011 0.001 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8338 (tp30) cc_final: 0.8015 (mm-30) REVERT: A 281 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: B 37 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7039 (pt) REVERT: B 59 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: B 186 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: B 217 MET cc_start: 0.8794 (pmt) cc_final: 0.8423 (pmm) REVERT: B 228 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8411 (m-30) REVERT: B 280 LYS cc_start: 0.8684 (tppp) cc_final: 0.8357 (tptp) REVERT: B 336 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8823 (mt) REVERT: P 16 GLU cc_start: 0.8539 (tp30) cc_final: 0.8258 (mm-30) REVERT: P 17 GLN cc_start: 0.8455 (tp40) cc_final: 0.8018 (mt0) REVERT: P 21 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8481 (tm-30) REVERT: G 21 MET cc_start: 0.7447 (tmm) cc_final: 0.7218 (ttm) REVERT: G 38 MET cc_start: 0.7667 (mtp) cc_final: 0.7412 (mtm) REVERT: N 65 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8956 (ttpp) REVERT: N 120 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8219 (mm-40) REVERT: R 42 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7658 (m-80) REVERT: R 112 GLN cc_start: 0.7374 (mm110) cc_final: 0.7023 (mm110) outliers start: 42 outliers final: 29 residues processed: 172 average time/residue: 1.1857 time to fit residues: 217.8154 Evaluate side-chains 172 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 135 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 74 ASP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN N 31 ASN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9364 Z= 0.214 Angle : 0.596 8.639 12724 Z= 0.314 Chirality : 0.041 0.211 1431 Planarity : 0.004 0.051 1619 Dihedral : 4.748 56.589 1278 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 3.43 % Allowed : 29.18 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1158 helix: 2.53 (0.25), residues: 429 sheet: 0.57 (0.34), residues: 227 loop : -0.95 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 243 HIS 0.001 0.000 HIS B 183 PHE 0.012 0.001 PHE A 189 TYR 0.020 0.001 TYR R 148 ARG 0.009 0.000 ARG R 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8301 (tp30) cc_final: 0.7984 (mm-30) REVERT: A 53 MET cc_start: 0.6342 (tmt) cc_final: 0.5756 (tmm) REVERT: A 281 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: B 37 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7027 (pt) REVERT: B 59 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: B 186 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: B 217 MET cc_start: 0.8815 (pmt) cc_final: 0.8426 (pmm) REVERT: B 228 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: B 280 LYS cc_start: 0.8662 (tppp) cc_final: 0.8345 (tptp) REVERT: B 336 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8808 (mt) REVERT: P 16 GLU cc_start: 0.8565 (tp30) cc_final: 0.8289 (mm-30) REVERT: P 17 GLN cc_start: 0.8406 (tp40) cc_final: 0.8002 (mt0) REVERT: P 21 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8488 (tm-30) REVERT: G 21 MET cc_start: 0.7488 (tmm) cc_final: 0.7264 (ttm) REVERT: G 38 MET cc_start: 0.7662 (mtp) cc_final: 0.7405 (mtm) REVERT: N 65 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8948 (ttpp) REVERT: N 120 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8198 (mm-40) REVERT: R 42 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: R 112 GLN cc_start: 0.7408 (mm110) cc_final: 0.7064 (mm110) REVERT: R 371 MET cc_start: 0.8313 (mpp) cc_final: 0.7861 (mmt) outliers start: 33 outliers final: 27 residues processed: 167 average time/residue: 1.2363 time to fit residues: 220.1623 Evaluate side-chains 171 residues out of total 1019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 106 ASP Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 422 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 64 optimal weight: 0.0570 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN N 31 ASN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.125944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081068 restraints weight = 15407.752| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.11 r_work: 0.2921 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9364 Z= 0.284 Angle : 0.610 9.629 12724 Z= 0.322 Chirality : 0.041 0.198 1431 Planarity : 0.004 0.051 1619 Dihedral : 4.779 56.789 1278 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 4.26 % Allowed : 28.56 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1158 helix: 2.52 (0.24), residues: 429 sheet: 0.46 (0.33), residues: 228 loop : -0.92 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.002 0.000 HIS B 183 PHE 0.013 0.001 PHE R 230 TYR 0.023 0.001 TYR R 148 ARG 0.007 0.000 ARG G 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.53 seconds wall clock time: 75 minutes 47.84 seconds (4547.84 seconds total)