Starting phenix.real_space_refine on Tue Apr 29 04:54:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxz_17269/04_2025/8oxz_17269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxz_17269/04_2025/8oxz_17269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oxz_17269/04_2025/8oxz_17269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxz_17269/04_2025/8oxz_17269.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxz_17269/04_2025/8oxz_17269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxz_17269/04_2025/8oxz_17269.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 5218 2.51 5 N 1417 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.42, per 1000 atoms: 0.65 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: 2.03 Conformation dependent library (CDL) restraints added in 935.0 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: 1.08 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: 2.34 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2735 1.34 - 1.46: 1816 1.46 - 1.58: 3891 1.58 - 1.70: 0 1.70 - 1.83: 61 Bond restraints: 8503 Sorted by residual: bond pdb=" C1 NAG P1105 " pdb=" O5 NAG P1105 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" CB ASN Q 305 " pdb=" CG ASN Q 305 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.46e+00 bond pdb=" CB ASN P 346 " pdb=" CG ASN P 346 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 bond pdb=" C1 NAG P1104 " pdb=" C2 NAG P1104 " ideal model delta sigma weight residual 1.532 1.560 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" N SER P 489 " pdb=" CA SER P 489 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.79e+00 ... (remaining 8498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 11332 2.62 - 5.24: 185 5.24 - 7.87: 10 7.87 - 10.49: 2 10.49 - 13.11: 2 Bond angle restraints: 11531 Sorted by residual: angle pdb=" CB MET Q 170 " pdb=" CG MET Q 170 " pdb=" SD MET Q 170 " ideal model delta sigma weight residual 112.70 124.48 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA LEU P 347 " pdb=" CB LEU P 347 " pdb=" CG LEU P 347 " ideal model delta sigma weight residual 116.30 129.41 -13.11 3.50e+00 8.16e-02 1.40e+01 angle pdb=" C ASN P 365 " pdb=" CA ASN P 365 " pdb=" CB ASN P 365 " ideal model delta sigma weight residual 110.42 117.61 -7.19 1.99e+00 2.53e-01 1.30e+01 angle pdb=" CA ASN Q 305 " pdb=" CB ASN Q 305 " pdb=" CG ASN Q 305 " ideal model delta sigma weight residual 112.60 115.68 -3.08 1.00e+00 1.00e+00 9.48e+00 angle pdb=" CA ILE Q 320 " pdb=" CB ILE Q 320 " pdb=" CG1 ILE Q 320 " ideal model delta sigma weight residual 110.40 105.23 5.17 1.70e+00 3.46e-01 9.24e+00 ... (remaining 11526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.61: 4627 21.61 - 43.22: 477 43.22 - 64.83: 93 64.83 - 86.44: 19 86.44 - 108.05: 14 Dihedral angle restraints: 5230 sinusoidal: 2173 harmonic: 3057 Sorted by residual: dihedral pdb=" CB CYS Q 261 " pdb=" SG CYS Q 261 " pdb=" SG CYS Q 301 " pdb=" CB CYS Q 301 " ideal model delta sinusoidal sigma weight residual 93.00 25.72 67.28 1 1.00e+01 1.00e-02 5.89e+01 dihedral pdb=" CB CYS Q 48 " pdb=" SG CYS Q 48 " pdb=" SG CYS Q 75 " pdb=" CB CYS Q 75 " ideal model delta sinusoidal sigma weight residual -86.00 -146.14 60.14 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" CB CYS P 151 " pdb=" SG CYS P 151 " pdb=" SG CYS P 160 " pdb=" CB CYS P 160 " ideal model delta sinusoidal sigma weight residual 93.00 35.79 57.21 1 1.00e+01 1.00e-02 4.40e+01 ... (remaining 5227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1132 0.078 - 0.156: 135 0.156 - 0.235: 6 0.235 - 0.313: 1 0.313 - 0.391: 2 Chirality restraints: 1276 Sorted by residual: chirality pdb=" C1 NAG P1105 " pdb=" ND2 ASN P 365 " pdb=" C2 NAG P1105 " pdb=" O5 NAG P1105 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C1 NAG P1102 " pdb=" ND2 ASN P 231 " pdb=" C2 NAG P1102 " pdb=" O5 NAG P1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE Q 182 " pdb=" CA ILE Q 182 " pdb=" CG1 ILE Q 182 " pdb=" CG2 ILE Q 182 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1273 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN P 365 " -0.051 2.00e-02 2.50e+03 4.69e-02 2.74e+01 pdb=" CG ASN P 365 " 0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN P 365 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN P 365 " 0.046 2.00e-02 2.50e+03 pdb=" C1 NAG P1105 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 