Starting phenix.real_space_refine on Tue Sep 24 18:00:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw4_39622/09_2024/8yw4_39622.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw4_39622/09_2024/8yw4_39622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw4_39622/09_2024/8yw4_39622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw4_39622/09_2024/8yw4_39622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw4_39622/09_2024/8yw4_39622.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yw4_39622/09_2024/8yw4_39622.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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 48 5.16 5 C 5466 2.51 5 N 1522 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8619 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2614 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2416 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 220 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'2ML:plan-1': 1, 'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.33, per 1000 atoms: 0.62 Number of scatterers: 8619 At special positions: 0 Unit cell: (84.609, 100.674, 162.792, 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 48 16.00 O 1583 8.00 N 1522 7.00 C 5466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 43.7% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 removed outlier: 3.722A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.717A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.679A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.598A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.578A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.882A pdb=" N ASP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.577A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.662A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.875A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 48 removed outlier: 3.689A pdb=" N TYR R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN R 37 " --> pdb=" O GLY R 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG R 43 " --> pdb=" O TRP R 39 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU R 45 " --> pdb=" O ARG R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 161 removed outlier: 3.512A pdb=" N LEU R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 194 Processing helix chain 'R' and resid 196 through 201 removed outlier: 3.891A pdb=" N TYR R 200 " --> pdb=" O ARG R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 246 removed outlier: 3.501A pdb=" N LEU R 235 " --> pdb=" O TYR R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 265 Processing helix chain 'R' and resid 265 through 282 removed outlier: 3.674A pdb=" N LEU R 269 " --> pdb=" O GLY R 265 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 292 through 297 removed outlier: 3.537A pdb=" N TRP R 296 " --> pdb=" O VAL R 292 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP R 297 " --> pdb=" O LYS R 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 292 through 297' Processing helix chain 'R' and resid 299 through 328 removed outlier: 3.677A pdb=" N ILE R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 351 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 358 removed outlier: 3.546A pdb=" N VAL R 356 " --> pdb=" O HIS R 353 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA R 358 " --> pdb=" O VAL R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 367 through 392 removed outlier: 3.886A pdb=" N PHE R 371 " --> pdb=" O GLY R 367 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 411 removed outlier: 3.947A pdb=" N ARG R 404 " --> pdb=" O GLN R 400 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 removed outlier: 3.513A pdb=" N ILE P 12 " --> pdb=" O SER P 8 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP P 15 " --> pdb=" O SER P 11 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS P 17 " --> pdb=" O 2ML P 13 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU P 24 " --> pdb=" O AIB P 20 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU P 27 " --> pdb=" O ILE P 23 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.860A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.613A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.503A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.548A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.248A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.341A 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: 6.788A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.679A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.709A 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: 3.629A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.992A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.687A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 423 hydrogen bonds defined for protein. 