Starting phenix.real_space_refine on Wed Feb 12 21:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxz_17269/02_2025/8oxz_17269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxz_17269/02_2025/8oxz_17269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oxz_17269/02_2025/8oxz_17269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxz_17269/02_2025/8oxz_17269.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxz_17269/02_2025/8oxz_17269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxz_17269/02_2025/8oxz_17269.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 47 5.16 5 C 5218 2.51 5 N 1417 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8324 Number of models: 1 Model: "" Number of chains: 4 Chain: "P" Number of atoms: 4542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4542 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 558} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3670 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 22, 'TRANS': 457} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "P" 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 Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.02, per 1000 atoms: 0.60 Number of scatterers: 8324 At special positions: 0 Unit cell: (113.984, 93.184, 125.632, 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 47 16.00 O 1642 8.00 N 1417 7.00 C 5218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS P 151 " - pdb=" SG CYS P 160 " distance=2.04 Simple disulfide: pdb=" SG CYS P 205 " - pdb=" SG CYS P 225 " distance=2.03 Simple disulfide: pdb=" SG CYS P 241 " - pdb=" SG CYS P 254 " distance=2.03 Simple disulfide: pdb=" SG CYS P 562 " - pdb=" SG CYS P 571 " distance=2.03 Simple disulfide: pdb=" SG CYS P 577 " - pdb=" SG CYS P 633 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 27 " - pdb=" SG CYS Q 45 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 35 " - pdb=" SG CYS Q 465 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 38 " - pdb=" SG CYS Q 64 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 48 " - pdb=" SG CYS Q 75 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 207 " - pdb=" SG CYS Q 213 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 261 " - pdb=" SG CYS Q 301 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 401 " - pdb=" SG CYS Q 415 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 467 " - pdb=" SG CYS Q 487 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 478 " - pdb=" SG CYS Q 490 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 492 " - pdb=" SG CYS Q 501 " 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 Links applied NAG-ASN " NAG P1101 " - " ASN P 136 " " NAG P1102 " - " ASN P 231 " " NAG P1103 " - " ASN P 346 " " NAG P1104 " - " ASN P 356 " " NAG P1105 " - " ASN P 365 " " NAG Q 800 " - " ASN Q 269 " " NAG Q 801 " - " ASN Q 363 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 960.7 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 13.6% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'P' and resid 274 through 279 removed outlier: 3.791A pdb=" N TRP P 278 " --> pdb=" O GLY P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 293 removed outlier: 3.597A pdb=" N ILE P 290 " --> pdb=" O THR P 286 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 317 removed outlier: 3.518A pdb=" N ASP P 317 " --> pdb=" O SER P 314 " (cutoff:3.500A) Processing helix chain 'P' and resid 467 through 471 removed outlier: 3.879A pdb=" N GLN P 471 " --> pdb=" O GLU P 468 " (cutoff:3.500A) Processing helix chain 'P' and resid 642 through 646 removed outlier: 3.621A pdb=" N PHE P 646 " --> pdb=" O GLU P 643 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.994A pdb=" N ASN Q 31 " --> pdb=" O CYS Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 40 Processing helix chain 'Q' and resid 59 through 64 removed outlier: 3.702A pdb=" N ARG Q 63 " --> pdb=" O THR Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 74 Processing helix chain 'Q' and resid 152 through 154 No H-bonds generated for 'chain 'Q' and resid 152 through 154' Processing helix chain 'Q' and resid 155 through 163 removed outlier: 3.641A pdb=" N GLU Q 160 " --> pdb=" O LYS Q 156 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN Q 161 " --> pdb=" O ASP Q 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS Q 163 " --> pdb=" O LEU Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 173 removed outlier: 3.526A pdb=" N MET Q 170 " --> pdb=" O GLY Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 176 No H-bonds generated for 'chain 'Q' and resid 174 through 176' Processing helix chain 'Q' and resid 228 through 237 removed outlier: 4.157A pdb=" N PHE Q 232 " --> pdb=" O ARG Q 228 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN Q 233 " --> pdb=" O GLY Q 229 " (cutoff:3.500A) Processing helix chain 'Q' and resid 251 through 261 removed outlier: 3.605A pdb=" N ALA Q 259 " --> pdb=" O ILE Q 255 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS Q 261 " --> pdb=" O GLN Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 320 through 328 Processing helix chain 'Q' and resid 338 through 340 No H-bonds generated for 'chain 'Q' and resid 338 through 340' Processing helix chain 'Q' and resid 341 through 352 removed outlier: 3.889A pdb=" N TYR Q 345 " --> pdb=" O PHE Q 341 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN Q 350 " --> pdb=" O LYS Q 346 " (cutoff:3.500A) Processing helix chain 'Q' and resid 366 through 380 removed outlier: 3.560A pdb=" N SER Q 380 " --> pdb=" O ASN Q 376 " (cutoff:3.500A) Processing helix chain 'Q' and resid 465 through 471 Processing sheet with id=AA1, first strand: chain 'P' and resid 115 through 119 removed outlier: 3.896A pdb=" N SER P 115 " --> pdb=" O GLY P 131 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA P 132 " --> pdb=" O ALA P 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 