305 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C ASN Q 305 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN Q 305 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN Q 306 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN P 365 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" CG ASN P 365 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN P 365 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN P 365 " -0.016 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 429 2.71 - 3.26: 8464 3.26 - 3.81: 13089 3.81 - 4.35: 15884 4.35 - 4.90: 26714 Nonbonded interactions: 64580 Sorted by model distance: nonbonded pdb=" NZ LYS Q 130 " pdb=" OE2 GLU Q 427 " model vdw 2.167 3.120 nonbonded pdb=" OG1 THR P 194 " pdb=" O GLY P 257 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASN Q 50 " pdb=" OG1 THR Q 52 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP P 333 " pdb=" N ASP P 334 " model vdw 2.207 3.120 nonbonded pdb=" O ASP P 383 " pdb=" ND2 ASN P 457 " model vdw 2.220 3.120 ... (remaining 64575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.180 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- 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 8525 Z= 0.220 Angle : 0.840 16.253 11582 Z= 0.436 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00927 ( 7) link_NAG-ASN : angle 4.83234 ( 21) hydrogen bonds : bond 0.25492 ( 213) hydrogen bonds : angle 9.62240 ( 546) SS BOND : bond 0.00359 ( 15) SS BOND : angle 0.94077 ( 30) covalent geometry : bond 0.00468 ( 8503) covalent geometry : angle 0.81505 (11531) *********************** 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 : 0.810 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: 0.2146 time to fit residues: 67.2650 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 : 0.809 ------------------------------------------------------------------------------- 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: 0.8980 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.0010 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 255 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 161 ASN Q 171 ASN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 376 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.156493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131879 restraints weight = 13698.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135941 restraints weight = 7243.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138594 restraints weight = 4534.124| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8525 Z= 0.182 Angle : 0.770 7.906 11582 Z= 0.388 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00813 ( 7) link_NAG-ASN : angle 3.37588 ( 21) hydrogen bonds : bond 0.04418 ( 213) hydrogen bonds : angle 7.00515 ( 546) SS BOND : bond 0.00344 ( 15) SS BOND : angle 1.02943 ( 30) covalent geometry : bond 0.00409 ( 8503) covalent geometry : angle 0.75617 (11531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 134 LYS cc_start: 0.8258 (tttm) cc_final: 0.7873 (tptm) REVERT: P 166 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.6847 (t70) REVERT: P 196 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7435 (mmt-90) REVERT: P 276 TYR cc_start: 0.7050 (m-80) cc_final: 0.6511 (m-80) REVERT: P 399 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7328 (tp) REVERT: P 407 ARG cc_start: 0.7004 (mtm180) cc_final: 0.6770 (ptp-110) REVERT: P 594 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: P 635 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6592 (mt-10) REVERT: P 662 ASP cc_start: 0.7873 (t0) cc_final: 0.7546 (t0) REVERT: Q 84 ARG cc_start: 0.5732 (mmm160) cc_final: 0.5396 (mmm160) REVERT: Q 102 MET cc_start: 0.0080 (ttp) cc_final: -0.0225 (ttp) REVERT: Q 149 MET cc_start: 0.6541 (ppp) cc_final: 0.6181 (ppp) REVERT: Q 155 MET cc_start: 0.7315 (mmt) cc_final: 0.6339 (mmp) REVERT: Q 163 LYS cc_start: 0.8378 (pptt) cc_final: 0.7917 (ptpp) REVERT: Q 174 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7212 (ttp80) REVERT: Q 289 LYS cc_start: 0.8423 (tttt) cc_final: 0.8123 (tttm) REVERT: Q 307 VAL cc_start: 0.8324 (t) cc_final: 0.7977 (m) REVERT: Q 322 LEU cc_start: 0.7966 (tp) cc_final: 0.7292 (tp) REVERT: Q 398 LYS cc_start: 0.7498 (mttp) cc_final: 0.7173 (mttp) REVERT: Q 486 GLU cc_start: 0.6155 (pt0) cc_final: 0.4441 (pt0) REVERT: Q 491 ARG