Starting phenix.real_space_refine on Sat Dec 28 11:10:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxz_17269/12_2024/8oxz_17269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxz_17269/12_2024/8oxz_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_17269/12_2024/8oxz_17269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxz_17269/12_2024/8oxz_17269.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxz_17269/12_2024/8oxz_17269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxz_17269/12_2024/8oxz_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.04, per 1000 atoms: 0.61 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: 2.22 Conformation dependent library (CDL) restraints added in 990.0 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: 1.01 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: 2.45 Time building geometry restraints manager: 2.53 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: 7.060 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.810 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- 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 : 0.910 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: 0.2403 time to fit residues: 75.9711 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 : 0.897 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 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 : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 134 LYS cc_start: 0.8253 (tttm) cc_final: 0.7887 (tptm) REVERT: P 166 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6830 (t70) REVERT: P 196 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7462 (mmt-90) REVERT: P 276 TYR cc_start: 0.6967 (m-80) cc_final: 0.6433 (m-80) REVERT: P 399 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7400 (tp) REVERT: P 594 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: P 635 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6460 (mt-10) REVERT: P 662 ASP cc_start: 0.7824 (t0) cc_final: 0.7535 (t0) REVERT: Q 84 ARG cc_start: 0.5676 (mmm160) cc_final: 0.5338 (mmm160) REVERT: Q 102 MET cc_start: 0.0010 (ttp) cc_final: -0.0275 (ttp) REVERT: Q 149 MET cc_start: 0.6589 (ppp) cc_final: 0.6222 (ppp) REVERT: Q 155 MET cc_start: 0.7261 (mmt) cc_final: 0.6304 (mmp) REVERT: Q 163 LYS cc_start: 0.8388 (pptt) cc_final: 0.7930 (ptpp) REVERT: Q 174 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7208 (ttp80) REVERT: Q 220 LYS cc_start: 0.7474 (ttpt) cc_final: 0.7268 (ttpt) REVERT: Q 289 LYS cc_start: 0.8436 (tttt) cc_final: 0.8147 (tttm) REVERT: Q 307 VAL cc_start: 0.8327 (t) cc_final: 0.7975 (m) REVERT: Q 322 LEU cc_start: 0.7959 (tp) cc_final: 0.7285 (tp) REVERT: Q 398 LYS cc_start: 0.7485 (mttp) cc_final: 0.7169 (mttp) REVERT: Q 486 GLU cc_start: 0.6199 (pt0) cc_final: 0.4453 (pt0) REVERT: Q 491 ARG cc_start: 0.6947 (ttp-170) cc_final: 0.6097 (ttp-110) outliers start: 55 outliers final: 28 residues processed: 237 average time/residue: 0.2292 time to fit residues: 72.6071 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 : 0.902 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 457 ASN Q 117 GLN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 342 GLN Q 350 ASN Q 460 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3222 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= 0.262 Angle : 0.717 12.396 11531 Z= 0.362 Chirality : 0.051 0.285 1276 Planarity : 0.006 0.065 1523 Dihedral : 7.820 70.472 1329 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 7.81 % Allowed : 23.88 % 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: -1.45 (0.24), residues: 1074 helix: -0.98 (0.49), residues: 103 sheet: -0.67 (0.28), residues: 318 loop : -1.09 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 211 HIS 0.008 0.002 HIS P 584 PHE 0.021 0.002 PHE P 528 TYR 0.017 0.002 TYR P 349 ARG 0.006 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 288 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7358 (mmt-90) REVERT: P 331 SER cc_start: 0.7664 (m) cc_final: 0.7369 (t) REVERT: P 393 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7655 (mt) REVERT: P 399 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7627 (tp) REVERT: P 411 VAL cc_start: 0.7608 (OUTLIER) cc_final: 0.7341 (m) REVERT: P 437 GLU cc_start: 0.7073 (tp30) cc_final: 0.6856 (tp30) REVERT: P 634 ARG cc_start: 0.5970 (mtp-110) cc_final: 0.5653 (mtp180) REVERT: P 662 ASP cc_start: 0.8195 (t0) cc_final: 0.6337 (m-30) REVERT: Q 84 ARG cc_start: 0.6147 (mmm160) cc_final: 0.5901 (mmm160) REVERT: Q 102 MET cc_start: 0.0008 (ttp) cc_final: -0.0268 (ttp) REVERT: Q 155 MET cc_start: 0.7338 (mmt) cc_final: 0.6397 (mmp) REVERT: Q 163 LYS cc_start: 0.8467 (pptt) cc_final: 0.8137 (ptpp) REVERT: Q 170 MET cc_start: 0.7379 (tpp) cc_final: 0.7114 (tpp) REVERT: Q 174 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7231 (ttp80) REVERT: Q 220 LYS cc_start: 0.7685 (ttpt) cc_final: 0.7461 (ttpt) REVERT: Q 287 ASP cc_start: 0.6586 (t0) cc_final: 0.6137 (t0) REVERT: Q 289 LYS cc_start: 0.8396 (tttt) cc_final: 0.8190 (tttm) REVERT: Q 305 ASN cc_start: 0.6875 (t0) cc_final: 0.6658 (t0) REVERT: Q 307 VAL cc_start: 0.8337 (t) cc_final: 0.7833 (m) REVERT: Q 347 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6423 (mt-10) REVERT: Q 366 ASN cc_start: 0.8094 (p0) cc_final: 0.7875 (p0) REVERT: Q 398 LYS cc_start: 0.7804 (mttp) cc_final: 0.7362 (mttp) REVERT: Q 486 GLU cc_start: 0.6437 (pt0) cc_final: 0.4835 (pt0) REVERT: Q 491 ARG cc_start: 0.6980 (ttp-170) cc_final: 0.6163 (ttp-110) outliers start: 70 outliers final: 35 residues processed: 253 average time/residue: 0.2348 time to fit residues: 78.8077 Evaluate side-chains 251 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 327 VAL 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 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 589 ILE Chi-restraints excluded: chain P residue 661 LEU Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 234 GLU 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 300 GLN Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 393 VAL Chi-restraints excluded: chain Q residue 401 CYS 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 96 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 311 GLN P 596 GLN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 350 ASN Q 406 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8503 Z= 0.389 Angle : 0.770 9.336 11531 Z= 0.395 Chirality : 0.052 0.237 1276 Planarity : 0.006 0.051 1523 Dihedral : 7.729 67.266 1328 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.81 % Allowed : 26.56 % Favored : 66.63 % 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: -1.67 (0.25), residues: 1074 helix: -1.17 (0.46), residues: 114 sheet: -0.83 (0.27), residues: 331 loop : -1.22 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP P 599 HIS 0.009 0.002 HIS P 584 PHE 0.025 0.003 PHE Q 426 TYR 0.019 0.002 TYR P 323 ARG 0.008 0.001 ARG Q 84 *********************** 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 283 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7565 (mtt90) REVERT: P 218 GLN cc_start: 0.8272 (mp10) cc_final: 0.7482 (mp10) REVERT: P 224 THR cc_start: 0.8199 (p) cc_final: 0.7914 (p) REVERT: P 231 ASN cc_start: 0.6075 (OUTLIER) cc_final: 0.5799 (t0) REVERT: P 308 GLN cc_start: 0.7053 (pp30) cc_final: 0.6796 (pp30) REVERT: P 331 SER cc_start: 0.7908 (m) cc_final: 0.7607 (t) REVERT: P 399 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7804 (tp) REVERT: P 411 VAL cc_start: 0.7694 (OUTLIER) cc_final: 0.7470 (m) REVERT: P 437 GLU cc_start: 0.7082 (tp30) cc_final: 0.6785 (tp30) REVERT: P 445 LEU cc_start: 0.8332 (mt) cc_final: 0.8127 (tp) REVERT: P 528 PHE cc_start: 0.8438 (p90) cc_final: 0.8127 (p90) REVERT: P 583 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.7045 (ptmm) REVERT: Q 35 CYS cc_start: 0.5168 (OUTLIER) cc_final: 0.4045 (t) REVERT: Q 102 MET cc_start: -0.0005 (ttp) cc_final: -0.0280 (ttp) REVERT: Q 134 LYS cc_start: 0.8372 (ptmm) cc_final: 0.8103 (ptmm) REVERT: Q 143 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.8000 (mt) REVERT: Q 155 MET cc_start: 0.7406 (mmt) cc_final: 0.6507 (mmp) REVERT: Q 170 MET cc_start: 0.7454 (tpp) cc_final: 0.7108 (tpp) REVERT: Q 174 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7274 (ttp80) REVERT: Q 257 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7396 (mt0) REVERT: Q 268 ARG cc_start: 0.7252 (ttp-170) cc_final: 0.7019 (ttp-110) REVERT: Q 279 ASP cc_start: 0.7709 (m-30) cc_final: 0.7449 (m-30) REVERT: Q 287 ASP cc_start: 0.6838 (t0) cc_final: 0.6351 (t0) REVERT: Q 328 GLU cc_start: 0.7314 (tp30) cc_final: 0.6957 (tp30) REVERT: Q 347 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6508 (mt-10) REVERT: Q 366 ASN cc_start: 0.8264 (p0) cc_final: 0.8012 (p0) REVERT: Q 398 LYS cc_start: 0.7914 (mttp) cc_final: 0.7377 (mttp) REVERT: Q 454 GLU cc_start: 0.7052 (pp20) cc_final: 0.6787 (pp20) REVERT: Q 455 VAL cc_start: 0.6204 (OUTLIER) cc_final: 0.5612 (p) REVERT: Q 491 ARG cc_start: 0.6959 (ttp-170) cc_final: 0.6117 (ttp-110) REVERT: Q 500 HIS cc_start: 0.5704 (OUTLIER) cc_final: 0.5413 (m90) outliers start: 61 outliers final: 35 residues processed: 249 average time/residue: 0.2496 time to fit residues: 82.0948 Evaluate side-chains 260 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 164 GLN 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 231 ASN Chi-restraints excluded: chain P residue 309 THR 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 418 LEU Chi-restraints excluded: chain P residue 451 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU 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 623 LEU Chi-restraints excluded: chain P residue 661 LEU Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain Q residue 35 CYS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 143 ILE 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 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 455 VAL Chi-restraints excluded: chain Q residue 500 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.0070 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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** Q 239 GLN Q 244 ASN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 479 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8503 Z= 0.241 Angle : 0.688 9.359 11531 Z= 0.349 Chirality : 0.049 0.234 1276 Planarity : 0.005 0.046 1523 Dihedral : 7.262 63.706 1328 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.70 % Allowed : 27.46 % Favored : 65.85 % 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: -1.62 (0.25), residues: 1074 helix: -0.98 (0.48), residues: 114 sheet: -0.90 (0.28), residues: 320 loop : -1.16 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 267 HIS 0.004 0.001 HIS P 584 PHE 0.021 0.002 PHE Q 232 TYR 0.021 0.002 TYR Q 308 ARG 0.007 0.001 ARG P 537 *********************** 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 282 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6650 (mtt90) REVERT: P 218 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: P 308 GLN cc_start: 0.7031 (pp30) cc_final: 0.6743 (pp30) REVERT: P 331 SER cc_start: 0.7860 (m) cc_final: 0.7569 (t) REVERT: P 411 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7369 (m) REVERT: P 528 PHE cc_start: 0.8453 (p90) cc_final: 0.8048 (p90) REVERT: P 583 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.7010 (ptmm) REVERT: Q 35 CYS cc_start: 0.4945 (OUTLIER) cc_final: 0.3777 (t) REVERT: Q 71 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7630 (tptt) REVERT: Q 102 MET cc_start: 0.0022 (ttp) cc_final: -0.0268 (ttp) REVERT: Q 134 LYS cc_start: 0.8381 (ptmm) cc_final: 0.8075 (ptmm) REVERT: Q 143 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7955 (mt) REVERT: Q 155 MET cc_start: 0.7331 (mmt) cc_final: 0.6435 (mmp) REVERT: Q 170 MET cc_start: 0.7442 (tpp) cc_final: 0.7096 (tpp) REVERT: Q 174 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7260 (ttp80) REVERT: Q 265 ILE cc_start: 0.8257 (mt) cc_final: 0.8032 (mt) REVERT: Q 287 ASP cc_start: 0.6773 (t0) cc_final: 0.6346 (t0) REVERT: Q 314 TYR cc_start: 0.8363 (m-10) cc_final: 0.7835 (m-10) REVERT: Q 328 GLU cc_start: 0.7297 (tp30) cc_final: 0.6971 (tp30) REVERT: Q 339 GLU cc_start: 0.7290 (tp30) cc_final: 0.7013 (tp30) REVERT: Q 347 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6435 (mt-10) REVERT: Q 349 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7410 (tptm) REVERT: Q 366 ASN cc_start: 0.8334 (p0) cc_final: 0.8041 (p0) REVERT: Q 398 LYS cc_start: 0.7841 (mttp) cc_final: 0.7615 (mttp) REVERT: Q 449 LEU cc_start: 0.7607 (mt) cc_final: 0.7385 (mp) REVERT: Q 454 GLU cc_start: 0.7076 (pp20) cc_final: 0.6833 (pp20) REVERT: Q 455 VAL cc_start: 0.6297 (OUTLIER) cc_final: 0.5922 (p) REVERT: Q 491 ARG cc_start: 0.6950 (ttp-170) cc_final: 0.6115 (ttp-110) outliers start: 60 outliers final: 30 residues processed: 253 average time/residue: 0.2490 time to fit residues: 81.9224 Evaluate side-chains 251 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 277 PHE 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 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 661 LEU 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 137 ARG Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 340 GLU 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 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 455 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 34 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 103 optimal weight: 0.0770 chunk 85 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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** Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 443 GLN Q 460 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8503 Z= 0.184 Angle : 0.661 8.606 11531 Z= 0.334 Chirality : 0.047 0.307 1276 Planarity : 0.005 0.044 1523 Dihedral : 6.895 59.166 1328 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 6.25 % Allowed : 27.34 % Favored : 66.41 % 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: -1.46 (0.25), residues: 1074 helix: -0.91 (0.47), residues: 115 sheet: -0.84 (0.28), residues: 318 loop : -1.01 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 267 HIS 0.004 0.001 HIS Q 500 PHE 0.020 0.002 PHE Q 232 TYR 0.009 0.001 TYR Q 141 ARG 0.005 0.000 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 279 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7491 (mtt90) REVERT: P 218 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7409 (mp10) REVERT: P 308 GLN cc_start: 0.7022 (pp30) cc_final: 0.6705 (pp30) REVERT: P 331 SER cc_start: 0.7746 (m) cc_final: 0.7451 (t) REVERT: P 367 SER cc_start: 0.6951 (t) cc_final: 0.6448 (m) REVERT: P 411 VAL cc_start: 0.7450 (OUTLIER) cc_final: 0.7221 (m) REVERT: P 437 GLU cc_start: 0.7026 (tp30) cc_final: 0.6652 (tp30) REVERT: P 445 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8033 (tp) REVERT: P 534 LEU cc_start: 0.8238 (mp) cc_final: 0.7961 (mt) REVERT: P 583 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7080 (ptmm) REVERT: Q 71 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7329 (tptt) REVERT: Q 84 ARG cc_start: 0.6777 (mmm160) cc_final: 0.6338 (mmm-85) REVERT: Q 102 MET cc_start: 0.0014 (ttp) cc_final: -0.0264 (ttp) REVERT: Q 143 ILE cc_start: 0.8137 (pt) cc_final: 0.7912 (mt) REVERT: Q 146 TYR cc_start: 0.8088 (t80) cc_final: 0.7820 (t80) REVERT: Q 155 MET cc_start: 0.7327 (mmt) cc_final: 0.6435 (mmp) REVERT: Q 170 MET cc_start: 0.7482 (tpp) cc_final: 0.7114 (tpp) REVERT: Q 174 ARG cc_start: 0.7361 (ttp80) cc_final: 0.7120 (ttp80) REVERT: Q 287 ASP cc_start: 0.6742 (t0) cc_final: 0.6345 (t0) REVERT: Q 314 TYR cc_start: 0.8315 (m-10) cc_final: 0.7871 (m-10) REVERT: Q 328 GLU cc_start: 0.7272 (tp30) cc_final: 0.6946 (tp30) REVERT: Q 339 GLU cc_start: 0.7260 (tp30) cc_final: 0.6973 (tp30) REVERT: Q 347 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6415 (mt-10) REVERT: Q 349 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7339 (tptm) REVERT: Q 366 ASN cc_start: 0.8379 (p0) cc_final: 0.8082 (p0) REVERT: Q 443 