Starting phenix.real_space_refine on Sun Jun 8 04:25:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyo_26190/06_2025/7tyo_26190.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyo_26190/06_2025/7tyo_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/cci-nas-00/data/ceres_data/7tyo_26190/06_2025/7tyo_26190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyo_26190/06_2025/7tyo_26190.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyo_26190/06_2025/7tyo_26190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyo_26190/06_2025/7tyo_26190.cif" } 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. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9052 Number of models: 1 Model: "" Number of chains: 8 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: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2837 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 14, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 11 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 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'NAG': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.21, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.2 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: 1.03 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: 2.78 Time building geometry restraints manager: 3.17 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: 2620 1.44 - 1.57: 5100 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9264 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 9259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 12318 1.39 - 2.79: 218 2.79 - 4.18: 32 4.18 - 5.57: 5 5.57 - 6.97: 2 Bond angle restraints: 12575 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 12570 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: 1594 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 1591 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 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR R 149 " pdb=" O LEU R 202 " model vdw 2.294 3.040 nonbonded pdb=" O PRO R 270 " pdb=" OG1 THR R 274 " model vdw 2.306 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.680 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.180 Process input model: 25.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.410 ------------------------------------------------------------------------------- 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 0.107 9273 Z= 0.161 Angle : 0.466 6.965 12592 Z= 0.287 Chirality : 0.039 0.222 1401 Planarity : 0.004 0.120 1593 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 0.61725 ( 3) hydrogen bonds : bond 0.27119 ( 441) hydrogen bonds : angle 9.01681 ( 1251) SS BOND : bond 0.00377 ( 7) SS BOND : angle 0.57567 ( 14) covalent geometry : bond 0.00204 ( 9264) covalent geometry : angle 0.46561 (12575) Misc. bond : bond 0.10707 ( 1) *********************** 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 to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.058 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: 1.7467 time to fit residues: 311.7941 Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 239 ASN A 294 GLN B 17 GLN B 36 ASN B 75 GLN G 24 ASN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123052 restraints weight = 10821.668| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.85 r_work: 0.3332 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9273 Z= 0.252 Angle : 0.711 8.632 12592 Z= 0.380 Chirality : 0.049 0.221 1401 Planarity : 0.006 0.066 1593 Dihedral : 6.946 58.684 1412 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.33 % Allowed : 14.16 % Favored : 81.50 % 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: -1.33 (0.23), residues: 1121 helix: -0.18 (0.23), residues: 437 sheet: -0.48 (0.32), residues: 231 loop : -1.73 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP R 236 HIS 0.008 0.002 HIS R 184 PHE 0.031 0.003 PHE A 212 TYR 0.013 0.002 TYR P 12 ARG 0.007 0.001 ARG B 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 1.77857 ( 3) hydrogen bonds : bond 0.06257 ( 441) hydrogen bonds : angle 5.47475 ( 1251) SS BOND : bond 0.00326 ( 7) SS BOND : angle 1.86076 ( 14) covalent geometry : bond 0.00584 ( 9264) covalent geometry : angle 0.70787 (12575) Misc. bond : bond 0.00029 ( 1) *********************** 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 162 