cc_start: 0.6933 (ttp-170) cc_final: 0.6085 (ttp-110) outliers start: 55 outliers final: 28 residues processed: 237 average time/residue: 0.2758 time to fit residues: 88.9896 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 : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 166 ASP Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 196 ARG Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 535 VAL Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 594 GLU Chi-restraints excluded: chain P residue 654 HIS Chi-restraints excluded: chain P residue 661 LEU Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 290 LEU Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.156620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131529 restraints weight = 13800.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135808 restraints weight = 7220.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.138406 restraints weight = 4511.457| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8525 Z= 0.178 Angle : 0.716 11.326 11582 Z= 0.359 Chirality : 0.050 0.282 1276 Planarity : 0.005 0.046 1523 Dihedral : 7.848 70.203 1329 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 7.25 % Allowed : 24.22 % Favored : 68.53 % 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: -1.42 (0.25), residues: 1074 helix: -0.92 (0.49), residues: 103 sheet: -0.68 (0.28), residues: 318 loop : -1.06 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 211 HIS 0.008 0.002 HIS P 584 PHE 0.019 0.002 PHE Q 232 TYR 0.015 0.002 TYR P 349 ARG 0.005 0.001 ARG Q 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 7) link_NAG-ASN : angle 2.96513 ( 21) hydrogen bonds : bond 0.04314 ( 213) hydrogen bonds : angle 6.46224 ( 546) SS BOND : bond 0.00429 ( 15) SS BOND : angle 1.02955 ( 30) covalent geometry : bond 0.00384 ( 8503) covalent geometry : angle 0.70454 (11531) *********************** 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 280 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7294 (mmt-90) REVERT: P 331 SER cc_start: 0.7575 (m) cc_final: 0.7211 (t) REVERT: P 393 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7549 (mp) REVERT: P 411 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7372 (m) REVERT: P 437 GLU cc_start: 0.7118 (tp30) cc_final: 0.6889 (tp30) REVERT: P 583 LYS cc_start: 0.7350 (ptmm) cc_final: 0.6989 (ptmm) REVERT: P 662 ASP cc_start: 0.8224 (t0) cc_final: 0.6449 (m-30) REVERT: Q 84 ARG cc_start: 0.6171 (mmm160) cc_final: 0.5875 (mmm160) REVERT: Q 102 MET cc_start: 0.0027 (ttp) cc_final: -0.0255 (ttp) REVERT: Q 134 LYS cc_start: 0.8127 (ptmm) cc_final: 0.7452 (ptmm) REVERT: Q 155 MET cc_start: 0.7424 (mmt) cc_final: 0.6447 (mmp) REVERT: Q 163 LYS cc_start: 0.8432 (pptt) cc_final: 0.8097 (ptpp) REVERT: Q 170 MET cc_start: 0.7334 (tpp) cc_final: 0.7078 (tpp) REVERT: Q 174 ARG cc_start: 0.7466 (ttp80) cc_final: 0.7228 (ttp80) REVERT: Q 287 ASP cc_start: 0.6442 (t0) cc_final: 0.6048 (t0) REVERT: Q 305 ASN cc_start: 0.6784 (t0) cc_final: 0.6569 (t0) REVERT: Q 307 VAL cc_start: 0.8314 (t) cc_final: 0.7824 (m) REVERT: Q 328 GLU cc_start: 0.7389 (tp30) cc_final: 0.7157 (tp30) REVERT: Q 347 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6403 (mt-10) REVERT: Q 398 LYS cc_start: 0.7738 (mttp) cc_final: 0.7302 (mttp) REVERT: Q 454 GLU cc_start: 0.7250 (pm20) cc_final: 0.6969 (pm20) REVERT: Q 486 GLU cc_start: 0.6376 (pt0) cc_final: 0.4799 (pt0) REVERT: Q 491 ARG cc_start: 0.6992 (ttp-170) cc_final: 0.6163 (ttp-110) outliers start: 65 outliers final: 34 residues processed: 245 average time/residue: 0.2919 time to fit residues: 94.5371 Evaluate side-chains 244 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 403 THR Chi-restraints excluded: chain P residue 411 VAL 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 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 535 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 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 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 234 GLU 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 327 SER 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 85 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 0.0020 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.154665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129278 restraints weight = 13853.