194 through 198 removed outlier: 4.034A pdb=" N THR P 194 " --> pdb=" O CYS P 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR P 224 " --> pdb=" O ALA P 206 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG P 234 " --> pdb=" O THR P 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 260 through 262 removed outlier: 3.646A pdb=" N VAL P 268 " --> pdb=" O ALA P 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 325 through 328 Processing sheet with id=AA5, first strand: chain 'P' and resid 379 through 382 removed outlier: 3.511A pdb=" N ARG P 413 " --> pdb=" O ALA P 396 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU P 430 " --> pdb=" O ILE P 416 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 444 through 448 removed outlier: 4.088A pdb=" N SER P 444 " --> pdb=" O GLY P 462 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 479 through 480 Processing sheet with id=AA8, first strand: chain 'P' and resid 505 through 509 removed outlier: 4.104A pdb=" N ALA P 508 " --> pdb=" O GLY P 526 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 609 through 611 Processing sheet with id=AB1, first strand: chain 'P' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'P' and resid 562 through 564 Processing sheet with id=AB3, first strand: chain 'Q' and resid 87 through 92 removed outlier: 6.740A pdb=" N GLN Q 118 " --> pdb=" O LYS Q 90 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ASN Q 92 " --> pdb=" O PRO Q 116 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU Q 119 " --> pdb=" O GLU Q 456 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU Q 444 " --> pdb=" O VAL Q 457 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 128 through 132 removed outlier: 3.510A pdb=" N LYS Q 398 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER Q 429 " --> pdb=" O ASN Q 396 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 220 through 226 removed outlier: 6.664A pdb=" N PHE Q 184 " --> pdb=" O VAL Q 222 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N SER Q 224 " --> pdb=" O ILE Q 182 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE Q 182 " --> pdb=" O SER Q 224 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR Q 226 " --> pdb=" O PHE Q 180 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N PHE Q 180 " --> pdb=" O THR Q 226 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE Q 143 " --> pdb=" O ARG Q 181 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N GLY Q 183 " --> pdb=" O ILE Q 143 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU Q 145 " --> pdb=" O GLY Q 183 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLY Q 185 " --> pdb=" O LEU Q 145 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR Q 147 " --> pdb=" O GLY Q 185 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE Q 187 " --> pdb=" O TYR Q 147 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N MET Q 149 " --> pdb=" O PHE Q 187 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP Q 144 " --> pdb=" O LEU Q 273 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL Q 275 " --> pdb=" O ASP Q 144 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR Q 146 " --> pdb=" O VAL Q 275 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER Q 277 " --> pdb=" O TYR Q 146 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU Q 148 " --> pdb=" O SER Q 277 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG Q 272 " --> pdb=" O GLN Q 332 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE Q 334 " --> pdb=" O ARG Q 272 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU Q 274 " --> pdb=" O ILE Q 334 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ALA Q 336 " --> pdb=" O LEU Q 274 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE Q 276 " --> pdb=" O ALA Q 336 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR Q 333 " --> pdb=" O ALA Q 356 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLY Q 358 " --> pdb=" O THR Q 333 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE Q 335 " --> pdb=" O GLY Q 358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 303 through 304 removed outlier: 3.519A pdb=" N GLU Q 304 " --> pdb=" O VAL Q 307 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL Q 307 " --> pdb=" O GLU Q 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'Q' and resid 483 through 486 213 hydrogen bonds defined for protein. 546 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: 2.30 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2735 1.34 - 1.46: 1816 1.46 - 1.58: 3891 1.58 - 1.70: 0 1.70 - 1.83: 61 Bond restraints: 8503 Sorted by residual: bond pdb=" C1 NAG P1105 " pdb=" O5 NAG P1105 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" CB ASN Q 305 " pdb=" CG ASN Q 305 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.46e+00 bond pdb=" CB ASN P 346 " pdb=" CG ASN P 346 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 bond pdb=" C1 NAG P1104 " pdb=" C2 NAG P1104 " ideal model delta sigma weight residual 1.532 1.560 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" N SER P 489 " pdb=" CA SER P 489 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.79e+00 ... (remaining 8498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 11332 2.62 - 5.24: 185 5.24 - 7.87: 10 7.87 - 10.49: 2 10.49 - 13.11: 2 Bond angle restraints: 11531 Sorted by residual: angle pdb=" CB MET Q 170 " pdb=" CG MET Q 170 " pdb=" SD MET Q 170 " ideal model delta sigma weight residual 112.70 124.48 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA LEU P 347 " pdb=" CB LEU P 347 " pdb=" CG LEU P 347 " ideal model delta sigma weight residual 116.30 129.41 -13.11 3.50e+00 8.16e-02 1.40e+01 angle pdb=" C ASN P 365 " pdb=" CA ASN P 365 " pdb=" CB ASN P 365 " ideal model delta sigma weight residual 110.42 117.61 -7.19 1.99e+00 2.53e-01 1.30e+01 angle pdb=" CA ASN Q 305 " pdb=" CB