Starting phenix.real_space_refine on Sun Mar 10 23:05:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oix_12935/03_2024/7oix_12935.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oix_12935/03_2024/7oix_12935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oix_12935/03_2024/7oix_12935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oix_12935/03_2024/7oix_12935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oix_12935/03_2024/7oix_12935.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oix_12935/03_2024/7oix_12935.pdb" } resolution = 3.6 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= 0.014 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 34 5.16 5 C 3814 2.51 5 N 937 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 408": "OD1" <-> "OD2" Residue "B ASP 411": "OD1" <-> "OD2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 495": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5869 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2097 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 21, 'TRANS': 243} Chain: "B" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3558 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain breaks: 1 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.85, per 1000 atoms: 0.66 Number of scatterers: 5869 At special positions: 0 Unit cell: (68.376, 74.888, 135.124, 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 34 16.00 O 1084 8.00 N 937 7.00 C 3814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 460 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA D 3 " - " MAN D 6 " " MAN D 6 " - " MAN D 7 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 601 " - " ASN A 146 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 220 " " NAG A 604 " - " ASN A 247 " " NAG A 605 " - " ASN A 241 " " NAG C 1 " - " ASN A 177 " " NAG D 1 " - " ASN A 312 " Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.2 seconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 6 sheets defined 57.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.624A pdb=" N THR A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 153 through 156 Processing helix chain 'A' and resid 192 through 196 removed outlier: 4.225A pdb=" N ARG A 196 " --> pdb=" O CYS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.693A pdb=" N ALA A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 Processing helix chain 'B' and resid 52 through 73 removed outlier: 4.436A pdb=" N TYR B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLN B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 107 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 115 through 135 removed outlier: 3.855A pdb=" N ILE B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.927A pdb=" N TRP B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 173 removed outlier: 4.240A pdb=" N TRP B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 4.393A pdb=" N THR B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N MET B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER B 173 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 206 Processing helix chain 'B' and resid 234 through 264 removed outlier: 3.957A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 Processing helix chain 'B' and resid 292 through 322 removed outlier: 3.917A pdb=" N PHE B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N THR B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 353 Proline residue: B 345 - end of helix Processing helix chain 'B' and resid 357 through 373 removed outlier: 4.134A pdb=" N ALA B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 368 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Proline residue: B 369 - end of helix Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 380 through 417 Proline residue: B 402 - end of helix removed outlier: 3.842A pdb=" N LEU B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Proline residue: B 407 - end of helix Processing helix chain 'B' and