1194 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: 2.41 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2532 1.33 - 1.45: 1521 1.45 - 1.57: 4675 1.57 - 1.69: 1 1.69 - 1.81: 66 Bond restraints: 8795 Sorted by residual: bond pdb=" N GLY R 198 " pdb=" CA GLY R 198 " ideal model delta sigma weight residual 1.444 1.475 -0.031 8.80e-03 1.29e+04 1.24e+01 bond pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " ideal model delta sigma weight residual 1.525 1.578 -0.053 2.10e-02 2.27e+03 6.26e+00 bond pdb=" N ASP B 38 " pdb=" CA ASP B 38 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.45e-02 4.76e+03 6.13e+00 bond pdb=" N AIB P 20 " pdb=" CA AIB P 20 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.96e+00 bond pdb=" N AIB P 2 " pdb=" CA AIB P 2 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.60e+00 ... (remaining 8790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11721 1.89 - 3.79: 159 3.79 - 5.68: 21 5.68 - 7.58: 5 7.58 - 9.47: 3 Bond angle restraints: 11909 Sorted by residual: angle pdb=" O GLY R 198 " pdb=" C GLY R 198 " pdb=" N PRO R 199 " ideal model delta sigma weight residual 121.07 122.28 -1.21 3.60e-01 7.72e+00 1.13e+01 angle pdb=" N PHE A 282 " pdb=" CA PHE A 282 " pdb=" C PHE A 282 " ideal model delta sigma weight residual 114.56 110.45 4.11 1.27e+00 6.20e-01 1.05e+01 angle pdb=" N GLY R 198 " pdb=" CA GLY R 198 " pdb=" C GLY R 198 " ideal model delta sigma weight residual 115.22 111.58 3.64 1.27e+00 6.20e-01 8.21e+00 angle pdb=" CA LEU R 261 " pdb=" CB LEU R 261 " pdb=" CG LEU R 261 " ideal model delta sigma weight residual 116.30 125.77 -9.47 3.50e+00 8.16e-02 7.32e+00 angle pdb=" N PRO R 199 " pdb=" CA PRO R 199 " pdb=" C PRO R 199 " ideal model delta sigma weight residual 113.81 109.90 3.91 1.45e+00 4.76e-01 7.28e+00 ... (remaining 11904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4370 17.59 - 35.19: 600 35.19 - 52.78: 201 52.78 - 70.37: 40 70.37 - 87.97: 10 Dihedral angle restraints: 5221 sinusoidal: 2080 harmonic: 3141 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 24.50 68.50 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 62.74 30.26 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA ASP R 129 " pdb=" CB ASP R 129 " pdb=" CG ASP R 129 " pdb=" OD1 ASP R 129 " ideal model delta sinusoidal sigma weight residual -30.00 -88.93 58.93 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 5218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1105 0.051 - 0.102: 181 0.102 - 0.153: 36 0.153 - 0.204: 0 0.204 - 0.255: 2 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA 2ML P 13 " pdb=" C 2ML P 13 " pdb=" CB1 2ML P 13 " pdb=" CB2 2ML P 13 " both_signs ideal model delta sigma weight residual False -2.84 -3.10 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU R 182 " pdb=" CB LEU R 182 " pdb=" CD1 LEU R 182 " pdb=" CD2 LEU R 182 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1321 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.039 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO G 60 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 236 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 39 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.022 5.00e-02 4.00e+02 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 531 2.73 - 3.27: 8572 3.27 - 3.82: 14119 3.82 - 4.36: 16719 4.36 - 4.90: 29320 Nonbonded interactions: 69261 Sorted by model distance: nonbonded pdb=" NH2 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.190 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR R 225 " pdb=" O TRP R 264 " model vdw 2.249 3.040 ... (remaining 69256 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.600 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8795 Z= 0.262 Angle : 0.561 9.472 11909 Z= 0.296 Chirality : 0.040 0.255 1324 Planarity : 0.003 0.061 1518 Dihedral : 18.345 87.967 3189 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 0.33 % Allowed : 33.88 % Favored : 65.80 % 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: -0.25 (0.27), residues: 1054 helix: 1.23 (0.25), residues: 406 sheet: -1.13 (0.36), residues: 222 loop : -0.91 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.002 0.001 HIS B 183 PHE 0.024 0.001 PHE R 379 TYR 0.015 0.001 TYR R 335 ARG 0.004 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.6332 (mtp) cc_final: 0.6113 (ttm) REVERT: N 94 TYR cc_start: 0.6910 (m-80) cc_final: 0.5985 (m-80) REVERT: R 297 TRP cc_start: 0.7098 (m100) cc_final: 0.5925 (m-10) outliers start: 3 outliers final: 0 residues processed: 212 average time/residue: 0.2617 time to fit residues: 70.9904 Evaluate side-chains 132 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 0.0020 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 17 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8795 