ASN Q 305 " pdb=" CG ASN Q 305 " ideal model delta sigma weight residual 112.60 115.68 -3.08 1.00e+00 1.00e+00 9.48e+00 angle pdb=" CA ILE Q 320 " pdb=" CB ILE Q 320 " pdb=" CG1 ILE Q 320 " ideal model delta sigma weight residual 110.40 105.23 5.17 1.70e+00 3.46e-01 9.24e+00 ... (remaining 11526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 4627 21.61 - 43.22: 477 43.22 - 64.83: 93 64.83 - 86.44: 19 86.44 - 108.05: 14 Dihedral angle restraints: 5230 sinusoidal: 2173 harmonic: 3057 Sorted by residual: dihedral pdb=" CB CYS Q 261 " pdb=" SG CYS Q 261 " pdb=" SG CYS Q 301 " pdb=" CB CYS Q 301 " ideal model delta sinusoidal sigma weight residual 93.00 25.72 67.28 1 1.00e+01 1.00e-02 5.89e+01 dihedral pdb=" CB CYS Q 48 " pdb=" SG CYS Q 48 " pdb=" SG CYS Q 75 " pdb=" CB CYS Q 75 " ideal model delta sinusoidal sigma weight residual -86.00 -146.14 60.14 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CB CYS P 151 " pdb=" SG CYS P 151 " pdb=" SG CYS P 160 " pdb=" CB CYS P 160 " ideal model delta sinusoidal sigma weight residual 93.00 35.79 57.21 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1132 0.078 - 0.156: 135 0.156 - 0.235: 6 0.235 - 0.313: 1 0.313 - 0.391: 2 Chirality restraints: 1276 Sorted by residual: chirality pdb=" C1 NAG P1105 " pdb=" ND2 ASN P 365 " pdb=" C2 NAG P1105 " pdb=" O5 NAG P1105 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C1 NAG P1102 " pdb=" ND2 ASN P 231 " pdb=" C2 NAG P1102 " pdb=" O5 NAG P1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE Q 182 " pdb=" CA ILE Q 182 " pdb=" CG1 ILE Q 182 " pdb=" CG2 ILE Q 182 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1273 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN P 365 " -0.051 2.00e-02 2.50e+03 4.69e-02 2.74e+01 pdb=" CG ASN P 365 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN P 365 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN P 365 " 0.046 2.00e-02 2.50e+03 pdb=" C1 NAG P1105 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 305 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C ASN Q 305 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN Q 305 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN Q 306 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN P 365 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" CG ASN P 365 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN P 365 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN P 365 " -0.016 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 429 2.71 - 3.26: 8464 3.26 - 3.81: 13089 3.81 - 4.35: 15884 4.35 - 4.90: 26714 Nonbonded interactions: 64580 Sorted by model distance: nonbonded pdb=" NZ LYS Q 130 " pdb=" OE2 GLU Q 427 " model vdw 2.167 3.120 nonbonded pdb=" OG1 THR P 194 " pdb=" O GLY P 257 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASN Q 50 " pdb=" OG1 THR Q 52 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP P 333 " pdb=" N ASP P 334 " model vdw 2.207 3.120 nonbonded pdb=" O ASP P 383 " pdb=" ND2 ASN P 457 " model vdw 2.220 3.120 ... (remaining 64575 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 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: 1.560 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 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 : 0.005 0.052 8503 Z= 0.309 Angle : 0.815 13.111 11531 Z= 0.431 Chirality : 0.052 0.391 1276 Planarity : 0.005 0.049 1523 Dihedral : 18.243 108.054 3245 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.23 % Allowed : 28.35 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.59 (0.24), residues: 1074 helix: -1.34 (0.49), residues: 102 sheet: -0.74 (0.28), residues: 307 loop : -1.16 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 153 HIS 0.004 0.001 HIS Q 321 PHE 0.021 0.002 PHE P 528 TYR 0.018 0.002 TYR P 323 ARG 0.006 0.001 ARG Q 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 231 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 117 GLU cc_start: 0.6447 (mp0) cc_final: 0.5613 (mp0) REVERT: P 196 ARG cc_start: 0.7291 (mtt90) cc_final: 0.6641 (mtt90) REVERT: P 276 TYR cc_start: 0.6814 (m-80) cc_final: 0.6509 (m-80) REVERT: P 518 ASN cc_start: 0.6903 (p0) cc_final: 0.6697 (p0) REVERT: P 635 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6438 (mt-10) REVERT: P 662 ASP cc_start: 0.7614 (t0) cc_final: 0.7223 (t0) REVERT: P 672 LEU cc_start: 0.7572 (mm) cc_final: 0.7366 (mm) REVERT: Q 84 ARG cc_start: 0.5640 (mmm160) cc_final: 0.4707 (mmt180) REVERT: Q 93 LYS cc_start: 0.7076 (tptp) cc_final: 0.6770 (tttm) REVERT: Q 102 MET cc_start: -0.0003 (ttp) cc_final: -0.0306 (ttp) REVERT: Q 134 LYS cc_start: 0.7177 (ptmm) cc_final: 0.6898 (ptmm) REVERT: Q 155 MET cc_start: 0.7055 (mmt) cc_final: 0.6214 (mmp) REVERT: Q 289 LYS cc_start: 0.8421 (tttt) cc_final: 0.8147 (tttm) REVERT: Q 322 LEU cc_start: 0.7820 (tp) cc_final: 0.7170 (tp) REVERT: Q 337 VAL cc_start: 0.7146 (m) cc_final: 0.6820 (m) REVERT: Q 371 ILE cc_start: 0.8577 (mm) cc_final: 0.8375 (mt) REVERT: Q 402 LYS cc_start: 0.6771 (tttt) cc_final: 0.6566 (tttt) REVERT: Q 443 GLN cc_start: 0.6602 (mm110) cc_final: 0.6147 (mm-40) outliers start: 11 outliers final: 3 residues processed: 236 average time/residue: 0.2330 time to fit residues: 72.9438 Evaluate side-chains 204 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 294 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 255 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 161 ASN Q 171 ASN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 376 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.156493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131887 restraints weight = 13698.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135914 restraints weight = 7243.