resid 423 through 453 removed outlier: 4.114A pdb=" N PHE B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 489 removed outlier: 3.951A pdb=" N LYS B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Proline residue: B 478 - end of helix Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.621A pdb=" N LYS B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 78 removed outlier: 6.999A pdb=" N GLY A 268 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS A 285 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR A 266 " --> pdb=" O HIS A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78 removed outlier: 3.682A pdb=" N THR A 290 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 136 removed outlier: 6.453A pdb=" N THR A 135 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR A 316 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE A 319 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE A 125 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA A 123 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N THR A 148 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ILE A 125 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N THR A 150 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N VAL A 127 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N ASP A 152 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N ALA A 129 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 177 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 136 removed outlier: 6.453A pdb=" N THR A 135 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR A 316 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AA6, first strand: chain 'A' and resid 216 through 217 318 hydrogen bonds defined for protein. 933 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: 1.53 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1743 1.34 - 1.46: 1525 1.46 - 1.58: 2713 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 6029 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C1 MAN D 5 " pdb=" C2 MAN D 5 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C1 NAG A 604 " pdb=" O5 NAG A 604 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" C2 BMA D 3 " pdb=" C3 BMA D 3 " ideal model delta sigma weight residual 1.544 1.502 0.042 2.00e-02 2.50e+03 4.35e+00 ... (remaining 6024 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.64: 231 106.64 - 113.53: 3402 113.53 - 120.42: 2329 120.42 - 127.31: 2177 127.31 - 134.20: 81 Bond angle restraints: 8220 Sorted by residual: angle pdb=" C LEU B 376 " pdb=" N MET B 377 " pdb=" CA MET B 377 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C ALA A 246 " pdb=" N ASN A 247 " pdb=" CA ASN A 247 " ideal model delta sigma weight residual 121.85 129.21 -7.36 1.77e+00 3.19e-01 1.73e+01 angle pdb=" CG ARG B 111 " pdb=" CD ARG B 111 " pdb=" NE ARG B 111 " ideal model delta sigma weight residual 112.00 121.12 -9.12 2.20e+00 2.07e-01 1.72e+01 angle pdb=" N GLY B 263 " pdb=" CA GLY B 263 " pdb=" C GLY B 263 " ideal model delta sigma weight residual 113.18 122.79 -9.61 2.37e+00 1.78e-01 1.64e+01 angle pdb=" CB ARG B 353 " pdb=" CG ARG B 353 " pdb=" CD ARG B 353 " ideal model delta sigma weight residual 111.30 119.90 -8.60 2.30e+00 1.89e-01 1.40e+01 ... (remaining 8215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 3470 24.55 - 49.10: 223 49.10 - 73.65: 31 73.65 - 98.20: 22 98.20 - 122.75: 6 Dihedral angle restraints: 3752 sinusoidal: 1668 harmonic: 2084 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 253 " pdb=" CB CYS A 253 " ideal model delta sinusoidal sigma weight residual 93.00 -179.48 -87.52 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 145 " pdb=" CB CYS A 145 " ideal model delta sinusoidal sigma weight residual 93.00 33.80 59.20 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CA VAL B 74 " pdb=" C VAL B 74 " pdb=" N ALA B 75 " pdb=" CA ALA B 75 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 880 0.092 - 0.183: 102 0.183 - 0.275: 4 