Starting phenix.real_space_refine on Wed Feb 14 10:24:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/02_2024/7tyo_26190.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/02_2024/7tyo_26190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/02_2024/7tyo_26190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/02_2024/7tyo_26190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/02_2024/7tyo_26190.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyo_26190/02_2024/7tyo_26190.pdb" } resolution = 2.7 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= 0.006 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 64 5.16 5 C 5781 2.51 5 N 1561 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9052 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1889 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 239 Unusual residues: {'NH2': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 2, 'TRANS': 29} Chain: "R" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2921 Unusual residues: {'NAG': 1, 'Y01': 2} Classifications: {'peptide': 359, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 14, 'TRANS': 344, None: 3} Not linked: pdbres="PHE R 409 " pdbres="NAG R 501 " Not linked: pdbres="NAG R 501 " pdbres="Y01 R 502 " Not linked: pdbres="Y01 R 502 " pdbres="Y01 R 503 " Chain breaks: 2 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 5.46, per 1000 atoms: 0.60 Number of scatterers: 9052 At special positions: 0 Unit cell: (116.086, 100.547, 140.766, 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 64 16.00 O 1646 8.00 N 1561 7.00 C 5781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.04 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 41.0% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.774A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.911A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.526A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.710A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.522A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.507A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 25 removed outlier: 4.068A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.526A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.516A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.623A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.607A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 18 removed outlier: 3.543A pdb=" N THR P 11 " --> pdb=" O CYS P 7 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS P 18 " --> pdb=" O GLN P 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 60 Processing helix chain 'R' and resid 140 through 173 Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.671A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE R 199 " --> pdb=" O SER R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.872A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 267 removed outlier: 4.134A pdb=" N TYR R 262 " --> pdb=" O ARG R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 298 through 329 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 removed outlier: 4.353A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 342 " --> pdb=" O TYR R 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 367 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 removed outlier: 3.526A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG R 404 " --> pdb=" O THR R 400 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA R 407 " --> pdb=" O LYS R 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.527A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.589A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.993A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.699A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.503A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.267A 