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138594 restraints weight = 4555.138| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8503 Z= 0.269 Angle : 0.756 7.692 11531 Z= 0.385 Chirality : 0.052 0.306 1276 Planarity : 0.006 0.063 1523 Dihedral : 9.937 77.437 1333 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.14 % Allowed : 25.56 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.43 (0.25), residues: 1074 helix: -1.08 (0.48), residues: 105 sheet: -0.74 (0.28), residues: 313 loop : -1.01 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP Q 267 HIS 0.006 0.001 HIS Q 321 PHE 0.021 0.002 PHE Q 217 TYR 0.017 0.002 TYR P 415 ARG 0.008 0.001 ARG P 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 134 LYS cc_start: 0.8259 (tttm) cc_final: 0.7873 (tptm) REVERT: P 166 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6845 (t70) REVERT: P 196 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7437 (mmt-90) REVERT: P 276 TYR cc_start: 0.7048 (m-80) cc_final: 0.6510 (m-80) REVERT: P 399 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7329 (tp) REVERT: P 407 ARG cc_start: 0.7001 (mtm180) cc_final: 0.6768 (ptp-110) REVERT: P 594 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: P 635 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6591 (mt-10) REVERT: P 662 ASP cc_start: 0.7872 (t0) cc_final: 0.7545 (t0) REVERT: Q 84 ARG cc_start: 0.5732 (mmm160) cc_final: 0.5395 (mmm160) REVERT: Q 102 MET cc_start: 0.0074 (ttp) cc_final: -0.0229 (ttp) REVERT: Q 149 MET cc_start: 0.6540 (ppp) cc_final: 0.6183 (ppp) REVERT: Q 155 MET cc_start: 0.7317 (mmt) cc_final: 0.6341 (mmp) REVERT: Q 163 LYS cc_start: 0.8377 (pptt) cc_final: 0.7917 (ptpp) REVERT: Q 174 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7215 (ttp80) REVERT: Q 289 LYS cc_start: 0.8423 (tttt) cc_final: 0.8125 (tttm) REVERT: Q 307 VAL cc_start: 0.8324 (t) cc_final: 0.7978 (m) REVERT: Q 322 LEU cc_start: 0.7968 (tp) cc_final: 0.7294 (tp) REVERT: Q 398 LYS cc_start: 0.7500 (mttp) cc_final: 0.7174 (mttp) REVERT: Q 486 GLU cc_start: 0.6153 (pt0) cc_final: 0.4436 (pt0) REVERT: Q 491 ARG cc_start: 0.6934 (ttp-170) cc_final: 0.6087 (ttp-110) outliers start: 55 outliers final: 28 residues processed: 237 average time/residue: 0.2278 time to fit residues: 71.5452 Evaluate side-chains 230 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 196 ARG Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 535 VAL Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 594 GLU Chi-restraints excluded: chain P residue 654 HIS Chi-restraints excluded: chain P residue 661 LEU Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 290 LEU Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 0.0980 chunk 97 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 0.0370 chunk 50 optimal weight: 0.0070 chunk 64 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.1476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 HIS ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 457 ASN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 244 ASN Q 257 GLN Q 350 ASN Q 460 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133614 restraints weight = 13854.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137869 restraints weight = 7219.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140609 restraints weight = 4481.693| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8503 Z= 0.181 Angle : 0.672 11.296 11531 Z= 0.338 Chirality : 0.048 0.275 1276 Planarity : 0.005 0.047 1523 Dihedral : 7.953 68.872 1329 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.70 % Allowed : 24.22 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.43 (0.25), residues: 1074 helix: -0.95 (0.48), residues: 103 sheet: -0.76 (0.28), residues: 320 loop : -1.02 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 211 HIS 0.005 0.001 HIS P 584 PHE 0.019 0.002 PHE Q 232 TYR 0.013 0.001 TYR P 349 ARG 0.011 0.001 ARG Q 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7811 (mtt90) cc_final: 0.7300 (mmt-90) REVERT: P 276 TYR cc_start: 0.7056 (m-80) cc_final: 0.6590 (m-10) REVERT: P 399 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7366 (tp) REVERT: P 411 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7155 (m) REVERT: P 430 LEU cc_start: 0.8366 (tp) cc_final: 0.8146 (tt) REVERT: P 583 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7015 (ptmm) REVERT: P 594 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: P 662 ASP cc_start: 0.7931 (t0) cc_final: 0.7227 (t0) REVERT: Q 84 ARG cc_start: 0.6188 (mmm160) cc_final: 0.5987 (mmm160) REVERT: Q 102 MET cc_start: 0.0054 (ttp) cc_final: -0.0239 (ttp) REVERT: Q 155 MET cc_start: 0.7327 (mmt) cc_final: 0.6364 (mmp) REVERT: Q 163 LYS cc_start: 0.8403 (pptt) cc_final: 0.7962 (ptpp) REVERT: Q 170 MET cc_start: 0.7318 (tpp) cc_final: 0.7080 (tpp) REVERT: Q 256 MET cc_start: 0.6932 (tpp) cc_final: 0.6703 (tpp) REVERT: Q 289 LYS cc_start: 0.8348 (tttt) cc_final: 0.8102 (tttm) REVERT: Q 307 VAL cc_start: 0.8249 (t) cc_final: 0.7789 (m) REVERT: Q 314 TYR cc_start: 0.8137 (m-10) cc_final: 0.7902 (m-10) REVERT: Q 328 GLU cc_start: 0.7341 (tp30) cc_final: 0.7099 (tp30) REVERT: Q 398 LYS cc_start: 0.7576 (mttp) cc_final: 0.7346 (mttp) REVERT: Q 429 SER cc_start: 0.5432 (OUTLIER) cc_final: 0.5228 (p) REVERT: Q 486 GLU cc_start: 0.6198 (pt0) cc_final: 0.4519 (pt0) REVERT: Q 491 ARG cc_start: 0.6915 (ttp-170) cc_final: 0.6083 (ttp-110) outliers start: 60 outliers final: 27 residues processed: 243 average time/residue: 0.2293 time to fit residues: 73.8971 Evaluate side-chains 236 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 496 TRP Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 535 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 594 GLU Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 327 SER Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 93 optimal weight: 0.9980 chunk 1 optimal weight: 0.0370 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 HIS ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 305 ASN Q 342 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.156707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131799 restraints weight = 13893.