0.275 - 0.366: 1 0.366 - 0.457: 2 Chirality restraints: 989 Sorted by residual: chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 241 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 220 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA ASN B 380 " pdb=" N ASN B 380 " pdb=" C ASN B 380 " pdb=" CB ASN B 380 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 986 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 477 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO B 478 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " -0.016 2.00e-02 2.50e+03 1.52e-02 4.65e+00 pdb=" CG TYR A 299 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 118 " 0.017 2.00e-02 2.50e+03 1.26e-02 4.00e+00 pdb=" CG TRP B 118 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 118 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 118 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 118 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 118 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 118 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 118 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 118 " 0.004 2.00e-02 2.50e+03 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 167 2.69 - 3.24: 6183 3.24 - 3.79: 9472 3.79 - 4.35: 11177 4.35 - 4.90: 19019 Nonbonded interactions: 46018 Sorted by model distance: nonbonded pdb=" OH TYR B 70 " pdb=" O TRP B 134 " model vdw 2.133 2.440 nonbonded pdb=" OH TYR B 49 " pdb=" OG1 THR B 169 " model vdw 2.258 2.440 nonbonded pdb=" OG SER A 198 " pdb=" OE1 GLN A 250 " model vdw 2.286 2.440 nonbonded pdb=" O GLN B 462 " pdb=" NZ LYS B 467 " model vdw 2.297 2.520 nonbonded pdb=" O4 NAG C 2 " pdb=" O5 BMA C 3 " model vdw 2.312 2.440 ... (remaining 46013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.400 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: 15.320 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.007 0.096 6029 Z= 0.479 Angle : 1.081 10.113 8220 Z= 0.547 Chirality : 0.060 0.457 989 Planarity : 0.007 0.057 1004 Dihedral : 17.878 122.750 2393 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.97 % Allowed : 8.86 % Favored : 90.18 % 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: -1.19 (0.28), residues: 710 helix: 0.08 (0.24), residues: 368 sheet: 0.41 (0.56), residues: 80 loop : -2.45 (0.31), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 118 HIS 0.012 0.002 HIS B 414 PHE 0.023 0.003 PHE B 135 TYR 0.036 0.003 TYR A 299 ARG 0.007 0.001 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 97 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8983 (mttt) REVERT: A 99 ASP cc_start: 0.8802 (t0) cc_final: 0.8572 (t0) REVERT: A 120 MET cc_start: 0.6624 (ptm) cc_final: 0.6161 (ptp) REVERT: A 226 GLU cc_start: 0.7434 (pt0) cc_final: 0.7086 (mt-10) REVERT: A 227 TRP cc_start: 0.8124 (p90) cc_final: 0.7557 (p90) REVERT: A 262 ILE cc_start: 0.8559 (tt) cc_final: 0.8323 (tt) REVERT: A 293 LYS cc_start: 0.8707 (tttt) cc_final: 0.8488 (ttpp) REVERT: B 69 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8879 (mt) REVERT: B 111 ARG cc_start: 0.4986 (ttm170) cc_final: 0.2973 (ttp-170) REVERT: B 155 GLU cc_start: 0.8912 (tp30) cc_final: 0.8376 (mm-30) REVERT: B 176 GLN cc_start: 0.7802 (mt0) cc_final: 0.7116 (tm-30) REVERT: B 239 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 289 MET cc_start: 0.3366 (tpt) cc_final: 0.2588 (tpt) REVERT: B 309 MET cc_start: 0.7070 (ptp) cc_final: 0.6702 (ptp) REVERT: B 370 PHE cc_start: 0.7494 (m-80) cc_final: 0.7280 (m-10) REVERT: B 377 MET cc_start: 0.1822 (ptt) cc_final: 0.1492 (ptt) REVERT: B 458 ARG cc_start: 0.7598 (mtp-110) cc_final: 0.7013 (ttm-80) outliers start: 6 outliers final: 1 residues processed: 150 average time/residue: 0.2187 time to fit residues: 40.9951 Evaluate side-chains 105 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 317 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 287 HIS B 57 GLN B 68 GLN B 214 GLN B 235 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6029 