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.057 Fit side-chains REVERT: A 283 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.7051 (mtt-85) REVERT: A 307 LYS cc_start: 0.5848 (tptt) cc_final: 0.5617 (tptt) REVERT: B 101 MET cc_start: 0.8629 (mtp) cc_final: 0.8243 (mtp) REVERT: G 47 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5462 (tm-30) REVERT: N 1 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6625 (tm-30) REVERT: R 79 TRP cc_start: 0.2955 (OUTLIER) cc_final: 0.1536 (m-90) REVERT: R 131 TYR cc_start: 0.3964 (m-80) cc_final: 0.2909 (m-10) REVERT: R 143 LYS cc_start: 0.5524 (tttm) cc_final: 0.4191 (tptm) REVERT: R 161 PHE cc_start: 0.6799 (t80) cc_final: 0.6589 (t80) REVERT: R 219 CYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4728 (t) REVERT: R 253 PHE cc_start: 0.6236 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: R 343 LYS cc_start: 0.6480 (mmtt) cc_final: 0.5842 (tttt) outliers start: 41 outliers final: 16 residues processed: 149 average time/residue: 1.4036 time to fit residues: 222.2365 Evaluate side-chains 134 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ARG 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 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 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 R residue 79 TRP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 253 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN N 5 GLN P 24 GLN R 179 GLN R 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124483 restraints weight = 11074.107| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.93 r_work: 0.3361 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9273 Z= 0.148 Angle : 0.558 6.184 12592 Z= 0.300 Chirality : 0.043 0.186 1401 Planarity : 0.004 0.048 1593 Dihedral : 6.596 58.286 1412 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.23 % Allowed : 16.28 % Favored : 79.49 % 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: -0.37 (0.25), residues: 1121 helix: 0.97 (0.25), residues: 437 sheet: -0.21 (0.33), residues: 227 loop : -1.45 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 236 HIS 0.004 0.001 HIS R 184 PHE 0.020 0.002 PHE A 212 TYR 0.014 0.001 TYR P 12 ARG 0.005 0.000 ARG N 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 1.57758 ( 3) hydrogen bonds : bond 0.04805 ( 441) hydrogen bonds : angle 4.92913 ( 1251) SS BOND : bond 0.00164 ( 7) SS BOND : angle 1.61483 ( 14) covalent geometry : bond 0.00333 ( 9264) covalent geometry : angle 0.55479 (12575) Misc. bond : bond 0.00018 ( 1) *********************** 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 159 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.976 Fit side-chains REVERT: A 283 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7095 (mtt-85) REVERT: A 300 LYS cc_start: 0.4959 (mtpt) cc_final: 0.4745 (mtpt) REVERT: B 101 MET cc_start: 0.8614 (mtp) cc_final: 0.8334 (mtp) REVERT: G 37 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7575 (mp) REVERT: G 47 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5472 (tm-30) REVERT: N 1 GLN cc_start: 0.7326 (tt0) cc_final: 0.6634 (tm-30) REVERT: N 89 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: R 79 TRP cc_start: 0.2970 (OUTLIER) cc_final: 0.1511 (m-90) REVERT: R 131 TYR cc_start: 0.3857 (m-80) cc_final: 0.2837 (m-10) REVERT: R 143 LYS cc_start: 0.5651 (tttm) cc_final: 0.4319 (tptm) REVERT: R 158 LEU cc_start: 0.7411 (tp) cc_final: 0.7108 (tt) REVERT: R 161 PHE cc_start: 0.6834 (t80) cc_final: 0.6620 (t80) REVERT: R 172 PHE cc_start: 0.5460 (t80) cc_final: 0.4943 (t80) REVERT: R 187 MET cc_start: 0.7766 (tpt) cc_final: 0.7311 (tpt) REVERT: R 219 CYS cc_start: 0.5186 (OUTLIER) cc_final: 0.4979 (t) REVERT: R 260 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6315 (ptm160) REVERT: R 343 LYS cc_start: 0.6472 (mmtt) cc_final: 0.5761 (tttt) REVERT: R 397 GLU cc_start: 0.6950 (tt0) cc_final: 0.6568 (tm-30) outliers start: 40 outliers final: 16 residues processed: 145 average time/residue: 1.3941 time to fit residues: 214.2978 Evaluate side-chains 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 367 VAL 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 196 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 37 LEU 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 219 CYS Chi-restraints excluded: chain R residue 253 PHE Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 179 GLN R 186 ASN