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135818 restraints weight = 7481.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138503 restraints weight = 4787.347| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8503 Z= 0.226 Angle : 0.676 10.055 11531 Z= 0.344 Chirality : 0.049 0.249 1276 Planarity : 0.005 0.046 1523 Dihedral : 7.371 66.714 1329 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.14 % Allowed : 25.89 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.41 (0.25), residues: 1074 helix: -1.00 (0.48), residues: 111 sheet: -0.75 (0.28), residues: 313 loop : -0.99 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 599 HIS 0.007 0.002 HIS P 584 PHE 0.018 0.002 PHE Q 461 TYR 0.011 0.001 TYR P 349 ARG 0.011 0.001 ARG Q 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7429 (mtt90) REVERT: P 218 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: P 231 ASN cc_start: 0.5914 (OUTLIER) cc_final: 0.5676 (t0) REVERT: P 399 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7544 (tp) REVERT: P 411 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7263 (m) REVERT: P 583 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7080 (ptmm) REVERT: P 634 ARG cc_start: 0.5882 (mtp-110) cc_final: 0.5552 (mtp180) REVERT: P 662 ASP cc_start: 0.8082 (t0) cc_final: 0.6350 (m-30) REVERT: Q 102 MET cc_start: 0.0070 (ttp) cc_final: -0.0219 (ttp) REVERT: Q 155 MET cc_start: 0.7364 (mmt) cc_final: 0.6430 (mmp) REVERT: Q 163 LYS cc_start: 0.8444 (pptt) cc_final: 0.8019 (pttm) REVERT: Q 170 MET cc_start: 0.7268 (tpp) cc_final: 0.6962 (tpp) REVERT: Q 174 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6599 (ttp80) REVERT: Q 287 ASP cc_start: 0.6424 (t0) cc_final: 0.6004 (t0) REVERT: Q 307 VAL cc_start: 0.8291 (t) cc_final: 0.7858 (m) REVERT: Q 314 TYR cc_start: 0.8274 (m-10) cc_final: 0.8012 (m-10) REVERT: Q 328 GLU cc_start: 0.7319 (tp30) cc_final: 0.7099 (tp30) REVERT: Q 347 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6355 (mt-10) REVERT: Q 398 LYS cc_start: 0.7717 (mttp) cc_final: 0.7279 (mttp) REVERT: Q 429 SER cc_start: 0.5546 (OUTLIER) cc_final: 0.5147 (p) REVERT: Q 486 GLU cc_start: 0.6348 (pt0) cc_final: 0.4781 (pt0) REVERT: Q 491 ARG cc_start: 0.6949 (ttp-170) cc_final: 0.6146 (ttp-110) outliers start: 55 outliers final: 34 residues processed: 234 average time/residue: 0.2374 time to fit residues: 73.5597 Evaluate side-chains 245 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 204 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 196 ARG Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 535 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 305 ASN Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 311 GLN ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 350 ASN ** Q 442 ASN ** 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 = 0.4036 r_free = 0.4036 target = 0.158137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133474 restraints weight = 13674.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137544 restraints weight = 7195.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140207 restraints weight = 4535.450| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8503 Z= 0.231 Angle : 0.685 12.865 11531 Z= 0.342 Chirality : 0.049 0.236 1276 Planarity : 0.005 0.045 1523 Dihedral : 7.058 64.186 1328 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 6.70 % Allowed : 26.56 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.37 (0.25), residues: 1074 helix: -1.03 (0.48), residues: 111 sheet: -0.72 (0.28), residues: 313 loop : -0.95 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 267 HIS 0.008 0.002 HIS P 198 PHE 0.022 0.002 PHE Q 426 TYR 0.020 0.001 TYR P 323 ARG 0.006 0.001 ARG Q 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7392 (mtt90) REVERT: P 218 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: P 308 GLN cc_start: 0.6592 (pp30) cc_final: 0.6251 (pp30) REVERT: P 367 SER cc_start: 0.6899 (t) cc_final: 0.6415 (m) REVERT: P 399 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7564 (tp) REVERT: P 411 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7253 (m) REVERT: P 583 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7047 (ptmm) REVERT: P 662 ASP cc_start: 0.8129 (t0) cc_final: 0.5615 (m-30) REVERT: Q 71 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7298 (tptt) REVERT: Q 102 MET cc_start: 0.0104 (ttp) cc_final: -0.0197 (ttp) REVERT: Q 134 LYS cc_start: 0.8179 (ptmm) cc_final: 0.7466 (ptmm) REVERT: Q 155 MET cc_start: 0.7311 (mmt) cc_final: 0.6415 (mmp) REVERT: Q 163 LYS cc_start: 0.8449 (pptt) cc_final: 0.8159 (ptpp) REVERT: Q 170 MET cc_start: 0.7247 (tpp) cc_final: 0.6860 (tpp) REVERT: Q 287 ASP cc_start: 0.6541 (t0) cc_final: 0.6103 (t0) REVERT: Q 314 TYR cc_start: 0.8321 (m-10) cc_final: 0.7960 (m-10) REVERT: Q 347 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6221 (mt-10) REVERT: Q 349 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7428 (tptm) REVERT: Q 398 LYS cc_start: 0.7786 (mttp) cc_final: 0.7427 (mttp) REVERT: Q 486 GLU cc_start: 0.6381 (pt0) cc_final: 0.4836 (pt0) REVERT: Q 491 ARG cc_start: 0.6919 (ttp-170) cc_final: 0.6157 (ttp-110) outliers start: 60 outliers final: 34 residues processed: 244 average time/residue: 0.2406 time to fit residues: 76.9121 Evaluate side-chains 253 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 196 ARG Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 283 LEU Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 175 ARG Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 0.0050 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 239 GLN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 443 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132678 restraints weight = 13643.