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6982 (mm-40) REVERT: Q 449 LEU cc_start: 0.7571 (mt) cc_final: 0.7126 (mp) REVERT: Q 491 ARG cc_start: 0.6844 (ttp-170) cc_final: 0.6051 (ttp-110) outliers start: 56 outliers final: 31 residues processed: 249 average time/residue: 0.2372 time to fit residues: 78.1094 Evaluate side-chains 270 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 224 THR Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE 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 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 P residue 661 LEU 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 119 LEU Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 443 GLN Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 453 GLU Chi-restraints excluded: chain Q residue 455 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 75 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN Q 257 GLN Q 350 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8503 Z= 0.234 Angle : 0.680 11.780 11531 Z= 0.342 Chirality : 0.048 0.320 1276 Planarity : 0.005 0.042 1523 Dihedral : 6.720 56.171 1328 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.92 % Allowed : 27.79 % Favored : 66.29 % 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: -1.40 (0.25), residues: 1074 helix: -0.87 (0.48), residues: 115 sheet: -0.79 (0.28), residues: 315 loop : -0.98 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 47 HIS 0.004 0.001 HIS Q 321 PHE 0.017 0.002 PHE Q 232 TYR 0.016 0.001 TYR P 276 ARG 0.005 0.000 ARG P 537 *********************** 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 275 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8489 (mp10) cc_final: 0.8201 (mp10) REVERT: P 196 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7486 (mtt90) REVERT: P 218 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: P 308 GLN cc_start: 0.7124 (pp30) cc_final: 0.6783 (pp30) REVERT: P 331 SER cc_start: 0.7752 (m) cc_final: 0.7477 (t) REVERT: P 367 SER cc_start: 0.7040 (t) cc_final: 0.6614 (m) REVERT: P 411 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7278 (m) REVERT: P 437 GLU cc_start: 0.7024 (tp30) cc_final: 0.6667 (tp30) REVERT: P 445 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8062 (tp) REVERT: P 534 LEU cc_start: 0.8270 (mp) cc_final: 0.8011 (mt) REVERT: P 583 LYS cc_start: 0.7355 (ptmm) cc_final: 0.7089 (ptmm) REVERT: Q 35 CYS cc_start: 0.4546 (OUTLIER) cc_final: 0.3245 (t) REVERT: Q 71 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7341 (tptt) REVERT: Q 102 MET cc_start: 0.0017 (ttp) cc_final: -0.0273 (ttp) REVERT: Q 134 LYS cc_start: 0.8449 (ptmm) cc_final: 0.8108 (ptmm) REVERT: Q 143 ILE cc_start: 0.8160 (pt) cc_final: 0.7927 (mt) REVERT: Q 155 MET cc_start: 0.7370 (mmt) cc_final: 0.6481 (mmp) REVERT: Q 163 LYS cc_start: 0.8519 (pptt) cc_final: 0.8046 (pttt) REVERT: Q 170 MET cc_start: 0.7466 (tpp) cc_final: 0.7055 (tpp) REVERT: Q 174 ARG cc_start: 0.7362 (ttp80) cc_final: 0.7129 (ttp80) REVERT: Q 268 ARG cc_start: 0.7290 (ttp-170) cc_final: 0.6989 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6864 (t0) cc_final: 0.6396 (t0) REVERT: Q 314 TYR cc_start: 0.8345 (m-10) cc_final: 0.7989 (m-10) REVERT: Q 325 LYS cc_start: 0.8221 (tppt) cc_final: 0.8009 (mmtp) REVERT: Q 328 GLU cc_start: 0.7246 (tp30) cc_final: 0.6939 (tp30) REVERT: Q 339 GLU cc_start: 0.7278 (tp30) cc_final: 0.7006 (tp30) REVERT: Q 347 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6483 (mt-10) REVERT: Q 349 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7323 (tptm) REVERT: Q 366 ASN cc_start: 0.8401 (p0) cc_final: 0.8081 (p0) REVERT: Q 491 ARG cc_start: 0.6895 (ttp-170) cc_final: 0.6079 (ttp-110) outliers start: 53 outliers final: 34 residues processed: 246 average time/residue: 0.2643 time to fit residues: 85.2663 Evaluate side-chains 255 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 194 THR 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 277 PHE 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 503 ASP 