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: 6.408A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.166A 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 234 removed outlier: 3.676A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.010A 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: 3.780A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG B 304 " --> 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 10 through 12 removed outlier: 6.806A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 75 through 77 removed outlier: 3.651A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP R 82 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 80 " --> pdb=" O ASP R 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 89 through 90 removed outlier: 3.778A pdb=" N VAL R 89 " --> pdb=" O CYS R 112 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1251 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: 2.48 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1454 1.32 - 1.44: 2621 1.44 - 1.57: 5100 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9265 Sorted by residual: bond pdb=" N LYS A 280 " pdb=" CA LYS A 280 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.27e-02 6.20e+03 6.96e+00 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.22e-02 6.72e+03 5.00e+00 bond pdb=" N ASP A 284 " pdb=" CA ASP A 284 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.16e-02 7.43e+03 4.80e+00 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.23e+00 bond pdb=" C VAL R 206 " pdb=" N PRO R 207 " ideal model delta sigma weight residual 1.335 1.353 -0.018 9.40e-03 1.13e+04 3.79e+00 ... (remaining 9260 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.50: 232 106.50 - 113.38: 4992 113.38 - 120.26: 3361 120.26 - 127.14: 3884 127.14 - 134.02: 108 Bond angle restraints: 12577 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 105.03 6.97 1.40e+00 5.10e-01 2.48e+01 angle pdb=" CA ASP A 274 " pdb=" C ASP A 274 " pdb=" O ASP A 274 " ideal model delta sigma weight residual 120.82 117.05 3.77 1.05e+00 9.07e-01 1.29e+01 angle pdb=" N VAL R 357 " pdb=" CA VAL R 357 " pdb=" C VAL R 357 " ideal model delta sigma weight residual 112.96 109.57 3.39 1.00e+00 1.00e+00 1.15e+01 angle pdb=" C ILE R 248 " pdb=" N VAL R 249 " pdb=" CA VAL R 249 " ideal model delta sigma weight residual 122.97 120.20 2.77 9.80e-01 1.04e+00 7.99e+00 angle pdb=" N ALA A 226 " pdb=" CA ALA A 226 " pdb=" C ALA A 226 " ideal model delta sigma weight residual 109.39 113.75 -4.36 1.59e+00 3.96e-01 7.53e+00 ... (remaining 12572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5168 17.91 - 35.81: 322 35.81 - 53.72: 73 53.72 - 71.63: 20 71.63 - 89.53: 7 Dihedral angle restraints: 5590 sinusoidal: 2266 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 50.74 42.26 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB CYS R 219 " pdb=" SG CYS R 219 " pdb=" SG CYS R 289 " pdb=" CB CYS R 289 " ideal model delta sinusoidal sigma weight residual 93.00 53.76 39.24 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual -86.00 -121.65 35.65 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 5587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1100 0.044 - 0.089: 233 0.089 - 0.133: 63 0.133 - 0.177: 4 0.177 - 0.222: 1 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CBE Y01 R 503 " pdb=" CAP Y01 R 503 " pdb=" CBB Y01 R 503 " pdb=" CBI Y01 R 503 " both_signs ideal model delta sigma weight residual False 2.57 2.35 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LYS A 280 " pdb=" N LYS A 280 " pdb=" C LYS A 280 " pdb=" CB LYS A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" C PRO P 32 " pdb=" CB PRO P 32 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 1398 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 31 " -0.082 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO P 32 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 138 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO R 139 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 139 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 139 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PRO B 236 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.020 5.00e-02 4.00e+02 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 287 2.72 - 3.27: 9093 3.27 - 3.81: 14602 3.81 - 4.36: 19203 4.36 - 4.90: 31737 Nonbonded interactions: 74922 Sorted by model distance: nonbonded pdb=" OH TYR P 12 " pdb=" O ALA R 145 " model vdw 2.176 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR R 149 " pdb=" O LEU R 202 " model vdw 2.294 2.440 nonbonded pdb=" O PRO R 270 " pdb=" OG1 THR R 274 " model vdw 2.306 2.440 ... (remaining 74917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.790 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: 4.130 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.240 Find NCS groups from input model: 0.250 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 : 0.002 0.034 9265 Z= 0.132 Angle : 0.466 6.965 12577 Z= 0.287 Chirality : 0.039 0.222 1401 Planarity : 0.004 0.120 1594 Dihedral : 12.868 89.532 3421 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.37 % Allowed : 10.78 % Favored : 87.84 % 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: -3.13 (0.21), residues: 1121 helix: -2.90 (0.16), residues: 427 sheet: -0.61 (0.31), residues: 239 loop : -1.84 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.002 0.000 HIS B 62 PHE 0.009 0.001 PHE B 151 TYR 0.007 0.001 TYR N 60 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.096 Fit side-chains REVERT: A 60 MET cc_start: 0.3277 (mtm) cc_final: 0.2369 (mtm) REVERT: A 356 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.6277 (mtm180) REVERT: A 372 ILE cc_start: 0.8158 (pt) cc_final: 0.7950 (pt) REVERT: B 101 MET cc_start: 0.8307 (mtp) cc_final: 0.7958 (mtp) REVERT: B 186 ASP cc_start: 0.7000 (m-30) cc_final: 0.6617 (m-30) REVERT: B 260 GLU cc_start: 0.7260 (pt0) cc_final: 0.7030 (pt0) REVERT: G 13 ARG cc_start: 0.6247 (mtt90) cc_final: 0.5784 (mmt90) REVERT: G 32 LYS cc_start: 0.7543 (tmtt) cc_final: 0.7326 (ttpp) REVERT: G 47 GLU cc_start: 0.6054 (mt-10) cc_final: 0.5582 (tm-30) REVERT: N 89 GLU cc_start: 0.6790 (mp0) cc_final: 0.6478 (mp0) REVERT: N 106 ASP cc_start: 0.8142 (p0) cc_final: 0.7853 (p0) REVERT: R 143 LYS cc_start: 0.6099 (tttm) cc_final: 0.4797 (tptm) REVERT: R 161 PHE cc_start: 0.6339 (t80) cc_final: 0.6107 (t80) REVERT: R 187 MET cc_start: 0.7339 (tpt) cc_final: 0.7104 (tpt) REVERT: R 210 GLU cc_start: 0.6556 (mp0) cc_final: 0.6314 (mp0) REVERT: R 214 ARG cc_start: 0.5122 (ttp-110) cc_final: 0.4675 (ttp-170) REVERT: R 343 LYS cc_start: 0.6465 (mmtt) cc_final: 0.6104 (tttt) outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 1.4536 time to fit residues: 259.3558 Evaluate side-chains 122 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 253 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 31 GLN A 294 GLN B 17 GLN B 36 ASN B 75 GLN G 24 ASN N 5 GLN N 13 GLN P 14 GLN R 135 ASN R 144 ASN R 179 GLN R 201 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9265 Z= 0.290 Angle : 0.616 7.648 12577 Z= 0.331 Chirality : 0.045 0.202 1401 Planarity : 0.005 0.060 1594 Dihedral : 6.749 57.610 1412 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.02 % Allowed : 14.69 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1121 helix: -0.06 (0.24), residues: 438 sheet: -0.50 (0.31), residues: 238 loop : -1.50 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 236 HIS 0.006 0.001 HIS R 184 PHE 0.026 0.002 PHE A 212 TYR 0.012 0.002 TYR R 391 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 1.059 Fit side-chains REVERT: A 60 MET cc_start: 0.3521 (mtm) cc_final: 0.2676 (mtm) REVERT: A 283 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6825 (mtt-85) REVERT: B 101 MET cc_start: 0.8296 (mtp) cc_final: 0.8032 (mtp) REVERT: B 260 GLU cc_start: 0.7308 (pt0) cc_final: 0.7065 (pt0) REVERT: G 32 LYS cc_start: 0.7526 (tmtt) cc_final: 0.7311 (ttpp) REVERT: G 47 GLU cc_start: 0.5945 (mt-10) cc_final: 0.5613 (tm-30) REVERT: G 59 ASN cc_start: 0.6285 (p0) cc_final: 0.6048 (p0) REVERT: N 1 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: P 12 TYR cc_start: 0.7052 (t80) cc_final: 0.6791 (t80) REVERT: R 79 TRP cc_start: 0.3045 (OUTLIER) cc_final: 0.1494 (m-90) REVERT: R 143 LYS cc_start: 0.5794 (tttm) cc_final: 0.4544 (tptm) REVERT: R 202 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7721 (tp) REVERT: R 210 GLU cc_start: 0.6584 (mp0) cc_final: 0.6306 (mp0) REVERT: R 214 ARG cc_start: 0.5159 (ttp-110) cc_final: 0.4768 (ttp-170) REVERT: R 343 LYS cc_start: 0.6609 (mmtt) cc_final: 0.6089 (tttt) outliers start: 38 outliers final: 14 residues processed: 152 average time/residue: 1.3023 time to fit residues: 209.8971 Evaluate side-chains 136 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 253 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN P 24 GLN R 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9265 Z= 0.239 Angle : 0.562 6.280 12577 Z= 0.301 Chirality : 0.044 0.188 1401 Planarity : 0.004 0.050 1594 Dihedral : 6.337 53.223 1409 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.86 % Allowed : 16.07 % Favored : 79.07 % 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: -0.32 (0.25), residues: 1121 helix: 1.01 (0.25), residues: 438 sheet: -0.41 (0.32), residues: 234 loop : -1.28 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 236 HIS 0.005 0.001 HIS R 184 PHE 0.023 0.002 PHE R 161 TYR 0.011 0.001 TYR R 149 ARG 0.004 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 time to evaluate : 1.148 Fit side-chains REVERT: A 60 MET cc_start: 0.3705 (mtm) cc_final: 0.2855 (mtm) REVERT: A 220 HIS cc_start: 0.7396 (t-170) cc_final: 0.7192 (t-90) REVERT: A 300 LYS cc_start: 0.5365 (mtpt) cc_final: 0.5163 (mtpt) REVERT: B 101 MET cc_start: 0.8283 (mtp) cc_final: 0.7980 (mtp) REVERT: B 260 GLU cc_start: 0.7302 (pt0) cc_final: 0.7067 (pt0) REVERT: G 47 GLU cc_start: 0.6062 (mt-10) cc_final: 0.5683 (tm-30) REVERT: N 1 GLN cc_start: 0.7274 (tt0) cc_final: 0.6493 (tm-30) REVERT: P 12 TYR cc_start: 0.7157 (t80) cc_final: 0.6921 (t80) REVERT: R 79 TRP cc_start: 0.3161 (OUTLIER) cc_final: 0.1469 (m-90) REVERT: R 131 TYR cc_start: 0.4182 (m-80) cc_final: 0.3053 (m-80) REVERT: R 143 LYS cc_start: 0.5939 (tttm) cc_final: 0.4693 (tptm) REVERT: R 158 LEU cc_start: 0.7481 (tp) cc_final: 0.7186 (tt) REVERT: R 172 PHE cc_start: 0.5352 (t80) cc_final: 0.4782 (t80) REVERT: R 187 MET cc_start: 0.7361 (tpt) cc_final: 0.7048 (tpt) REVERT: R 202 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7702 (tp) REVERT: R 210 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: R 260 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.6105 (ptm160) REVERT: R 397 GLU cc_start: 0.6748 (tt0) cc_final: 0.6435 (tm-30) outliers start: 46 outliers final: 21 residues processed: 154 average time/residue: 1.3307 time to fit residues: 218.8234 Evaluate side-chains 141 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 210 GLU Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.0270 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9265 Z= 0.210 Angle : 0.535 6.688 12577 Z= 0.287 Chirality : 0.043 0.189 1401 Planarity : 0.004 0.064 1594 Dihedral : 6.165 54.768 1406 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.86 % Allowed : 17.12 % Favored : 78.01 % 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: 0.02 (0.25), residues: 1121 helix: 1.44 (0.26), residues: 431 sheet: -0.17 (0.32), residues: 228 loop : -1.26 