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136783 restraints weight = 7161.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139452 restraints weight = 4489.729| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8503 Z= 0.233 Angle : 0.697 13.295 11531 Z= 0.346 Chirality : 0.049 0.293 1276 Planarity : 0.005 0.051 1523 Dihedral : 6.962 59.827 1328 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.14 % Allowed : 26.67 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.36 (0.25), residues: 1074 helix: -0.95 (0.49), residues: 114 sheet: -0.75 (0.28), residues: 313 loop : -0.93 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 267 HIS 0.005 0.001 HIS Q 321 PHE 0.019 0.002 PHE P 528 TYR 0.017 0.001 TYR P 323 ARG 0.011 0.001 ARG P 537 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 218 GLN cc_start: 0.8057 (mp10) cc_final: 0.7184 (mp10) REVERT: P 308 GLN cc_start: 0.6780 (pp30) cc_final: 0.6446 (pp30) REVERT: P 331 SER cc_start: 0.7726 (m) cc_final: 0.7370 (t) REVERT: P 367 SER cc_start: 0.6890 (t) cc_final: 0.6394 (m) REVERT: P 399 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7485 (tp) REVERT: P 411 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7313 (m) REVERT: P 583 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7012 (ptmm) REVERT: Q 40 GLN cc_start: 0.6860 (tt0) cc_final: 0.6651 (tt0) REVERT: Q 71 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7419 (tptt) REVERT: Q 102 MET cc_start: 0.0112 (ttp) cc_final: -0.0192 (ttp) REVERT: Q 124 ARG cc_start: 0.5497 (OUTLIER) cc_final: 0.4851 (mtm180) REVERT: Q 134 LYS cc_start: 0.8290 (ptmm) cc_final: 0.7416 (ptmm) REVERT: Q 143 ILE cc_start: 0.8072 (pt) cc_final: 0.7753 (mt) REVERT: Q 144 ASP cc_start: 0.6919 (m-30) cc_final: 0.6688 (m-30) REVERT: Q 155 MET cc_start: 0.7446 (mmt) cc_final: 0.6686 (mmp) REVERT: Q 163 LYS cc_start: 0.8509 (pptt) cc_final: 0.8079 (ptpp) REVERT: Q 170 MET cc_start: 0.7249 (tpp) cc_final: 0.6844 (tpp) REVERT: Q 232 PHE cc_start: 0.7663 (t80) cc_final: 0.7391 (t80) REVERT: Q 268 ARG cc_start: 0.6915 (ttp-170) cc_final: 0.6541 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6614 (t0) cc_final: 0.6203 (t0) REVERT: Q 314 TYR cc_start: 0.8356 (m-10) cc_final: 0.7953 (m-10) REVERT: Q 328 GLU cc_start: 0.7202 (tp30) cc_final: 0.6830 (tp30) REVERT: Q 347 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6203 (mt-10) REVERT: Q 349 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7427 (tptm) REVERT: Q 375 TYR cc_start: 0.7394 (t80) cc_final: 0.7162 (t80) REVERT: Q 398 LYS cc_start: 0.7780 (mttp) cc_final: 0.7411 (mttp) REVERT: Q 429 SER cc_start: 0.5564 (OUTLIER) cc_final: 0.5363 (p) REVERT: Q 486 GLU cc_start: 0.6390 (pt0) cc_final: 0.4893 (pt0) REVERT: Q 491 ARG cc_start: 0.6940 (ttp-170) cc_final: 0.6118 (ttp-110) outliers start: 55 outliers final: 32 residues processed: 242 average time/residue: 0.2375 time to fit residues: 76.1400 Evaluate side-chains 255 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 222 VAL Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 48 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: ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 332 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 479 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.154028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130115 restraints weight = 13734.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133995 restraints weight = 7332.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136574 restraints weight = 4622.890| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8503 Z= 0.280 Angle : 0.715 14.302 11531 Z= 0.356 Chirality : 0.050 0.259 1276 Planarity : 0.005 0.075 1523 Dihedral : 6.690 55.170 1328 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.69 % Allowed : 27.79 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.36 (0.25), residues: 1074 helix: -0.98 (0.49), residues: 114 sheet: -0.80 (0.28), residues: 318 loop : -0.89 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 278 HIS 0.004 0.001 HIS P 584 PHE 0.019 0.002 PHE Q 426 TYR 0.014 0.001 TYR P 349 ARG 0.008 0.001 ARG Q 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7385 (mmt-90) REVERT: P 218 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: P 231 ASN cc_start: 0.6065 (OUTLIER) cc_final: 0.5853 (t0) REVERT: P 308 GLN cc_start: 0.7005 (pp30) cc_final: 0.6693 (pp30) REVERT: P 331 SER cc_start: 0.7776 (m) cc_final: 0.7424 (t) REVERT: P 399 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7591 (tp) REVERT: P 411 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7324 (m) REVERT: P 437 GLU cc_start: 0.7063 (tp30) cc_final: 0.6763 (tp30) REVERT: P 583 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7006 (ptmm) REVERT: Q 35 CYS cc_start: 0.4892 (OUTLIER) cc_final: 0.3603 (t) REVERT: Q 40 GLN cc_start: 0.6978 (tt0) cc_final: 0.6753 (tt0) REVERT: Q 71 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7502 (tptt) REVERT: Q 102 MET cc_start: 0.0093 (ttp) cc_final: -0.0206 (ttp) REVERT: Q 124 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.4680 (mtm180) REVERT: Q 134 LYS cc_start: 0.8391 (ptmm) cc_final: 0.8038 (ptmm) REVERT: Q 143 ILE cc_start: 0.8140 (pt) cc_final: 0.7871 (mt) REVERT: Q 155 MET cc_start: 0.7377 (mmt) cc_final: 0.6495 (mmp) REVERT: Q 163 LYS cc_start: 0.8500 (pptt) cc_final: 0.7925 (ptpp) REVERT: Q 170 MET cc_start: 0.7295 (tpp) cc_final: 0.6893 (tpp) REVERT: Q 232 PHE cc_start: 0.7670 (t80) cc_final: 0.7458 (t80) REVERT: Q 268 ARG cc_start: 0.7145 (ttp-170) cc_final: 0.6854 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6676 (t0) cc_final: 0.6247 (t0) REVERT: Q 314 TYR cc_start: 0.8407 (m-10) cc_final: 0.8012 (m-10) REVERT: Q 328 GLU cc_start: 0.7186 (tp30) cc_final: 0.6830 (tp30) REVERT: Q 341 PHE cc_start: 0.6864 (m-80) cc_final: 0.6527 (m-80) REVERT: Q 347 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6307 (mt-10) REVERT: Q 349 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7423 (tptm) REVERT: Q 491 ARG cc_start: 0.6951 (ttp-170) cc_final: 0.6134 (ttp-110) outliers start: 51 outliers final: 35 residues processed: 249 average time/residue: 0.2437 time to fit residues: 79.3363 Evaluate side-chains 265 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain Q residue 35 CYS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 101 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.0060 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.153823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129603 restraints weight = 13885.