R 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.163028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.125274 restraints weight = 10848.913| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.98 r_work: 0.3357 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9273 Z= 0.191 Angle : 0.614 7.072 12592 Z= 0.328 Chirality : 0.046 0.206 1401 Planarity : 0.004 0.049 1593 Dihedral : 6.639 55.242 1410 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.97 % Allowed : 16.60 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1121 helix: 1.06 (0.25), residues: 437 sheet: -0.20 (0.33), residues: 228 loop : -1.41 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 236 HIS 0.005 0.001 HIS R 184 PHE 0.024 0.002 PHE P 19 TYR 0.014 0.002 TYR P 12 ARG 0.005 0.001 ARG N 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 1.85459 ( 3) hydrogen bonds : bond 0.04966 ( 441) hydrogen bonds : angle 5.00016 ( 1251) SS BOND : bond 0.00225 ( 7) SS BOND : angle 1.30083 ( 14) covalent geometry : bond 0.00438 ( 9264) covalent geometry : angle 0.61250 (12575) Misc. bond : bond 0.00025 ( 1) *********************** 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 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 1.090 Fit side-chains REVERT: A 283 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.7096 (mtt-85) REVERT: A 307 LYS cc_start: 0.5984 (tptt) cc_final: 0.5334 (pmtt) REVERT: A 372 ILE cc_start: 0.7968 (pt) cc_final: 0.7470 (mp) REVERT: B 101 MET cc_start: 0.8590 (mtp) cc_final: 0.8332 (mtp) REVERT: B 130 GLU cc_start: 0.4928 (OUTLIER) cc_final: 0.3904 (mm-30) REVERT: B 280 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7876 (ttpp) REVERT: N 1 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: N 89 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: R 79 TRP cc_start: 0.2951 (OUTLIER) cc_final: 0.1394 (m-90) REVERT: R 131 TYR cc_start: 0.3723 (m-80) cc_final: 0.2811 (m-10) REVERT: R 143 LYS cc_start: 0.5646 (tttm) cc_final: 0.4344 (tptt) REVERT: R 161 PHE cc_start: 0.6812 (t80) cc_final: 0.6599 (t80) REVERT: R 172 PHE cc_start: 0.5484 (t80) cc_final: 0.4920 (t80) REVERT: R 187 MET cc_start: 0.7757 (tpt) cc_final: 0.7354 (tpt) REVERT: R 260 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6424 (ptm160) REVERT: R 343 LYS cc_start: 0.6484 (mmtt) cc_final: 0.5800 (tttt) REVERT: R 397 GLU cc_start: 0.6922 (tt0) cc_final: 0.6520 (tm-30) outliers start: 47 outliers final: 20 residues processed: 146 average time/residue: 1.3425 time to fit residues: 208.1965 Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 283 ARG 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 280 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 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 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 260 ARG Chi-restraints excluded: chain R residue 337 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127501 restraints weight = 10822.642| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.04 r_work: 0.3385 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9273 Z= 0.121 Angle : 0.518 6.575 12592 Z= 0.278 Chirality : 0.042 0.184 1401 Planarity : 0.004 0.047 1593 Dihedral : 6.073 46.438 1407 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.86 % Allowed : 17.86 % Favored : 77.27 % 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: 0.20 (0.25), residues: 1121 helix: 1.61 (0.26), residues: 431 sheet: -0.12 (0.33), residues: 232 loop : -1.16 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 236 HIS 0.004 0.001 HIS A 41 PHE 0.021 0.001 PHE P 19 TYR 0.012 0.001 TYR P 12 ARG 0.005 0.000 ARG R 404 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 1.50789 ( 3) hydrogen bonds : bond 0.04111 ( 441) hydrogen bonds : angle 4.61254 ( 1251) SS BOND : bond 0.00180 ( 7) SS BOND : angle 0.94713 ( 14) covalent geometry : bond 0.00268 ( 9264) covalent geometry : angle 0.51641 (12575) Misc. bond : bond 0.00013 ( 1) *********************** 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 to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 1.262 Fit side-chains REVERT: A 265 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6564 (ttt-90) REVERT: A 283 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7127 (mtt-85) REVERT: A 307 LYS cc_start: 0.5884 (tptt) cc_final: 0.5338 (pmtt) REVERT: A 372 ILE cc_start: 0.7862 (pt) cc_final: 0.7422 (mp) REVERT: B 15 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6998 (mttm) REVERT: B 101 MET cc_start: 0.8584 (mtp) cc_final: 0.8291 (mtp) REVERT: B 130 GLU cc_start: 0.4944 (OUTLIER) cc_final: 0.3931 (mm-30) REVERT: G 19 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7447 (mm) REVERT: G 37 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7556 (mp) REVERT: G 62 ARG cc_start: 0.3679 (pmm-80) cc_final: 0.3386 (pmm-80) REVERT: N 1 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: N 12 VAL cc_start: 0.8094 (p) cc_final: 0.7887 (p) REVERT: N 89 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: P 19 PHE cc_start: 0.6973 (m-80) cc_final: 0.6712 (m-80) REVERT: R 131 TYR cc_start: 0.3747 (m-80) cc_final: 0.2835 (m-10) REVERT: R 143 LYS cc_start: 0.5587 (tttm) cc_final: 0.4298 (tptt) REVERT: R 161 PHE cc_start: 0.6773 (t80) cc_final: 0.6551 (t80) REVERT: R 172 PHE cc_start: 0.5396 (t80) cc_final: 0.4855 (t80) REVERT: R 260 ARG cc_start: 0.6833 (OUTLIER) cc_final: 0.6311 (ptm160) REVERT: R 271 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6337 (mt) outliers start: 46 outliers final: 17 residues processed: 144 average time/residue: 1.6289 time to fit residues: 249.6136 Evaluate side-chains 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 283 ARG 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 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 B residue 318 LEU Chi-restraints excluded: chain G residue 19 LEU 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 89 GLU Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.3500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN R 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127035 restraints weight = 10797.506| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.95 r_work: 0.3389 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9273 Z= 0.119 Angle : 0.518 6.782 12592 Z= 0.276 Chirality : 0.042 0.184 1401 Planarity : 0.003 0.046 1593 Dihedral : 5.877 45.894 1407 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.97 % Allowed : 17.65 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1121 helix: 1.80 (0.26), residues: 433 sheet: 0.00 (0.33), residues: 226 loop : -1.09 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.003 0.001 HIS R 184 PHE 0.018 0.001 PHE P 19 TYR 0.011 0.001 TYR P 12 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 1.42904 ( 3) hydrogen bonds : bond 0.03941 ( 441) hydrogen bonds : angle 4.51378 ( 1251) SS BOND : bond 0.00152 ( 7) SS BOND : angle 0.89807 ( 14) covalent geometry : bond 0.00265 ( 9264) covalent geometry : angle 0.51679 (12575) Misc. bond : bond 0.00009 ( 1) *********************** 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 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 1.054 Fit side-chains REVERT: A 60 MET cc_start: 0.3490 (mtm) cc_final: 0.2715 (mtm) REVERT: A 265 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6562 (ttt-90) REVERT: A 307 LYS cc_start: 0.5845 (tptt) cc_final: 0.5291 (pmtt) REVERT: A 372 ILE cc_start: 0.7841 (pt) cc_final: 0.7429 (mp) REVERT: B 3 GLU cc_start: 0.4611 (OUTLIER) cc_final: 0.4354 (tp30) REVERT: B 15 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6981 (mttm) REVERT: B 101 MET cc_start: 0.8592 (mtp) cc_final: 0.8315 (mtp) REVERT: B 130 GLU cc_start: 0.4887 (OUTLIER) cc_final: 0.3861 (mm-30) REVERT: G 19 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7438 (mm) REVERT: G 37 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7483 (mp) REVERT: N 1 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6629 (tm-30) REVERT: N 89 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: R 79 TRP cc_start: 0.2715 (OUTLIER) cc_final: 0.1406 (m100) REVERT: R 131 TYR cc_start: 0.3820 (m-80) cc_final: 0.2959 (m-10) REVERT: R 161 PHE cc_start: 0.6764 (t80) cc_final: 0.6510 (t80) REVERT: R 172 PHE cc_start: 0.5286 (t80) cc_final: 0.4757 (t80) REVERT: R 260 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6312 (ptm160) REVERT: R 300 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8119 (mt) outliers start: 47 outliers final: 20 residues processed: 144 average time/residue: 1.6872 time to fit residues: 260.7852 Evaluate side-chains 141 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 367 VAL Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 15 LYS 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 