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 236 HIS 0.004 0.001 HIS R 184 PHE 0.022 0.002 PHE P 19 TYR 0.010 0.001 TYR R 149 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 1.051 Fit side-chains REVERT: A 60 MET cc_start: 0.3547 (mtm) cc_final: 0.2846 (mtm) REVERT: A 307 LYS cc_start: 0.5943 (tptt) cc_final: 0.5590 (pmtt) REVERT: A 372 ILE cc_start: 0.7849 (pt) cc_final: 0.7461 (mp) REVERT: B 101 MET cc_start: 0.8274 (mtp) cc_final: 0.7922 (mtp) REVERT: B 130 GLU cc_start: 0.4441 (OUTLIER) cc_final: 0.3427 (mt-10) REVERT: B 260 GLU cc_start: 0.7306 (pt0) cc_final: 0.7071 (pt0) REVERT: G 20 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7403 (mttt) REVERT: G 37 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7566 (mp) REVERT: G 47 GLU cc_start: 0.6117 (mt-10) cc_final: 0.5710 (tm-30) REVERT: G 62 ARG cc_start: 0.3699 (pmm-80) cc_final: 0.3344 (pmm-80) REVERT: N 1 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6445 (tm-30) REVERT: N 12 VAL cc_start: 0.8210 (p) cc_final: 0.7974 (p) REVERT: P 19 PHE cc_start: 0.6964 (m-80) cc_final: 0.6750 (m-80) REVERT: R 131 TYR cc_start: 0.4129 (m-80) cc_final: 0.2937 (m-80) REVERT: R 143 LYS cc_start: 0.6016 (tttm) cc_final: 0.4667 (tptt) REVERT: R 172 PHE cc_start: 0.5318 (t80) cc_final: 0.4738 (t80) REVERT: R 187 MET cc_start: 0.7351 (tpt) cc_final: 0.7009 (tpt) REVERT: R 202 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7744 (tp) REVERT: R 210 GLU cc_start: 0.6673 (mp0) cc_final: 0.6413 (mp0) REVERT: R 260 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.6064 (ptm160) REVERT: R 397 GLU cc_start: 0.6737 (tt0) cc_final: 0.6421 (tm-30) outliers start: 46 outliers final: 22 residues processed: 147 average time/residue: 1.4123 time to fit residues: 221.8121 Evaluate side-chains 141 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9265 Z= 0.287 Angle : 0.600 7.008 12577 Z= 0.319 Chirality : 0.045 0.197 1401 Planarity : 0.004 0.056 1594 Dihedral : 6.343 46.925 1406 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.29 % Allowed : 17.55 % Favored : 77.17 % 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: -0.09 (0.25), residues: 1121 helix: 1.25 (0.25), residues: 437 sheet: -0.19 (0.32), residues: 229 loop : -1.26 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 236 HIS 0.006 0.001 HIS R 184 PHE 0.025 0.002 PHE A 212 TYR 0.016 0.002 TYR A 358 ARG 0.005 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 112 time to evaluate : 1.255 Fit side-chains REVERT: A 60 MET cc_start: 0.3527 (mtm) cc_final: 0.2835 (mtm) REVERT: A 307 LYS cc_start: 0.5855 (tptt) cc_final: 0.5637 (pmtt) REVERT: A 372 ILE cc_start: 0.7855 (pt) cc_final: 0.7496 (mp) REVERT: B 101 MET cc_start: 0.8258 (mtp) cc_final: 0.8006 (mtp) REVERT: B 130 GLU cc_start: 0.4424 (OUTLIER) cc_final: 0.3385 (mt-10) REVERT: B 260 GLU cc_start: 0.7295 (pt0) cc_final: 0.7030 (pt0) REVERT: G 20 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7522 (mmtt) REVERT: N 1 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: N 89 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: R 79 TRP cc_start: 0.2873 (OUTLIER) cc_final: 0.1420 (m100) REVERT: R 131 TYR cc_start: 0.4086 (m-80) cc_final: 0.2900 (m-80) REVERT: R 143 LYS cc_start: 0.5938 (tttm) cc_final: 0.4682 (tptt) REVERT: R 172 PHE cc_start: 0.5390 (t80) cc_final: 0.4772 (t80) REVERT: R 187 MET cc_start: 0.7371 (tpt) cc_final: 0.7080 (tpt) REVERT: R 202 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7653 (tp) REVERT: R 210 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: R 260 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6111 (ptm160) REVERT: R 300 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8189 (mt) outliers start: 50 outliers final: 23 residues processed: 146 average time/residue: 1.5062 time to fit residues: 235.0025 Evaluate side-chains 141 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 