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133576 restraints weight = 7321.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136211 restraints weight = 4601.600| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8503 Z= 0.258 Angle : 0.710 15.604 11531 Z= 0.351 Chirality : 0.049 0.266 1276 Planarity : 0.005 0.052 1523 Dihedral : 6.518 51.006 1328 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.47 % Allowed : 27.34 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.34 (0.25), residues: 1074 helix: -1.06 (0.48), residues: 114 sheet: -0.72 (0.28), residues: 320 loop : -0.90 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 267 HIS 0.004 0.001 HIS Q 321 PHE 0.023 0.002 PHE Q 426 TYR 0.016 0.002 TYR P 276 ARG 0.012 0.001 ARG Q 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 218 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: P 231 ASN cc_start: 0.5945 (OUTLIER) cc_final: 0.5739 (t0) REVERT: P 236 LEU cc_start: 0.8040 (mt) cc_final: 0.7690 (mm) REVERT: P 308 GLN cc_start: 0.7058 (pp30) cc_final: 0.6722 (pp30) REVERT: P 331 SER cc_start: 0.7823 (m) cc_final: 0.7451 (t) REVERT: P 367 SER cc_start: 0.7122 (t) cc_final: 0.6644 (m) REVERT: P 399 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7557 (tp) REVERT: P 411 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7299 (m) REVERT: P 437 GLU cc_start: 0.7083 (tp30) cc_final: 0.6767 (tp30) REVERT: P 583 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7073 (ptmm) REVERT: Q 35 CYS cc_start: 0.4896 (OUTLIER) cc_final: 0.3662 (t) REVERT: Q 40 GLN cc_start: 0.7010 (tt0) cc_final: 0.6809 (tt0) REVERT: Q 71 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.6894 (tptm) REVERT: Q 102 MET cc_start: 0.0075 (ttp) cc_final: -0.0223 (ttp) REVERT: Q 124 ARG cc_start: 0.5590 (OUTLIER) cc_final: 0.4647 (mtm180) REVERT: Q 143 ILE cc_start: 0.8176 (pt) cc_final: 0.7949 (mt) REVERT: Q 145 LEU cc_start: 0.8376 (tp) cc_final: 0.8165 (tt) REVERT: Q 155 MET cc_start: 0.7425 (mmt) cc_final: 0.6540 (mmp) REVERT: Q 163 LYS cc_start: 0.8495 (pptt) cc_final: 0.8061 (pttt) REVERT: Q 170 MET cc_start: 0.7307 (tpp) cc_final: 0.6884 (tpp) REVERT: Q 232 PHE cc_start: 0.7736 (t80) cc_final: 0.7532 (t80) REVERT: Q 265 ILE cc_start: 0.8236 (mt) cc_final: 0.8036 (mt) REVERT: Q 268 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6915 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6702 (t0) cc_final: 0.6294 (t0) REVERT: Q 314 TYR cc_start: 0.8385 (m-10) cc_final: 0.8048 (m-10) REVERT: Q 341 PHE cc_start: 0.6944 (m-80) cc_final: 0.6567 (m-80) REVERT: Q 347 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6364 (mt-10) REVERT: Q 349 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7348 (tptm) REVERT: Q 422 ASP cc_start: 0.6200 (t0) cc_final: 0.5926 (m-30) REVERT: Q 449 LEU cc_start: 0.7157 (mp) cc_final: 0.6712 (mp) REVERT: Q 454 GLU cc_start: 0.7419 (pm20) cc_final: 0.7184 (pm20) REVERT: Q 491 ARG cc_start: 0.6962 (ttp-170) cc_final: 0.6151 (ttp-110) outliers start: 58 outliers final: 34 residues processed: 244 average time/residue: 0.2300 time to fit residues: 74.6226 Evaluate side-chains 257 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain Q residue 35 CYS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 268 ARG Chi-restraints excluded: chain Q residue 289 LYS Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 0.0870 chunk 59 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130884 restraints weight = 13854.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134890 restraints weight = 7281.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137522 restraints weight = 4574.461| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8503 Z= 0.213 Angle : 0.703 16.795 11531 Z= 0.344 Chirality : 0.048 0.249 1276 Planarity : 0.005 0.042 1523 Dihedral : 6.248 46.467 1328 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.25 % Allowed : 29.13 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.25 (0.25), residues: 1074 helix: -1.04 (0.48), residues: 115 sheet: -0.64 (0.28), residues: 317 loop : -0.85 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 496 HIS 0.003 0.001 HIS Q 500 PHE 0.018 0.002 PHE Q 426 TYR 0.009 0.001 TYR P 349 ARG 0.012 0.001 ARG Q 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8491 (mp10) cc_final: 0.8209 (mp10) REVERT: P 196 ARG cc_start: 0.7581 (mtt90) cc_final: 0.7258 (mmt-90) REVERT: P 218 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: P 231 ASN cc_start: 0.5933 (OUTLIER) cc_final: 0.5727 (t0) REVERT: P 308 GLN cc_start: 0.7121 (pp30) cc_final: 0.6786 (pp30) REVERT: P 331 SER cc_start: 0.7805 (m) cc_final: 0.7441 (t) REVERT: P 399 LEU cc_start: 0.7777 (tp) cc_final: 0.7505 (tp) REVERT: P 411 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7337 (m) REVERT: P 437 GLU cc_start: 0.7060 (tp30) cc_final: 0.6814 (tp30) REVERT: P 534 LEU cc_start: 0.8250 (mp) cc_final: 0.8044 (mt) REVERT: P 583 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7153 (ptmm) REVERT: Q 35 CYS cc_start: 0.4678 (OUTLIER) cc_final: 0.3399 (t) REVERT: Q 71 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.6907 (tptm) REVERT: Q 102 MET cc_start: 0.0068 (ttp) cc_final: -0.0229 (ttp) REVERT: Q 124 ARG cc_start: 0.5542 (OUTLIER) cc_final: 0.4745 (mtm180) REVERT: Q 143 ILE cc_start: 0.8116 (pt) cc_final: 0.7906 (mt) REVERT: Q 145 LEU cc_start: 0.8430 (tp) cc_final: 0.8141 (tt) REVERT: Q 146 TYR cc_start: 0.8007 (t80) cc_final: 0.7604 (t80) REVERT: Q 155 MET cc_start: 0.7368 (mmt) cc_final: 0.6485 (mmp) REVERT: Q 163 LYS cc_start: 0.8533 (pptt) cc_final: 0.8034 (pttt) REVERT: Q 170 MET cc_start: 0.7296 (tpp) cc_final: 0.6851 (tpp) REVERT: Q 265 ILE cc_start: 0.8211 (mt) cc_final: 0.7876 (mt) REVERT: Q 268 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6959 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6754 (t0) cc_final: 0.6280 (t0) REVERT: Q 314 TYR cc_start: 0.8382 (m-10) cc_final: 0.8066 (m-10) REVERT: Q 340 GLU cc_start: 0.7148 (mp0) cc_final: 0.6853 (mp0) REVERT: Q 347 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6282 (mt-10) REVERT: Q 349 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7296 (tptm) REVERT: Q 422 ASP cc_start: 0.6268 (t0) cc_final: 0.5915 (m-30) REVERT: Q 491 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.6144 (ttp-110) outliers start: 47 outliers final: 35 residues processed: 245 average time/residue: 0.2373 time to fit residues: 76.5757 Evaluate side-chains 263 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain Q residue 35 CYS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 225 LEU Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 268 ARG Chi-restraints excluded: chain Q residue 289 LYS Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.0030 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 GLN ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131220 restraints weight = 13836.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135323 restraints weight = 7275.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.138002 restraints weight = 4541.064| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8503 Z= 0.223 Angle : 0.710 17.110 11531 Z= 0.348 Chirality : 0.048 0.237 1276 Planarity : 0.004 0.043 1523 Dihedral : 6.160 44.794 1328 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.80 % Allowed : 29.35 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.29 (0.25), residues: 1074 helix: -1.07 (0.48), residues: 115 sheet: -0.69 (0.28), residues: 317 loop : -0.86 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 267 HIS 0.003 0.001 HIS Q 321 PHE 0.023 0.002 PHE Q 426 TYR 0.027 0.001 TYR P 209 ARG 0.012 0.001 ARG Q 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8506 (mp10) cc_final: 0.8194 (mp10) REVERT: P 218 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: P 231 ASN cc_start: 0.5960 (OUTLIER) cc_final: 0.5751 (t0) REVERT: P 308 GLN cc_start: 0.7143 (pp30) cc_final: 0.6825 (pp30) REVERT: P 331 SER cc_start: 0.7821 (m) cc_final: 0.7437 (t) REVERT: P 399 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7556 (tp) REVERT: P 411 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7319 (m) REVERT: P 437 GLU cc_start: 0.7099 (tp30) cc_final: 0.6839 (tp30) REVERT: P 583 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7164 (ptmm) REVERT: P 677 HIS cc_start: 0.7850 (t-90) cc_final: 0.7495 (t-90) REVERT: Q 35 CYS cc_start: 0.4870 (OUTLIER) cc_final: 0.3604 (t) REVERT: Q 67 LEU cc_start: 0.7699 (pt) cc_final: 0.7475 (pp) REVERT: Q 102 MET cc_start: 0.0075 (ttp) cc_final: -0.0221 (ttp) REVERT: Q 112 THR cc_start: 0.7423 (p) cc_final: 0.5416 (p) REVERT: Q 124 ARG cc_start: 0.5500 (OUTLIER) cc_final: 0.4663 (mtm180) REVERT: Q 134 LYS cc_start: 0.8514 (ptmm) cc_final: 0.8174 (ptmm) REVERT: Q 145 LEU cc_start: 0.8403 (tp) cc_final: 0.8176 (tt) REVERT: Q 155 MET cc_start: 0.7364 (mmt) cc_final: 0.6478 (mmp) REVERT: Q 163 LYS cc_start: 0.8534 (pptt) cc_final: 0.8060 (pttt) REVERT: Q 170 MET cc_start: 0.7287 (tpp) cc_final: 0.6887 (tpp) REVERT: Q 174 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6844 (ttp80) REVERT: Q 268 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6849 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6739 (t0) cc_final: 0.6268 (t0) REVERT: Q 314 TYR cc_start: 0.8433 (m-10) cc_final: 0.8077 (m-10) REVERT: Q 347 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6375 (mt-10) REVERT: Q 349 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7319 (tptm) REVERT: Q 422 ASP cc_start: 0.6302 (t0) cc_final: 0.5940 (m-30) REVERT: Q 491 ARG cc_start: 0.6843 (ttp-170) cc_final: 0.6150 (ttp-110) outliers start: 52 outliers final: 33 residues processed: 259 average time/residue: 0.2339 time to fit residues: 80.1546 Evaluate side-chains 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain Q residue 35 CYS Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 225 LEU Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 268 ARG Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.154214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129929 restraints weight = 13948.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133990 restraints weight = 7469.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136602 restraints weight = 4699.016| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8503 Z= 0.260 Angle : 0.733 16.073 11531 Z= 0.359 Chirality : 0.048 0.227 1276 Planarity : 0.005 0.042 1523 Dihedral : 6.112 46.043 1328 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.91 % Allowed : 29.02 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.36 (0.25), residues: 1074 helix: -1.06 (0.48), residues: 115 sheet: -0.72 (0.28), residues: 319 loop : -0.92 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 496 HIS 0.005 0.001 HIS Q 321 PHE 0.029 0.002 PHE Q 341 TYR 0.029 0.002 TYR P 276 ARG 0.011 0.001 ARG Q 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.74 seconds wall clock time: 57 minutes 21.98 seconds (3441.98 seconds total)