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 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 80 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 144 ASP 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 271 THR Chi-restraints excluded: chain Q residue 289 LYS Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 340 GLU 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 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.0980 chunk 31 optimal weight: 0.0060 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.0010 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.1980 overall best weight: 0.0680 ------------------------------------------------------------------------------- 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 ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8503 Z= 0.175 Angle : 0.685 13.429 11531 Z= 0.341 Chirality : 0.048 0.426 1276 Planarity : 0.004 0.041 1523 Dihedral : 6.382 52.373 1328 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.02 % Allowed : 29.02 % Favored : 65.96 % 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: -1.35 (0.25), residues: 1074 helix: -0.81 (0.48), residues: 116 sheet: -0.72 (0.28), residues: 327 loop : -0.97 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 496 HIS 0.004 0.001 HIS Q 321 PHE 0.016 0.002 PHE Q 232 TYR 0.015 0.001 TYR Q 308 ARG 0.005 0.000 ARG Q 499 *********************** 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 262 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8446 (mp10) cc_final: 0.8239 (mp10) REVERT: P 218 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: P 236 LEU cc_start: 0.7969 (mt) cc_final: 0.7588 (mm) REVERT: P 308 GLN cc_start: 0.7077 (pp30) cc_final: 0.6734 (pp30) REVERT: P 331 SER cc_start: 0.7709 (m) cc_final: 0.7442 (t) REVERT: P 411 VAL cc_start: 0.7385 (OUTLIER) cc_final: 0.7157 (m) REVERT: P 437 GLU cc_start: 0.6986 (tp30) cc_final: 0.6617 (tp30) REVERT: P 531 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6339 (m-30) REVERT: P 534 LEU cc_start: 0.8236 (mp) cc_final: 0.7985 (mt) REVERT: P 583 LYS cc_start: 0.7309 (ptmm) cc_final: 0.7047 (ptmm) REVERT: Q 71 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7259 (tptp) REVERT: Q 93 LYS cc_start: 0.7620 (tptp) cc_final: 0.7284 (tptp) REVERT: Q 102 MET cc_start: 0.0015 (ttp) cc_final: -0.0261 (ttp) REVERT: Q 143 ILE cc_start: 0.8118 (pt) cc_final: 0.7885 (mt) REVERT: Q 155 MET cc_start: 0.7313 (mmt) cc_final: 0.6431 (mmp) REVERT: Q 163 LYS cc_start: 0.8532 (pptt) cc_final: 0.8033 (pttt) REVERT: Q 170 MET cc_start: 0.7443 (tpp) cc_final: 0.7052 (tpp) REVERT: Q 174 ARG cc_start: 0.7214 (ttp80) cc_final: 0.7006 (ttp80) REVERT: Q 268 ARG cc_start: 0.7220 (ttp-170) cc_final: 0.6933 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6791 (t0) cc_final: 0.6333 (t0) REVERT: Q 314 TYR cc_start: 0.8311 (m-10) cc_final: 0.7907 (m-10) REVERT: Q 339 GLU cc_start: 0.7232 (tp30) cc_final: 0.6938 (tp30) REVERT: Q 347 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6407 (mt-10) REVERT: Q 349 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7333 (tptm) REVERT: Q 366 ASN cc_start: 0.8401 (p0) cc_final: 0.8104 (p0) REVERT: Q 398 LYS cc_start: 0.7848 (mttp) cc_final: 0.7608 (mttp) REVERT: Q 443 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7124 (mm-40) REVERT: Q 449 LEU cc_start: 0.7240 (mp) cc_final: 0.6744 (mp) REVERT: Q 491 ARG cc_start: 0.6887 (ttp-170) cc_final: 0.6077 (ttp-110) outliers start: 45 outliers final: 31 residues processed: 240 average time/residue: 0.2422 time to fit residues: 76.0804 Evaluate side-chains 252 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain P residue 194 THR 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 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 509 LEU Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET 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 124 ARG Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 144 ASP 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 271 