210 GLU Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9265 Z= 0.141 Angle : 0.479 6.543 12577 Z= 0.255 Chirality : 0.041 0.185 1401 Planarity : 0.003 0.045 1594 Dihedral : 5.772 45.890 1404 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.81 % Allowed : 19.34 % Favored : 76.85 % 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: 0.45 (0.25), residues: 1121 helix: 1.86 (0.26), residues: 431 sheet: 0.12 (0.33), residues: 216 loop : -1.10 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.003 0.001 HIS A 41 PHE 0.024 0.001 PHE R 161 TYR 0.011 0.001 TYR R 149 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.109 Fit side-chains REVERT: A 60 MET cc_start: 0.3443 (mtm) cc_final: 0.2785 (mtm) REVERT: A 307 LYS cc_start: 0.5788 (tptt) cc_final: 0.5568 (pmtt) REVERT: A 372 ILE cc_start: 0.7699 (pt) cc_final: 0.7434 (mp) REVERT: B 15 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7200 (mttm) REVERT: B 101 MET cc_start: 0.8270 (mtp) cc_final: 0.7985 (mtp) REVERT: B 130 GLU cc_start: 0.4551 (OUTLIER) cc_final: 0.3540 (mt-10) REVERT: B 260 GLU cc_start: 0.7288 (pt0) cc_final: 0.6963 (pt0) REVERT: G 19 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7518 (mm) REVERT: G 20 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7474 (mttt) REVERT: N 1 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: N 3 GLN cc_start: 0.7415 (tt0) cc_final: 0.7131 (tp40) REVERT: P 19 PHE cc_start: 0.6922 (m-80) cc_final: 0.6688 (m-80) REVERT: R 79 TRP cc_start: 0.2800 (OUTLIER) cc_final: 0.1439 (m100) REVERT: R 131 TYR cc_start: 0.4118 (m-80) cc_final: 0.2953 (m-80) REVERT: R 172 PHE cc_start: 0.5242 (t80) cc_final: 0.4688 (t80) REVERT: R 202 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7644 (tp) REVERT: R 210 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6272 (mp0) REVERT: R 260 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6046 (ptm160) REVERT: R 320 VAL cc_start: 0.7768 (p) cc_final: 0.7559 (t) outliers start: 36 outliers final: 14 residues processed: 147 average time/residue: 1.2367 time to fit residues: 194.0775 Evaluate side-chains 136 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 210 GLU Chi-restraints excluded: chain R residue 260 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.0070 chunk 65 optimal weight: 0.2980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9265 Z= 0.121 Angle : 0.455 7.252 12577 Z= 0.243 Chirality : 0.040 0.170 1401 Planarity : 0.003 0.043 1594 Dihedral : 5.392 44.489 1404 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.38 % Allowed : 20.61 % Favored : 76.00 % 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: 0.86 (0.26), residues: 1121 helix: 2.19 (0.26), residues: 432 sheet: 0.27 (0.33), residues: 220 loop : -0.84 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.003 0.001 HIS A 220 PHE 0.014 0.001 PHE P 19 TYR 0.009 0.001 TYR N 60 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.017 Fit side-chains REVERT: A 60 MET cc_start: 0.3380 (mtm) cc_final: 0.2817 (mtm) REVERT: A 220 HIS cc_start: 0.7475 (t-90) cc_final: 0.6980 (t-90) REVERT: A 265 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6463 (ttt-90) REVERT: A 307 LYS cc_start: 0.5782 (tptt) cc_final: 0.5530 (pmtt) REVERT: A 372 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7453 (mp) REVERT: B 9 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.6208 (mm-40) REVERT: B 101 MET cc_start: 0.8258 (mtp) cc_final: 0.7936 (mtp) REVERT: B 130 GLU cc_start: 0.4529 (OUTLIER) cc_final: 0.3553 (mt-10) REVERT: B 217 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7300 (pp-130) REVERT: B 260 GLU cc_start: 0.7259 (pt0) cc_final: 0.7001 (pt0) REVERT: G 19 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7521 (mm) REVERT: G 20 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7366 (mttt) REVERT: N 1 GLN cc_start: 0.7311 (tt0) cc_final: 0.6469 (tm-30) REVERT: N 3 GLN cc_start: 0.7392 (tt0) cc_final: 0.7113 (tp40) REVERT: P 19 PHE cc_start: 0.7003 (m-80) cc_final: 0.6796 (m-80) REVERT: R 79 TRP cc_start: 0.2653 (OUTLIER) cc_final: 0.1445 (m100) REVERT: R 131 TYR cc_start: 0.4106 (m-80) cc_final: 0.2877 (m-80) REVERT: R 202 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7643 (tp) REVERT: R 229 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7130 (tpp) REVERT: R 320 VAL cc_start: 0.7753 (p) cc_final: 0.7543 (t) outliers start: 32 outliers final: 11 residues processed: 147 average time/residue: 1.2975 time to fit residues: 202.8875 Evaluate side-chains 129 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 229 MET Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9265 Z= 0.269 Angle : 0.578 8.380 12577 Z= 0.306 Chirality : 0.044 0.198 1401 Planarity : 0.004 0.049 1594 Dihedral : 5.816 45.390 1403 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.65 % Allowed : 19.56 % Favored : 75.79 % 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: 0.47 (0.25), residues: 1121 helix: 1.72 (0.25), residues: 439 sheet: 0.19 (0.33), residues: 217 loop : -1.00 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 236 HIS 0.005 0.001 HIS R 184 PHE 0.023 0.002 PHE R 161 TYR 0.015 0.002 TYR A 358 ARG 0.005 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 108 time to evaluate : 1.098 Fit side-chains REVERT: A 60 MET cc_start: 0.3363 (mtm) cc_final: 0.2797 (mtm) REVERT: A 265 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6478 (ttt-90) REVERT: A 372 ILE cc_start: 0.7739 (pt) cc_final: 0.7456 (mp) REVERT: B 9 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6261 (mm-40) REVERT: B 130 GLU cc_start: 0.4249 (OUTLIER) cc_final: 0.3216 (mt-10) REVERT: B 154 ASP cc_start: 0.7387 (m-30) cc_final: 0.7070 (m-30) REVERT: B 260 GLU cc_start: 0.7320 (pt0) cc_final: 0.7048 (pt0) REVERT: G 19 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7543 (mm) REVERT: G 20 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7250 (mmtt) REVERT: G 37 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7611 (mp) REVERT: N 1 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: N 83 MET cc_start: 0.8172 (mtp) cc_final: 0.7939 (mtp) REVERT: R 79 TRP cc_start: 0.2720 (OUTLIER) cc_final: 0.1406 (m100) REVERT: R 131 TYR cc_start: 0.4153 (m-80) cc_final: 0.3001 (m-80) REVERT: R 202 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7585 (tp) REVERT: R 300 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8239 (mt) outliers start: 44 outliers final: 21 residues processed: 138 average time/residue: 1.2697 time to fit residues: 187.1115 Evaluate side-chains 140 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9265 Z= 0.136 Angle : 0.483 8.281 12577 Z= 0.255 Chirality : 0.041 0.178 1401 Planarity : 0.003 0.043 1594 Dihedral : 5.412 44.487 1403 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.75 % Allowed : 21.67 % Favored : 75.58 % 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: 1121 helix: 2.16 (0.26), residues: 434 sheet: 0.40 (0.33), residues: 218 loop : -0.81 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 236 HIS 0.002 0.001 HIS R 302 PHE 0.026 0.001 PHE R 161 TYR 0.010 0.001 TYR N 60 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 1.116 Fit side-chains REVERT: A 60 MET cc_start: 0.3334 (mtm) cc_final: 0.2801 (mtm) REVERT: A 209 GLU cc_start: 0.6674 (mp0) cc_final: 0.6302 (mp0) REVERT: A 265 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6495 (ttt-90) REVERT: A 307 LYS cc_start: 0.5872 (pmtt) cc_final: 0.5518 (tptt) REVERT: A 372 ILE cc_start: 0.7705 (pt) cc_final: 0.7463 (mp) REVERT: B 9 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.6231 (mm-40) REVERT: B 130 GLU cc_start: 0.4250 (OUTLIER) cc_final: 0.3253 (mt-10) REVERT: B 260 GLU cc_start: 0.7227 (pt0) cc_final: 0.6889 (pt0) REVERT: G 19 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7597 (mm) REVERT: G 20 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7255 (mmtt) REVERT: N 1 GLN cc_start: 0.7293 (tt0) cc_final: 0.6566 (tm-30) REVERT: N 3 GLN cc_start: 0.7403 (tt0) cc_final: 0.7117 (tp40) REVERT: P 19 PHE cc_start: 0.6909 (m-80) cc_final: 0.6655 (m-80) REVERT: R 79 TRP cc_start: 0.2698 (OUTLIER) cc_final: 0.1604 (m100) REVERT: R 131 TYR cc_start: 0.4218 (m-80) cc_final: 0.3025 (m-80) REVERT: R 172 PHE cc_start: 0.5188 (t80) cc_final: 0.4615 (t80) REVERT: R 202 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7643 (tp) REVERT: R 300 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8025 (mp) REVERT: R 320 VAL cc_start: 0.7753 (p) cc_final: 0.7544 (t) REVERT: R 397 GLU cc_start: 0.6720 (tt0) cc_final: 0.6443 (tm-30) outliers start: 26 outliers final: 12 residues processed: 129 average time/residue: 1.3400 time to fit residues: 183.8151 Evaluate side-chains 128 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9265 Z= 0.205 Angle : 0.535 9.612 12577 Z= 0.283 Chirality : 0.043 0.186 1401 Planarity : 0.004 0.044 1594 Dihedral : 5.601 45.312 1403 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.85 % Allowed : 21.56 % Favored : 75.58 % 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: 0.75 (0.25), residues: 1121 helix: 2.03 (0.26), residues: 434 sheet: 0.35 (0.34), residues: 216 loop : -0.91 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 236 HIS 0.004 0.001 HIS R 184 PHE 0.019 0.002 PHE P 19 TYR 0.013 0.001 TYR A 358 ARG 0.005 0.000 ARG B 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 1.125 Fit side-chains REVERT: A 34 LYS cc_start: 0.7383 (tttt) cc_final: 0.7175 (ttpp) REVERT: A 60 MET cc_start: 0.3354 (mtm) cc_final: 0.2844 (mtm) REVERT: A 209 GLU cc_start: 0.6744 (mp0) cc_final: 0.6451 (mp0) REVERT: A 265 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6488 (ttt-90) REVERT: A 372 ILE cc_start: 0.7724 (pt) cc_final: 0.7478 (mp) REVERT: B 9 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6354 (mm-40) REVERT: B 130 GLU cc_start: 0.4153 (OUTLIER) cc_final: 0.3220 (mt-10) REVERT: B 260 GLU cc_start: 0.7292 (pt0) cc_final: 0.6964 (pt0) REVERT: G 19 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7564 (mm) REVERT: G 20 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7260 (mmtt) REVERT: N 1 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: P 19 PHE cc_start: 0.6948 (m-80) cc_final: 0.6655 (m-80) REVERT: R 79 TRP cc_start: 0.2690 (OUTLIER) cc_final: 0.1515 (m100) REVERT: R 131 TYR cc_start: 0.4159 (m-80) cc_final: 0.2959 (m-80) REVERT: R 202 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7609 (tp) REVERT: R 300 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8177 (mt) REVERT: R 397 GLU cc_start: 0.6680 (tt0) cc_final: 0.6372 (tm-30) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 1.3847 time to fit residues: 189.9453 Evaluate side-chains 131 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.0270 chunk 77 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126275 restraints weight = 10816.100| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.74 r_work: 0.3405 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9265 Z= 0.129 Angle : 0.472 7.382 12577 Z= 0.249 Chirality : 0.040 0.179 1401 Planarity : 0.003 0.042 1594 Dihedral : 5.275 44.559 1403 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.64 % Allowed : 21.99 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1121 helix: 2.30 (0.26), residues: 434 sheet: 0.46 (0.34), residues: 220 loop : -0.73 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 236 HIS 0.002 0.001 HIS R 302 PHE 0.027 0.001 PHE R 161 TYR 0.010 0.001 TYR N 60 ARG 0.005 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.91 seconds wall clock time: 70 minutes 32.09 seconds (4232.09 seconds total)