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 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 89 GLU Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 179 GLN Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 179 GLN R 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.164502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125758 restraints weight = 10999.524| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.96 r_work: 0.3375 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9273 Z= 0.147 Angle : 0.554 7.062 12592 Z= 0.296 Chirality : 0.043 0.193 1401 Planarity : 0.004 0.046 1593 Dihedral : 5.875 45.164 1404 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.86 % Allowed : 18.60 % Favored : 76.53 % 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: 0.35 (0.25), residues: 1121 helix: 1.75 (0.26), residues: 432 sheet: 0.01 (0.33), residues: 222 loop : -1.11 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 236 HIS 0.005 0.001 HIS R 184 PHE 0.021 0.002 PHE P 19 TYR 0.013 0.001 TYR A 358 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00002 ( 1) link_NAG-ASN : angle 1.51015 ( 3) hydrogen bonds : bond 0.04214 ( 441) hydrogen bonds : angle 4.61749 ( 1251) SS BOND : bond 0.00206 ( 7) SS BOND : angle 1.03862 ( 14) covalent geometry : bond 0.00335 ( 9264) covalent geometry : angle 0.55241 (12575) Misc. bond : bond 0.00013 ( 1) *********************** 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 158 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 1.022 Fit side-chains REVERT: A 60 MET cc_start: 0.3501 (mtm) cc_final: 0.2729 (mtm) REVERT: A 265 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6578 (ttt-90) REVERT: A 307 LYS cc_start: 0.5840 (tptt) cc_final: 0.5296 (pmtt) REVERT: A 372 ILE cc_start: 0.7860 (pt) cc_final: 0.7433 (mp) REVERT: B 3 GLU cc_start: 0.4636 (OUTLIER) cc_final: 0.4371 (tp30) REVERT: B 15 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6943 (mttm) REVERT: B 101 MET cc_start: 0.8574 (mtp) cc_final: 0.8299 (mtp) REVERT: B 130 GLU cc_start: 0.4933 (OUTLIER) cc_final: 0.3934 (mm-30) REVERT: B 217 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7870 (pp-130) REVERT: G 19 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7470 (mm) REVERT: G 37 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7471 (mp) REVERT: N 1 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: N 89 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: R 79 TRP cc_start: 0.2626 (OUTLIER) cc_final: 0.1325 (m100) REVERT: R 161 PHE cc_start: 0.6764 (t80) cc_final: 0.6534 (t80) REVERT: R 172 PHE cc_start: 0.5362 (t80) cc_final: 0.4809 (t80) REVERT: R 260 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6456 (ptm160) REVERT: R 300 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8149 (mt) outliers start: 46 outliers final: 20 residues processed: 144 average time/residue: 1.8991 time to fit residues: 290.8075 Evaluate side-chains 138 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 3 GLU 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 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 217 MET 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 19 LEU 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 89 GLU Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 300 ILE Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125932 restraints weight = 11036.069| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.00 r_work: 0.3364 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9273 Z= 0.173 Angle : 0.591 7.455 12592 Z= 0.315 Chirality : 0.045 0.201 1401 Planarity : 0.004 0.047 1593 Dihedral : 6.012 44.198 1404 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.44 % Allowed : 19.13 % Favored : 76.43 % 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: 0.16 (0.25), residues: 1121 helix: 1.49 (0.26), residues: 439 sheet: -0.11 (0.33), residues: 230 loop : -1.15 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 236 HIS 0.008 0.001 HIS A 220 PHE 0.024 0.002 PHE P 19 TYR 0.017 0.002 TYR A 358 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 1) link_NAG-ASN : angle 1.58730 ( 3) hydrogen bonds : bond 0.04540 ( 441) hydrogen bonds : angle 4.77025 ( 1251) SS BOND : bond 0.00226 ( 7) SS BOND : angle 1.17717 ( 14) covalent geometry : bond 0.00397 ( 9264) covalent geometry : angle 0.58913 (12575) Misc. bond : bond 0.00018 ( 1) *********************** 