Z= 0.221 Angle : 0.736 7.696 8220 Z= 0.360 Chirality : 0.044 0.261 989 Planarity : 0.005 0.044 1004 Dihedral : 13.137 108.961 1114 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.90 % Allowed : 17.71 % Favored : 79.39 % 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: -0.39 (0.29), residues: 710 helix: 0.89 (0.25), residues: 372 sheet: 0.27 (0.57), residues: 80 loop : -2.19 (0.31), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 118 HIS 0.006 0.001 HIS A 287 PHE 0.021 0.001 PHE B 468 TYR 0.020 0.001 TYR A 299 ARG 0.005 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 114 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: A 120 MET cc_start: 0.6653 (ptm) cc_final: 0.6148 (ptp) REVERT: A 262 ILE cc_start: 0.8532 (tt) cc_final: 0.8102 (tt) REVERT: A 266 TYR cc_start: 0.9139 (m-80) cc_final: 0.8777 (m-80) REVERT: B 111 ARG cc_start: 0.4877 (ttm170) cc_final: 0.2116 (ttp-170) REVERT: B 176 GLN cc_start: 0.7778 (mt0) cc_final: 0.7256 (tm-30) REVERT: B 239 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 289 MET cc_start: 0.3285 (tpt) cc_final: 0.2532 (tpt) REVERT: B 309 MET cc_start: 0.7168 (ptp) cc_final: 0.6938 (ptp) REVERT: B 458 ARG cc_start: 0.7564 (mtp-110) cc_final: 0.7141 (ttm-80) outliers start: 18 outliers final: 11 residues processed: 128 average time/residue: 0.2027 time to fit residues: 33.0058 Evaluate side-chains 118 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6029 Z= 0.215 Angle : 0.709 8.655 8220 Z= 0.343 Chirality : 0.044 0.283 989 Planarity : 0.005 0.075 1004 Dihedral : 10.858 101.161 1110 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.22 % Allowed : 21.74 % Favored : 75.04 % 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: -0.27 (0.30), residues: 710 helix: 1.02 (0.26), residues: 371 sheet: 0.12 (0.57), residues: 80 loop : -2.11 (0.32), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 118 HIS 0.004 0.001 HIS B 291 PHE 0.021 0.001 PHE B 468 TYR 0.019 0.001 TYR A 299 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8716 (t0) cc_final: 0.8502 (t0) REVERT: A 114 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: A 262 ILE cc_start: 0.8537 (tt) cc_final: 0.8152 (tt) REVERT: A 266 TYR cc_start: 0.9148 (m-80) cc_final: 0.8826 (m-80) REVERT: B 111 ARG cc_start: 0.4950 (ttm170) cc_final: 0.1955 (ttp-110) REVERT: B 176 GLN cc_start: 0.7812 (mt0) cc_final: 0.7336 (tm-30) REVERT: B 187 MET cc_start: 0.8358 (mmm) cc_final: 0.8128 (mmm) REVERT: B 239 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 289 MET cc_start: 0.3203 (tpt) cc_final: 0.2416 (tpt) REVERT: B 414 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7666 (t-90) REVERT: B 431 TYR cc_start: 0.8135 (t80) cc_final: 0.7742 (t80) REVERT: B 458 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.7180 (ttm-80) outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 0.1887 time to fit residues: 30.6654 Evaluate side-chains 118 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6029 Z= 0.189 Angle : 0.681 12.720 8220 Z= 0.323 Chirality : 0.043 0.266 989 Planarity : 0.005 0.079 1004 Dihedral : 9.475 93.537 1110 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.86 % Allowed : 22.87 % Favored : 73.27 % 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: -0.26 (0.30), residues: 710 helix: 1.11 (0.26), residues: 365 sheet: 0.13 (0.58), residues: 80 loop : -2.16 (0.32), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 118 HIS 0.006 0.001 HIS B 414 PHE 0.020 0.001 PHE B 468 TYR 0.014 0.001 TYR A 299 ARG 0.006 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8697 (t0) cc_final: 0.8473 (t0) REVERT: A 114 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: A 262 ILE cc_start: 0.8543 (tt) cc_final: 0.8149 (tt) REVERT: A 266 TYR cc_start: 0.9142 (m-80) cc_final: 0.8865 (m-80) REVERT: B 111 ARG cc_start: 0.5055 (ttm170) cc_final: 0.1198 (ttp80) REVERT: B 176 GLN cc_start: 0.7807 (mt0) cc_final: 0.7304 (tm-30) REVERT: B 187 MET cc_start: 0.8413 (mmm) cc_final: 0.8161 (mmm) REVERT: B 239 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 289 MET cc_start: 0.3160 (tpt) cc_final: 0.2354 (tpt) REVERT: B 370 PHE cc_start: 0.7085 (m-10) cc_final: 0.6740 (m-10) REVERT: B 431 TYR cc_start: 0.8178 (t80) cc_final: 0.7768 (t80) REVERT: B 437 PHE cc_start: 0.8656 (t80) cc_final: 0.8406 (t80) REVERT: B 458 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.7184 (ttm-80) outliers start: 24 outliers final: 15 residues processed: 127 average time/residue: 0.1883 time to fit residues: 31.0419 Evaluate side-chains 118 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS B 501 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 6029 Z= 0.444 Angle : 0.843 9.785 8220 Z= 0.408 Chirality : 0.052 0.557 989 Planarity : 0.006 0.090 1004 Dihedral : 9.307 71.690 1110 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.83 % Allowed : 22.54 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.30), residues: 710 helix: 0.93 (0.26), residues: 363 sheet: -0.02 (0.58), residues: 80 loop : -2.22 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 118 HIS 0.015 0.001 HIS B 414 PHE 0.017 0.002 PHE B 102 TYR 0.018 0.002 TYR B 70 ARG 0.005 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8788 (t0) cc_final: 0.8522 (t0) REVERT: A 114 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: B 68 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8393 (tp40) REVERT: B 111 ARG cc_start: 0.5107 (ttm170) cc_final: 0.2146 (ttp-170) REVERT: B 176 GLN cc_start: 0.7886 (mt0) cc_final: 0.7454 (tm-30) REVERT: B 187 MET cc_start: 0.8465 (mmm) cc_final: 0.8210 (mmm) REVERT: B 239 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 289 MET cc_start: 0.3424 (tpt) cc_final: 0.2612 (tpt) REVERT: B 309 MET cc_start: 0.7884 (ptp) cc_final: 0.7283 (ptp) REVERT: B 370 PHE cc_start: 0.7247 (m-10) cc_final: 0.6888 (m-10) REVERT: B 377 MET cc_start: 0.1896 (OUTLIER) cc_final: 0.1260 (ttp) REVERT: B 378 GLU cc_start: 0.3662 (OUTLIER) cc_final: 0.1060 (mt-10) REVERT: B 431 TYR cc_start: 0.8304 (t80) cc_final: 0.8025 (t80) REVERT: B 437 PHE cc_start: 0.8741 (t80) cc_final: 0.8528 (t80) REVERT: B 458 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7220 (ttm-80) outliers start: 30 outliers final: 23 residues processed: 131 average time/residue: 0.1725 time to fit residues: 29.7384 Evaluate side-chains 134 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6029 Z= 0.239 Angle : 0.712 9.065 8220 Z= 0.341 Chirality : 0.045 0.337 989 Planarity : 0.005 0.073 1004 Dihedral : 8.257 59.259 1110 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.15 % Allowed : 24.15 % Favored : 70.69 % 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: -0.48 (0.30), residues: 710 helix: 0.95 (0.26), residues: 365 sheet: -0.05 (0.59), residues: 80 loop : -2.27 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 118 HIS 0.006 0.001 HIS B 414 PHE 0.018 0.001 PHE B 468 TYR 0.015 0.001 TYR A 299 ARG 0.003 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 114 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: A 266 TYR cc_start: 0.9100 (m-80) cc_final: 0.8750 (m-80) REVERT: B 111 ARG cc_start: 0.5079 (ttm170) cc_final: 0.2451 (ttp-170) REVERT: B 176 GLN cc_start: 0.7912 (mt0) cc_final: 0.7518 (tm-30) REVERT: B 239 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 285 LEU cc_start: 0.4310 (OUTLIER) cc_final: 0.3729 (tt) REVERT: B 289 MET cc_start: 0.3257 (tpt) cc_final: 0.2434 (tpt) REVERT: B 309 MET cc_start: 0.7817 (ptp) cc_final: 0.7332 (ptp) REVERT: B 370 PHE cc_start: 0.7162 (m-10) cc_final: 0.6742 (m-10) REVERT: B 378 GLU cc_start: 0.3247 (OUTLIER) cc_final: 0.1019 (mt-10) REVERT: B 431 TYR cc_start: 0.8195 (t80) cc_final: 0.7832 (t80) REVERT: B 437 PHE cc_start: 0.8699 (t80) cc_final: 0.8465 (t80) REVERT: B 458 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7131 (ttm-80) outliers start: 32 outliers final: 20 residues processed: 133 average time/residue: 0.1846 time to fit residues: 31.8255 Evaluate side-chains 129 