THR Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 455 VAL 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 90 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 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 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 GLN P 490 GLN ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5373 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= 0.250 Angle : 0.705 13.251 11531 Z= 0.353 Chirality : 0.049 0.342 1276 Planarity : 0.005 0.042 1523 Dihedral : 6.367 49.081 1328 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.02 % Allowed : 29.58 % Favored : 65.40 % 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: -1.33 (0.25), residues: 1074 helix: -0.83 (0.48), residues: 115 sheet: -0.74 (0.28), residues: 314 loop : -0.93 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 496 HIS 0.003 0.001 HIS Q 470 PHE 0.021 0.002 PHE Q 232 TYR 0.019 0.001 TYR Q 308 ARG 0.006 0.000 ARG P 196 *********************** 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 269 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8530 (mp10) cc_final: 0.8264 (mp10) REVERT: P 218 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: P 308 GLN cc_start: 0.7129 (pp30) cc_final: 0.6803 (pp30) REVERT: P 331 SER cc_start: 0.7749 (m) cc_final: 0.7516 (t) REVERT: P 411 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.7188 (m) REVERT: P 437 GLU cc_start: 0.7001 (tp30) cc_final: 0.6649 (tp30) REVERT: P 534 LEU cc_start: 0.8316 (mp) cc_final: 0.8056 (mt) REVERT: P 583 LYS cc_start: 0.7339 (ptmm) cc_final: 0.7031 (ptmm) REVERT: Q 71 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7557 (tptt) REVERT: Q 93 LYS cc_start: 0.7513 (tptp) cc_final: 0.7228 (tptp) REVERT: Q 102 MET cc_start: 0.0015 (ttp) cc_final: -0.0265 (ttp) REVERT: Q 134 LYS cc_start: 0.8520 (ptmm) cc_final: 0.8056 (ptmm) REVERT: Q 143 ILE cc_start: 0.8173 (pt) cc_final: 0.7933 (mt) REVERT: Q 155 MET cc_start: 0.7378 (mmt) cc_final: 0.6526 (mmp) REVERT: Q 163 LYS cc_start: 0.8565 (pptt) cc_final: 0.8059 (pttt) REVERT: Q 170 MET cc_start: 0.7442 (tpp) cc_final: 0.7052 (tpp) REVERT: Q 174 ARG cc_start: 0.7276 (ttp80) cc_final: 0.7056 (ttp80) REVERT: Q 268 ARG cc_start: 0.7347 (ttp-170) cc_final: 0.7031 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6861 (t0) cc_final: 0.6379 (t0) REVERT: Q 314 TYR cc_start: 0.8406 (m-10) cc_final: 0.8060 (m-10) REVERT: Q 339 GLU cc_start: 0.7241 (tp30) cc_final: 0.6983 (tp30) REVERT: Q 347 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6506 (mt-10) REVERT: Q 349 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7384 (tptm) REVERT: Q 366 ASN cc_start: 0.8419 (p0) cc_final: 0.8145 (p0) REVERT: Q 398 LYS cc_start: 0.7856 (mttp) cc_final: 0.7628 (mttp) REVERT: Q 449 LEU cc_start: 0.7280 (mp) cc_final: 0.6842 (mp) REVERT: Q 491 ARG cc_start: 0.6884 (ttp-170) cc_final: 0.6092 (ttp-110) outliers start: 45 outliers final: 31 residues processed: 247 average time/residue: 0.2409 time to fit residues: 78.1131 Evaluate side-chains 252 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 126 VAL Chi-restraints excluded: chain P residue 194 THR 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 277 PHE Chi-restraints excluded: chain P residue 306 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 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 589 ILE 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 144 ASP 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 271 THR Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 455 VAL 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 62 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 287 GLN P 306 GLN P 409 GLN ** P 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN Q 332 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8503 Z= 0.317 Angle : 0.762 14.620 11531 Z= 0.379 Chirality : 0.050 0.311 1276 Planarity : 0.005 0.045 1523 Dihedral : 6.496 48.708 1328 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.69 % Allowed : 29.24 % 