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 156 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.980 Fit side-chains REVERT: A 265 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6538 (ttt-90) REVERT: A 307 LYS cc_start: 0.5865 (tptt) cc_final: 0.5348 (pmtt) REVERT: A 372 ILE cc_start: 0.7855 (pt) cc_final: 0.7420 (mp) REVERT: B 101 MET cc_start: 0.8559 (mtp) cc_final: 0.8335 (mtp) REVERT: B 130 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.3905 (mm-30) REVERT: B 217 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7901 (pp-130) REVERT: G 19 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7476 (mm) REVERT: N 1 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: N 89 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: P 17 ASN cc_start: 0.7710 (t0) cc_final: 0.7467 (t0) REVERT: R 79 TRP cc_start: 0.2590 (OUTLIER) cc_final: 0.1384 (m100) REVERT: R 161 PHE cc_start: 0.6806 (t80) cc_final: 0.6580 (t80) REVERT: R 172 PHE cc_start: 0.5455 (t80) cc_final: 0.4896 (t80) REVERT: R 187 MET cc_start: 0.7771 (tpt) cc_final: 0.7338 (tpt) REVERT: R 260 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6318 (ptm160) REVERT: R 300 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8190 (mt) outliers start: 42 outliers final: 20 residues processed: 143 average time/residue: 1.3266 time to fit residues: 201.7482 Evaluate side-chains 137 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 214 ARG Chi-restraints excluded: chain B residue 217 MET 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 19 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 89 GLU Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 182 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN P 17 ASN R 179 GLN R 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127752 restraints weight = 10924.104| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.84 r_work: 0.3390 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9273 Z= 0.101 Angle : 0.499 7.518 12592 Z= 0.267 Chirality : 0.041 0.180 1401 Planarity : 0.003 0.043 1593 Dihedral : 5.581 44.119 1404 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.75 % Allowed : 20.93 % Favored : 76.32 % 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: 0.62 (0.26), residues: 1121 helix: 1.98 (0.26), residues: 434 sheet: 0.18 (0.33), residues: 223 loop : -1.00 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 236 HIS 0.004 0.001 HIS A 220 PHE 0.025 0.001 PHE A 222 TYR 0.011 0.001 TYR N 60 ARG 0.004 0.000 ARG G 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 1) link_NAG-ASN : angle 1.21744 ( 3) hydrogen bonds : bond 0.03642 ( 441) hydrogen bonds : angle 4.41673 ( 1251) SS BOND : bond 0.00160 ( 7) SS BOND : angle 0.80270 ( 14) covalent geometry : bond 0.00219 ( 9264) covalent geometry : angle 0.49846 (12575) Misc. bond : bond 0.00012 ( 1) *********************** 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 144 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.006 Fit side-chains REVERT: A 60 MET cc_start: 0.3426 (mtm) cc_final: 0.2601 (mtm) REVERT: A 265 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6595 (ttt-90) REVERT: A 307 LYS cc_start: 0.5802 (tptt) cc_final: 0.5322 (pmtt) REVERT: A 372 ILE cc_start: 0.7825 (pt) cc_final: 0.7431 (mp) REVERT: B 101 MET cc_start: 0.8619 (mtp) cc_final: 0.8363 (mtp) REVERT: B 217 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7801 (pp-130) REVERT: G 19 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7455 (mm) REVERT: N 1 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: N 3 GLN cc_start: 0.7859 (tt0) cc_final: 0.7497 (tp40) REVERT: P 17 ASN cc_start: 0.7784 (t0) cc_final: 0.7533 (t0) REVERT: P 19 PHE cc_start: 0.6989 (m-80) cc_final: 0.6705 (m-80) REVERT: R 79 TRP cc_start: 0.2475 (OUTLIER) cc_final: 0.1318 (m100) REVERT: R 161 PHE cc_start: 0.6778 (t80) cc_final: 0.6544 (t80) REVERT: R 172 PHE cc_start: 0.5228 (t80) cc_final: 0.4715 (t80) REVERT: R 221 ILE cc_start: 0.6165 (pp) cc_final: 0.5929 (mt) REVERT: R 260 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6340 (ptm160) REVERT: R 300 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8136 (mt) REVERT: R 334 GLU cc_start: 0.6173 (mp0) cc_final: 0.5942 (mp0) REVERT: R 397 GLU cc_start: 0.6950 (tt0) cc_final: 0.6644 (tm-30) outliers start: 26 outliers final: 11 residues processed: 136 average time/residue: 1.3299 time to fit