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 68 GLN Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6029 Z= 0.195 Angle : 0.688 7.952 8220 Z= 0.330 Chirality : 0.043 0.282 989 Planarity : 0.005 0.067 1004 Dihedral : 7.279 47.874 1110 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.35 % Allowed : 25.28 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.30), residues: 710 helix: 1.08 (0.26), residues: 362 sheet: -0.07 (0.58), residues: 80 loop : -2.23 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 118 HIS 0.005 0.001 HIS B 414 PHE 0.015 0.001 PHE B 318 TYR 0.014 0.001 TYR A 299 ARG 0.006 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8684 (t0) cc_final: 0.8434 (t0) REVERT: A 114 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: A 266 TYR cc_start: 0.9084 (m-80) cc_final: 0.8810 (m-80) REVERT: B 111 ARG cc_start: 0.5070 (ttm170) cc_final: 0.1906 (ttp-170) REVERT: B 132 LEU cc_start: 0.8899 (tp) cc_final: 0.8564 (tp) REVERT: B 176 GLN cc_start: 0.7887 (mt0) cc_final: 0.7480 (tm-30) REVERT: B 239 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7978 (tm-30) REVERT: B 289 MET cc_start: 0.3258 (tpt) cc_final: 0.2470 (tpt) REVERT: B 309 MET cc_start: 0.7720 (ptp) cc_final: 0.7340 (ptp) REVERT: B 370 PHE cc_start: 0.7109 (m-10) cc_final: 0.6665 (m-10) REVERT: B 431 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7822 (t80) REVERT: B 437 PHE cc_start: 0.8668 (t80) cc_final: 0.8416 (t80) REVERT: B 458 ARG cc_start: 0.7620 (mtp-110) cc_final: 0.7083 (ttm-80) outliers start: 27 outliers final: 18 residues processed: 133 average time/residue: 0.1809 time to fit residues: 31.4463 Evaluate side-chains 127 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 497 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.0040 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6029 Z= 0.199 Angle : 0.693 8.734 8220 Z= 0.330 Chirality : 0.043 0.271 989 Planarity : 0.004 0.063 1004 Dihedral : 6.837 45.503 1110 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.03 % Allowed : 25.28 % Favored : 70.69 % 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: -0.33 (0.30), residues: 710 helix: 1.09 (0.26), residues: 362 sheet: -0.02 (0.58), residues: 80 loop : -2.19 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 118 HIS 0.003 0.001 HIS B 291 PHE 0.014 0.001 PHE B 318 TYR 0.014 0.001 TYR A 299 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8681 (t0) cc_final: 0.8426 (t0) REVERT: A 114 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: A 266 TYR cc_start: 0.9075 (m-80) cc_final: 0.8829 (m-80) REVERT: B 111 ARG cc_start: 0.5070 (ttm170) cc_final: 0.1884 (ttp-170) REVERT: B 132 LEU cc_start: 0.8863 (tp) cc_final: 0.8507 (tp) REVERT: B 176 GLN cc_start: 0.7856 (mt0) cc_final: 0.7459 (tm-30) REVERT: B 239 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 285 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.3716 (tt) REVERT: B 289 MET cc_start: 0.3336 (tpt) cc_final: 0.2476 (tpt) REVERT: B 309 MET cc_start: 0.7651 (ptp) cc_final: 0.7226 (ptp) REVERT: B 370 PHE cc_start: 0.7108 (m-80) cc_final: 0.6643 (m-10) REVERT: B 377 MET cc_start: 0.1953 (OUTLIER) cc_final: 0.1218 (ttp) REVERT: B 431 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7715 (t80) REVERT: B 437 PHE cc_start: 0.8666 (t80) cc_final: 0.8422 (t80) REVERT: B 458 ARG cc_start: 0.7474 (mtp-110) cc_final: 0.6995 (ttm-80) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.1943 time to fit residues: 31.3214 Evaluate side-chains 125 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 497 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6029 Z= 0.224 Angle : 0.695 8.005 8220 Z= 0.335 Chirality : 0.044 0.293 989 Planarity : 0.005 0.063 1004 Dihedral : 6.704 46.135 1110 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.86 % Allowed : 25.60 % Favored : 70.53 % 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: -0.32 (0.30), residues: 710 helix: 1.12 (0.26), residues: 362 sheet: -0.01 (0.58), residues: 80 loop : -2.21 