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: -1.47 (0.25), residues: 1074 helix: -0.86 (0.49), residues: 114 sheet: -0.84 (0.28), residues: 315 loop : -1.03 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 599 HIS 0.006 0.001 HIS P 584 PHE 0.022 0.002 PHE Q 426 TYR 0.030 0.002 TYR P 209 ARG 0.007 0.001 ARG P 196 ********************** 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 261 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 218 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: P 287 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6866 (mt0) REVERT: P 331 SER cc_start: 0.7800 (m) cc_final: 0.7570 (t) REVERT: P 367 SER cc_start: 0.7191 (t) cc_final: 0.6829 (m) REVERT: P 411 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7268 (m) REVERT: P 583 LYS cc_start: 0.7186 (ptmm) cc_final: 0.6908 (ptmm) REVERT: Q 102 MET cc_start: 0.0012 (ttp) cc_final: -0.0274 (ttp) REVERT: Q 134 LYS cc_start: 0.8487 (ptmm) cc_final: 0.8003 (ptmm) REVERT: Q 143 ILE cc_start: 0.8219 (pt) cc_final: 0.8003 (mt) REVERT: Q 155 MET cc_start: 0.7393 (mmt) cc_final: 0.6486 (mmp) REVERT: Q 163 LYS cc_start: 0.8564 (pptt) cc_final: 0.8037 (pttt) REVERT: Q 170 MET cc_start: 0.7407 (tpp) cc_final: 0.6996 (tpp) REVERT: Q 268 ARG cc_start: 0.7313 (ttp-170) cc_final: 0.7006 (ttp-110) REVERT: Q 279 ASP cc_start: 0.7542 (m-30) cc_final: 0.7274 (m-30) REVERT: Q 287 ASP cc_start: 0.6887 (t0) cc_final: 0.6377 (t0) REVERT: Q 314 TYR cc_start: 0.8419 (m-10) cc_final: 0.8047 (m-10) REVERT: Q 339 GLU cc_start: 0.7294 (tp30) cc_final: 0.7081 (tp30) REVERT: Q 347 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6588 (mt-10) REVERT: Q 349 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7405 (tptm) REVERT: Q 366 ASN cc_start: 0.8472 (p0) cc_final: 0.8193 (p0) REVERT: Q 398 LYS cc_start: 0.7829 (mttp) cc_final: 0.7585 (mttp) REVERT: Q 454 GLU cc_start: 0.6930 (pp20) cc_final: 0.6674 (pp20) REVERT: Q 491 ARG cc_start: 0.6924 (ttp-170) cc_final: 0.6139 (ttp-110) outliers start: 42 outliers final: 32 residues processed: 238 average time/residue: 0.2321 time to fit residues: 73.3021 Evaluate side-chains 248 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 194 THR 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 277 PHE Chi-restraints excluded: chain P residue 287 GLN Chi-restraints excluded: chain P residue 306 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 371 MET 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 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 589 ILE 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 144 ASP 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 271 THR Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 340 GLU 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 452 THR Chi-restraints excluded: chain Q residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 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 Q 350 ASN Q 369 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.154004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129206 restraints weight = 13652.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133210 restraints weight = 7216.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135869 restraints weight = 4575.363| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5783 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= 0.307 Angle : 0.772 14.108 11531 Z= 0.388 Chirality : 0.050 0.285 1276 Planarity : 0.005 0.044 1523 Dihedral : 6.475 48.773 1328 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.46 % Allowed : 29.91 % 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: -1.54 (0.25), residues: 1074 helix: -0.96 (0.48), residues: 113 sheet: -0.85 (0.28), residues: 318 loop : -1.09 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 496 HIS 0.005 0.001 HIS P 584 PHE 0.022 0.002 PHE Q 426 TYR 0.025 0.002 TYR P 209 ARG 0.012 0.001 ARG Q 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2475.82 seconds wall clock time: 45 minutes 34.29 seconds (2734.29 seconds total)