residues: 192.3856 Evaluate side-chains 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG 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 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 63 SER Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain R residue 79 TRP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.165297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126737 restraints weight = 10969.396| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.97 r_work: 0.3381 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9273 Z= 0.139 Angle : 0.550 8.672 12592 Z= 0.294 Chirality : 0.043 0.189 1401 Planarity : 0.004 0.046 1593 Dihedral : 5.729 44.741 1404 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.64 % Allowed : 21.14 % Favored : 76.22 % 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: 0.55 (0.25), residues: 1121 helix: 1.87 (0.26), residues: 434 sheet: 0.12 (0.33), residues: 227 loop : -0.97 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 236 HIS 0.004 0.001 HIS R 184 PHE 0.021 0.002 PHE A 222 TYR 0.012 0.001 TYR A 358 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00016 ( 1) link_NAG-ASN : angle 1.37887 ( 3) hydrogen bonds : bond 0.04081 ( 441) hydrogen bonds : angle 4.56159 ( 1251) SS BOND : bond 0.00182 ( 7) SS BOND : angle 0.96488 ( 14) covalent geometry : bond 0.00316 ( 9264) covalent geometry : angle 0.54911 (12575) Misc. bond : bond 0.00011 ( 1) ********************** 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 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.962 Fit side-chains REVERT: A 60 MET cc_start: 0.3217 (mtm) cc_final: 0.2503 (mtm) REVERT: A 265 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6562 (ttt-90) REVERT: A 307 LYS cc_start: 0.5809 (tptt) cc_final: 0.5318 (pmtt) REVERT: A 372 ILE cc_start: 0.7844 (pt) cc_final: 0.7458 (mp) REVERT: B 15 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6943 (mttm) REVERT: B 101 MET cc_start: 0.8608 (mtp) cc_final: 0.8349 (mtp) REVERT: B 217 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7695 (pp-130) REVERT: G 19 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7499 (mm) REVERT: N 1 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6651 (tm-30) REVERT: P 17 ASN cc_start: 0.7960 (t0) cc_final: 0.7634 (t0) REVERT: R 79 TRP cc_start: 0.2479 (OUTLIER) cc_final: 0.1323 (m100) REVERT: R 161 PHE cc_start: 0.6786 (t80) cc_final: 0.6545 (t80) REVERT: R 172 PHE cc_start: 0.5274 (t80) cc_final: 0.4717 (t80) REVERT: R 260 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6380 (ptm160) REVERT: R 300 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8132 (mt) REVERT: R 334 GLU cc_start: 0.6166 (mp0) cc_final: 0.5933 (mp0) REVERT: R 397 GLU cc_start: 0.6927 (tt0) cc_final: 0.6601 (tm-30) outliers start: 25 outliers final: 14 residues processed: 128 average time/residue: 1.3653 time to fit residues: 185.7497 Evaluate side-chains 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 196 THR Chi-restraints excluded: chain B residue 217 MET 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 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 181 VAL Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 260 ARG Chi-restraints excluded: chain R residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128562 restraints weight = 10930.924| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.99 r_work: 0.3404 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9273 Z= 0.103 Angle : 0.505 8.555 12592 Z= 0.270 Chirality : 0.042 0.179 1401 Planarity : 0.003 0.044 1593 Dihedral : 5.411 44.294 1403 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.22 % Allowed : 21.67 % Favored : 76.11 % 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: 0.74 (0.26), residues: 1121 helix: 2.11 (0.26), residues: 433 sheet: 0.28 (0.34), residues: 222 loop : -0.97 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.018 0.001 PHE A 222 TYR 0.010 0.001 TYR N 60 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 1) link_NAG-ASN : angle 1.05684 ( 3) hydrogen bonds : bond 0.03571 ( 441) hydrogen bonds : angle 4.35509 ( 1251) SS BOND : bond 0.00145 ( 7) SS BOND : angle 0.78466 ( 14) covalent geometry : bond 0.00226 ( 9264) covalent geometry : angle 0.50401 (12575) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8849.63 seconds wall clock time: 156 minutes 9.80 seconds (9369.80 seconds total)