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 118 HIS 0.005 0.001 HIS B 414 PHE 0.013 0.001 PHE B 318 TYR 0.014 0.001 TYR A 299 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8709 (t0) cc_final: 0.8459 (t0) REVERT: A 114 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: B 111 ARG cc_start: 0.5058 (ttm170) cc_final: 0.2373 (ttp-170) REVERT: B 132 LEU cc_start: 0.8891 (tp) cc_final: 0.8557 (tp) REVERT: B 176 GLN cc_start: 0.7860 (mt0) cc_final: 0.7467 (tm-30) REVERT: B 239 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 285 LEU cc_start: 0.4333 (OUTLIER) cc_final: 0.3737 (tt) REVERT: B 289 MET cc_start: 0.3385 (tpt) cc_final: 0.3114 (tpt) REVERT: B 309 MET cc_start: 0.7675 (ptp) cc_final: 0.7253 (ptp) REVERT: B 370 PHE cc_start: 0.7125 (m-80) cc_final: 0.6663 (m-10) REVERT: B 377 MET cc_start: 0.1985 (OUTLIER) cc_final: 0.1229 (ttp) REVERT: B 431 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7785 (t80) REVERT: B 437 PHE cc_start: 0.8663 (t80) cc_final: 0.8447 (t80) REVERT: B 458 ARG cc_start: 0.7569 (mtp-110) cc_final: 0.7100 (ttm-80) outliers start: 24 outliers final: 20 residues processed: 121 average time/residue: 0.1902 time to fit residues: 29.8202 Evaluate side-chains 130 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 497 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6029 Z= 0.284 Angle : 0.728 7.794 8220 Z= 0.354 Chirality : 0.046 0.344 989 Planarity : 0.005 0.064 1004 Dihedral : 6.911 49.762 1110 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.03 % Allowed : 26.25 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.30), residues: 710 helix: 1.02 (0.26), residues: 363 sheet: -0.05 (0.57), residues: 80 loop : -2.23 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 118 HIS 0.007 0.001 HIS B 414 PHE 0.013 0.001 PHE B 468 TYR 0.018 0.001 TYR A 266 ARG 0.004 0.000 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8745 (t0) cc_final: 0.8498 (t0) REVERT: A 114 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: B 111 ARG cc_start: 0.5039 (ttm170) cc_final: 0.2408 (ttp-170) REVERT: B 132 LEU cc_start: 0.8917 (tp) cc_final: 0.8572 (tp) REVERT: B 176 GLN cc_start: 0.7895 (mt0) cc_final: 0.7491 (tm-30) REVERT: B 239 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 285 LEU cc_start: 0.4514 (OUTLIER) cc_final: 0.3899 (tt) REVERT: B 289 MET cc_start: 0.3438 (tpt) cc_final: 0.3176 (tpt) REVERT: B 309 MET cc_start: 0.7704 (ptp) cc_final: 0.7340 (ptp) REVERT: B 431 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 437 PHE cc_start: 0.8709 (t80) cc_final: 0.8506 (t80) REVERT: B 458 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.7139 (ttm-80) outliers start: 25 outliers final: 21 residues processed: 121 average time/residue: 0.1826 time to fit residues: 29.0792 Evaluate side-chains 127 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 180 PHE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 497 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.0270 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.144112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.133056 restraints weight = 11884.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136121 restraints weight = 5814.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137420 restraints weight = 3544.841| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6029 Z= 0.210 Angle : 0.685 7.418 8220 Z= 0.332 Chirality : 0.043 0.294 989 Planarity : 0.005 0.060 1004 Dihedral : 6.684 49.738 1110 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.86 % Allowed : 26.25 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.30), residues: 710 helix: 1.04 (0.26), residues: 363 sheet: -0.01 (0.58), residues: 80 loop : -2.21 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 118 HIS 0.003 0.001 HIS B 291 PHE 0.013 0.001 PHE B 318 TYR 0.018 0.001 TYR A 266 ARG 0.004 0.000 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.88 seconds wall clock time: 30 minutes 39.49 seconds (1839.49 seconds total)