Z= 0.242 Angle : 0.644 11.033 11909 Z= 0.337 Chirality : 0.042 0.155 1324 Planarity : 0.005 0.042 1518 Dihedral : 4.037 36.374 1199 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.26 % Rotamer: Outliers : 5.75 % Allowed : 28.99 % Favored : 65.26 % 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: 0.42 (0.27), residues: 1054 helix: 2.01 (0.25), residues: 412 sheet: -1.15 (0.35), residues: 231 loop : -0.56 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.003 0.001 HIS R 242 PHE 0.014 0.002 PHE B 199 TYR 0.011 0.001 TYR P 25 ARG 0.006 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 157 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7200 (pt) REVERT: A 198 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7138 (tmm) REVERT: B 87 THR cc_start: 0.8330 (m) cc_final: 0.8035 (m) REVERT: B 338 ILE cc_start: 0.8066 (mt) cc_final: 0.7669 (mt) REVERT: N 89 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6692 (pm20) REVERT: R 140 MET cc_start: 0.8318 (tmm) cc_final: 0.8071 (tmm) REVERT: R 297 TRP cc_start: 0.7117 (m100) cc_final: 0.6356 (m-10) outliers start: 53 outliers final: 19 residues processed: 192 average time/residue: 0.2013 time to fit residues: 53.1736 Evaluate side-chains 152 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 36 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 95 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8795 Z= 0.190 Angle : 0.565 9.404 11909 Z= 0.295 Chirality : 0.041 0.266 1324 Planarity : 0.004 0.053 1518 Dihedral : 4.025 43.870 1199 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.36 % Favored : 95.45 % Rotamer: Outliers : 4.78 % Allowed : 28.34 % Favored : 66.88 % 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 (0.27), residues: 1054 helix: 2.12 (0.25), residues: 409 sheet: -0.97 (0.34), residues: 237 loop : -0.54 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS R 166 PHE 0.025 0.002 PHE A 343 TYR 0.017 0.001 TYR N 32 ARG 0.004 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7596 (tmm) REVERT: A 345 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8301 (t0) REVERT: B 87 THR cc_start: 0.8597 (m) cc_final: 0.8280 (m) REVERT: B 338 ILE cc_start: 0.8478 (mt) cc_final: 0.8087 (mt) REVERT: R 164 ARG cc_start: 0.5032 (mtt180) cc_final: 0.4528 (mmt180) outliers start: 44 outliers final: 25 residues processed: 186 average time/residue: 0.2336 time to fit residues: 57.7742 Evaluate side-chains 168 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8795 Z= 0.245 Angle : 0.587 9.390 11909 Z= 0.301 Chirality : 0.043 0.214 1324 Planarity : 0.004 0.044 1518 Dihedral : 4.104 40.087 1199 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 5.75 % Allowed : 26.60 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1054 helix: 2.26 (0.25), residues: 411 sheet: -0.92 (0.35), residues: 226 loop : -0.49 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 233 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.002 PHE N 68 TYR 0.011 0.001 TYR A 306 ARG 0.003 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 159 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8447 (tpp) REVERT: A 344 ASN cc_start: 0.8568 (t0) cc_final: 0.8329 (t0) REVERT: A 353 MET cc_start: 0.8010 (ttm) cc_final: 0.7599 (ttm) REVERT: B 17 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7553 (tt0) REVERT: B 87 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8464 (m) REVERT: B 155 ASN cc_start: 0.8232 (t0) cc_final: 0.7823 (t0) REVERT: B 290 ASP cc_start: 0.8515 (m-30) cc_final: 0.8308 (m-30) REVERT: B 338 ILE cc_start: 0.8694 (mt) cc_final: 0.8321 (mt) REVERT: N 105 ARG cc_start: 0.7759 (mpp80) cc_final: 0.7310 (mpp80) REVERT: R 164 ARG cc_start: 0.5321 (mtt180) cc_final: 0.4729 (mmt180) REVERT: R 181 MET cc_start: 0.7622 (ttm) cc_final: 0.7347 (ttm) REVERT: R 297 TRP cc_start: 0.7432 (m100) cc_final: 0.6437 (m-10) outliers start: 53 outliers final: 35 residues processed: 195 average time/residue: 0.2363 time to fit residues: 61.3289 Evaluate side-chains 177 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 299 ILE Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN R 173 HIS ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8795 Z= 0.307 Angle : 0.616 9.420 11909 Z= 0.320 Chirality : 0.043 0.193 1324 Planarity : 0.004 0.040 1518 Dihedral : 4.165 36.978 1199 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 5.65 % Allowed : 29.75 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 1054 helix: 2.20 (0.25), residues: 409 sheet: -0.94 (0.35), residues: 231 loop : -0.53 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 287 HIS 0.005 0.001 HIS B 54 PHE 0.018 0.002 PHE B 241 TYR 0.013 0.001 TYR A 306 ARG 0.009 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 162 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7638 (ttmm) cc_final: 0.7420 (mttt) REVERT: A 22 GLN cc_start: 0.8545 (tp40) cc_final: 0.8319 (tp-100) REVERT: A 198 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8609 (tpp) REVERT: A 344 ASN cc_start: 0.8454 (t0) cc_final: 0.8166 (m-40) REVERT: A 353 MET cc_start: 0.8268 (ttm) cc_final: 0.7919 (ttm) REVERT: B 87 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8910 (m) REVERT: B 266 HIS cc_start: 0.7814 (OUTLIER) cc_final: 0.7482 (t-90) REVERT: G 62 ARG cc_start: 0.7251 (tpp-160) cc_final: 0.7028 (tpp-160) REVERT: N 105 ARG cc_start: 0.7988 (mpp80) cc_final: 0.7660 (ptp-170) REVERT: R 141 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6659 (p90) REVERT: R 164 ARG cc_start: 0.5521 (mtt180) cc_final: 0.4672 (mmt180) REVERT: R 190 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6624 (ttp-170) outliers start: 52 outliers final: 34 residues processed: 196 average time/residue: 0.2107 time to fit residues: 55.9748 Evaluate side-chains 192 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 190 GLN A 259 ASN A 338 ASN G 18 GLN ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8795 Z= 0.187 Angle : 0.537 10.527 11909 Z= 0.277 Chirality : 0.040 0.144 1324 Planarity : 0.003 0.039 1518 Dihedral : 4.002 35.729 1199 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.12 % Favored : 94.69 % Rotamer: Outliers : 4.45 % Allowed : 30.29 % Favored : 65.26 % 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: 0.58 (0.27), residues: 1054 helix: 2.16 (0.26), residues: 416 sheet: -0.79 (0.35), residues: 228 loop : -0.72 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.001 PHE R 379 TYR 0.011 0.001 TYR R 281 ARG 0.004 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8477 (tp40) cc_final: 0.8174 (tp-100) REVERT: A 198 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8519 (tpp) REVERT: A 344 ASN cc_start: 0.8391 (t0) cc_final: 0.8046 (m-40) REVERT: A 353 MET cc_start: 0.8304 (ttm) cc_final: 0.8033 (ttm) REVERT: B 87 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8865 (m) REVERT: B 266 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7579 (t-90) REVERT: G 62 ARG cc_start: 0.7157 (tpp-160) cc_final: 0.6931 (tpp-160) REVERT: N 105 ARG cc_start: 0.7924 (mpp80) cc_final: 0.7686 (ptp-170) REVERT: R 147 LEU cc_start: 0.8648 (tp) cc_final: 0.8430 (tt) REVERT: R 164 ARG cc_start: 0.5490 (mtt180) cc_final: 0.4621 (mmt180) outliers start: 41 outliers final: 27 residues processed: 187 average time/residue: 0.2147 time to fit residues: 54.5189 Evaluate side-chains 182 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 173 HIS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.7656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8795 Z= 0.234 Angle : 0.563 11.991 11909 Z= 0.288 Chirality : 0.042 0.264 1324 Planarity : 0.003 0.041 1518 Dihedral : 4.028 35.128 1199 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.60 % Favored : 94.21 % Rotamer: Outliers : 4.78 % Allowed : 29.97 % Favored : 65.26 % 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: 0.63 (0.27), residues: 1054 helix: 2.22 (0.26), residues: 417 sheet: -0.78 (0.35), residues: 229 loop : -0.72 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.004 0.001 HIS B 54 PHE 0.023 0.001 PHE P 6 TYR 0.011 0.001 TYR R 281 ARG 0.002 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8542 (tp40) cc_final: 0.8305 (tp-100) REVERT: A 198 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8565 (tpp) REVERT: A 344 ASN cc_start: 0.8385 (t0) cc_final: 0.8064 (m-40) REVERT: A 353 MET cc_start: 0.8338 (ttm) cc_final: 0.8093 (ttm) REVERT: B 87 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8957 (m) REVERT: B 266 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7570 (t-90) REVERT: G 62 ARG cc_start: 0.7196 (tpp-160) cc_final: 0.6972 (tpp-160) REVERT: N 105 ARG cc_start: 0.7987 (mpp80) cc_final: 0.7759 (ptp-170) REVERT: R 147 LEU cc_start: 0.8708 (tp) cc_final: 0.8492 (tt) REVERT: R 164 ARG cc_start: 0.5550 (mtt180) cc_final: 0.4777 (mmt180) outliers start: 44 outliers final: 34 residues processed: 199 average time/residue: 0.2130 time to fit residues: 57.6424 Evaluate side-chains 196 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 146 SER Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 173 HIS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 284 THR Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain R residue 381 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.7895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8795 Z= 0.188 Angle : 0.544 11.460 11909 Z= 0.278 Chirality : 0.040 0.259 1324 Planarity : 0.003 0.039 1518 Dihedral : 3.912 34.316 1199 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.12 % Favored : 94.69 % Rotamer: Outliers : 4.56 % Allowed : 30.73 % Favored : 64.71 % 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: 0.68 (0.27), residues: 1054 helix: 2.31 (0.26), residues: 417 sheet: -0.76 (0.35), residues: 229 loop : -0.74 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.016 0.001 PHE R 379 TYR 0.010 0.001 TYR N 60 ARG 0.003 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8504 (tp40) cc_final: 0.8260 (tp-100) REVERT: A 198 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8589 (tpp) REVERT: A 353 MET cc_start: 0.8351 (ttm) cc_final: 0.8132 (ttm) REVERT: B 87 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8971 (m) REVERT: B 266 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7509 (t-90) REVERT: G 62 ARG cc_start: 0.7143 (tpp-160) cc_final: 0.6592 (mmp80) REVERT: R 164 ARG cc_start: 0.5442 (mtt180) cc_final: 0.4749 (mmt180) outliers start: 42 outliers final: 31 residues processed: 189 average time/residue: 0.2169 time to fit residues: 55.7395 Evaluate side-chains 189 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 166 HIS Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 173 HIS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8795 Z= 0.188 Angle : 0.553 11.956 11909 Z= 0.281 Chirality : 0.040 0.264 1324 Planarity : 0.003 0.039 1518 Dihedral : 3.878 33.854 1199 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.41 % Favored : 94.40 % Rotamer: Outliers : 3.58 % Allowed : 31.70 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1054 helix: 2.38 (0.26), residues: 418 sheet: -0.75 (0.35), residues: 229 loop : -0.72 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 54 PHE 0.024 0.001 PHE P 6 TYR 0.010 0.001 TYR N 60 ARG 0.003 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8509 (tp40) cc_final: 0.8288 (tp-100) REVERT: A 198 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8537 (tpp) REVERT: A 353 MET cc_start: 0.8357 (ttm) cc_final: 0.8138 (ttm) REVERT: B 87 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8990 (m) REVERT: B 266 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7512 (t-90) REVERT: G 62 ARG cc_start: 0.7152 (tpp-160) cc_final: 0.6640 (mmp80) REVERT: R 164 ARG cc_start: 0.5464 (mtt180) cc_final: 0.4985 (mmt180) outliers start: 33 outliers final: 27 residues processed: 188 average time/residue: 0.2221 time to fit residues: 57.4561 Evaluate side-chains 188 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 167 CYS Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.0870 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 0.0030 chunk 83 optimal weight: 0.0040 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 0.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.8169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8795 Z= 0.140 Angle : 0.550 14.503 11909 Z= 0.273 Chirality : 0.040 0.260 1324 Planarity : 0.003 0.037 1518 Dihedral : 3.738 34.108 1199 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.26 % Rotamer: Outliers : 2.93 % Allowed : 32.68 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.28), residues: 1054 helix: 2.53 (0.26), residues: 414 sheet: -0.59 (0.35), residues: 228 loop : -0.69 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.003 0.000 HIS B 183 PHE 0.018 0.001 PHE R 379 TYR 0.008 0.001 TYR N 95 ARG 0.003 0.000 ARG A 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 286 THR cc_start: 0.8415 (m) cc_final: 0.8205 (m) REVERT: A 313 LEU cc_start: 0.8819 (mm) cc_final: 0.8530 (mm) REVERT: B 87 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8848 (m) REVERT: B 124 TYR cc_start: 0.8613 (m-80) cc_final: 0.7679 (m-80) REVERT: B 266 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7513 (t-90) REVERT: G 62 ARG cc_start: 0.7171 (tpp-160) cc_final: 0.6697 (mmp80) outliers start: 27 outliers final: 19 residues processed: 185 average time/residue: 0.2223 time to fit residues: 56.3375 Evaluate side-chains 181 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 52 GLN B 17 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.160260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118406 restraints weight = 9909.097| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.86 r_work: 0.3043 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.8443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8795 Z= 0.390 Angle : 0.660 13.238 11909 Z= 0.335 Chirality : 0.044 0.265 1324 Planarity : 0.004 0.045 1518 Dihedral : 4.177 33.196 1199 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.79 % Favored : 94.02 % Rotamer: Outliers : 3.47 % Allowed : 32.25 % Favored : 64.28 % 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: 0.66 (0.27), residues: 1054 helix: 2.31 (0.26), residues: 418 sheet: -0.83 (0.34), residues: 231 loop : -0.76 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.007 0.001 HIS B 54 PHE 0.023 0.002 PHE B 241 TYR 0.025 0.002 TYR B 85 ARG 0.004 0.000 ARG A 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2275.23 seconds wall clock time: 41 minutes 1.99 seconds (2461.99 seconds total)