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133452 restraints weight = 7361.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136247 restraints weight = 4654.082| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8525 Z= 0.174 Angle : 0.706 8.872 11582 Z= 0.356 Chirality : 0.049 0.241 1276 Planarity : 0.005 0.046 1523 Dihedral : 7.384 67.180 1328 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.14 % Allowed : 25.78 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.24), residues: 1074 helix: -1.03 (0.47), residues: 114 sheet: -0.75 (0.28), residues: 318 loop : -1.10 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 599 HIS 0.007 0.001 HIS P 584 PHE 0.018 0.002 PHE Q 426 TYR 0.020 0.002 TYR P 323 ARG 0.008 0.001 ARG Q 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00579 ( 7) link_NAG-ASN : angle 2.78868 ( 21) hydrogen bonds : bond 0.03910 ( 213) hydrogen bonds : angle 6.24254 ( 546) SS BOND : bond 0.00385 ( 15) SS BOND : angle 1.06093 ( 30) covalent geometry : bond 0.00397 ( 8503) covalent geometry : angle 0.69559 (11531) *********************** 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 266 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7262 (mmt-90) REVERT: P 231 ASN cc_start: 0.6051 (OUTLIER) cc_final: 0.5811 (t0) REVERT: P 331 SER cc_start: 0.7745 (m) cc_final: 0.7365 (t) REVERT: P 411 VAL cc_start: 0.7557 (OUTLIER) cc_final: 0.7334 (m) REVERT: P 437 GLU cc_start: 0.7126 (tp30) cc_final: 0.6764 (tp30) REVERT: P 528 PHE cc_start: 0.8416 (p90) cc_final: 0.8180 (p90) REVERT: P 583 LYS cc_start: 0.7451 (ptmm) cc_final: 0.7066 (ptmm) REVERT: Q 102 MET cc_start: 0.0058 (ttp) cc_final: -0.0234 (ttp) REVERT: Q 134 LYS cc_start: 0.8236 (ptmm) cc_final: 0.7423 (ptmm) REVERT: Q 155 MET cc_start: 0.7450 (mmt) cc_final: 0.6451 (mmp) REVERT: Q 163 LYS cc_start: 0.8514 (pptt) cc_final: 0.8072 (ptpp) REVERT: Q 170 MET cc_start: 0.7401 (tpp) cc_final: 0.7038 (tpp) REVERT: Q 174 ARG cc_start: 0.7495 (ttp80) cc_final: 0.7243 (ttp80) REVERT: Q 232 PHE cc_start: 0.7841 (t80) cc_final: 0.7640 (t80) REVERT: Q 287 ASP cc_start: 0.6679 (t0) cc_final: 0.6211 (t0) REVERT: Q 314 TYR cc_start: 0.8399 (m-10) cc_final: 0.7997 (m-10) REVERT: Q 347 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6333 (mt-10) REVERT: Q 398 LYS cc_start: 0.7849 (mttp) cc_final: 0.7340 (mttp) REVERT: Q 454 GLU cc_start: 0.7256 (pm20) cc_final: 0.6830 (pm20) REVERT: Q 486 GLU cc_start: 0.6461 (pt0) cc_final: 0.4970 (pt0) REVERT: Q 491 ARG cc_start: 0.6963 (ttp-170) cc_final: 0.6127 (ttp-110) outliers start: 55 outliers final: 35 residues processed: 237 average time/residue: 0.2878 time to fit residues: 92.6854 Evaluate side-chains 249 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 231 ASN Chi-restraints excluded: chain P residue 309 THR 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 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 444 SER 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 527 SER 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 667 MET Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 294 VAL 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 401 CYS Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.0010 chunk 8 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 311 GLN ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 239 GLN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 443 GLN Q 479 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131224 restraints weight = 13600.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135220 restraints weight = 7139.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137914 restraints weight = 4503.734| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8525 Z= 0.166 Angle : 0.686 8.649 11582 Z= 0.345 Chirality : 0.048 0.234 1276 Planarity : 0.005 0.043 1523 Dihedral : 7.072 63.520 1328 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 6.81 % Allowed : 26.12 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.25), residues: 1074 helix: -0.92 (0.48), residues: 113 sheet: -0.87 (0.27), residues: 323 loop : -0.97 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 267 HIS 0.005 0.001 HIS P 584 PHE 0.023 0.002 PHE Q 426 TYR 0.015 0.001 TYR P 349 ARG 0.004 0.000 ARG P 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 7) link_NAG-ASN : angle 2.69244 ( 21) hydrogen bonds : bond 0.03689 ( 213) hydrogen bonds : angle 6.14277 ( 546) SS BOND : bond 0.00407 ( 15) SS BOND : angle 0.98917 ( 30) covalent geometry : bond 0.00378 ( 8503) covalent geometry : angle 0.67615 (11531) *********************** 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 277 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7515 (mmt-90) REVERT: P 218 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: P 231 ASN cc_start: 0.5994 (OUTLIER) cc_final: 0.5753 (t0) REVERT: P 331 SER cc_start: 0.7770 (m) cc_final: 0.7467 (t) REVERT: P 347 LEU cc_start: 0.8136 (pp) cc_final: 0.7932 (pp) REVERT: P 437 GLU cc_start: 0.7088 (tp30) cc_final: 0.6777 (tp30) REVERT: P 528 PHE cc_start: 0.8427 (p90) cc_final: 0.8035 (p90) REVERT: P 583 LYS cc_start: 0.7417 (ptmm) cc_final: 0.7092 (ptmm) REVERT: Q 71 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7494 (tptt) REVERT: Q 102 MET cc_start: 0.0125 (ttp) cc_final: -0.0185 (ttp) REVERT: Q 134 LYS cc_start: 0.8289 (ptmm) cc_final: 0.7972 (ptmm) REVERT: Q 155 MET cc_start: 0.7351 (mmt) cc_final: 0.6419 (mmp) REVERT: Q 163 LYS cc_start: 0.8506 (pptt) cc_final: 0.8031 (ptpp) REVERT: Q 170 MET cc_start: 0.7283 (tpp) cc_final: 0.6892 (tpp) REVERT: Q 174 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7188 (ttp80) REVERT: Q 232 PHE cc_start: 0.7758 (t80) cc_final: 0.7479 (t80) REVERT: Q 287 ASP cc_start: 0.6596 (t0) cc_final: 0.6245 (t0) REVERT: Q 314 TYR cc_start: 0.8365 (m-10) cc_final: 0.7908 (m-10) REVERT: Q 328 GLU cc_start: 0.7219 (tp30) cc_final: 0.6859 (tp30) REVERT: Q 347 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6365 (mt-10) REVERT: Q 349 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7436 (tptm) REVERT: Q 398 LYS cc_start: 0.7822 (mttp) cc_final: 0.7373 (mttp) REVERT: Q 449 LEU cc_start: 0.7690 (mt) cc_final: 0.7194 (mp) REVERT: Q 454 GLU cc_start: 0.7280 (pm20) cc_final: 0.6834 (pm20) REVERT: Q 491 ARG cc_start: 0.6940 (ttp-170) cc_final: 0.6104 (ttp-110) outliers start: 61 outliers final: 39 residues processed: 245 average time/residue: 0.2520 time to fit residues: 82.7956 Evaluate side-chains 260 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 196 ARG Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 309 THR 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 403 THR Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 445 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 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 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 257 GLN Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 332 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130560 restraints weight = 13595.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134674 restraints weight = 7111.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137248 restraints weight = 4444.764| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8525 Z= 0.164 Angle : 0.692 8.706 11582 Z= 0.347 Chirality : 0.048 0.224 1276 Planarity : 0.005 0.053 1523 Dihedral : 6.876 59.782 1328 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 6.14 % Allowed : 27.01 % Favored : 66.85 % 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: -1.43 (0.25), residues: 1074 helix: -0.95 (0.48), residues: 113 sheet: -0.86 (0.28), residues: 322 loop : -0.96 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP P 278 HIS 0.004 0.001 HIS P 584 PHE 0.018 0.002 PHE Q 426 TYR 0.018 0.002 TYR Q 308 ARG 0.009 0.001 ARG Q 272 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 7) link_NAG-ASN : angle 2.73494 ( 21) hydrogen bonds : bond 0.03619 ( 213) hydrogen bonds : angle 6.07847 ( 546) SS BOND : bond 0.00310 ( 15) SS BOND : angle 1.04775 ( 30) covalent geometry : bond 0.00374 ( 8503) covalent geometry : angle 0.68192 (11531) *********************** 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 280 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 218 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: P 308 GLN cc_start: 0.7020 (pp30) cc_final: 0.6673 (pp30) REVERT: P 331 SER cc_start: 0.7785 (m) cc_final: 0.7492 (t) REVERT: P 430 LEU cc_start: 0.8353 (tt) cc_final: 0.8087 (tt) REVERT: P 437 GLU cc_start: 0.7108 (tp30) cc_final: 0.6691 (tp30) REVERT: P 528 PHE cc_start: 0.8431 (p90) cc_final: 0.8073 (p90) REVERT: P 583 LYS cc_start: 0.7420 (ptmm) cc_final: 0.7106 (ptmm) REVERT: Q 71 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7531 (tptt) REVERT: Q 102 MET cc_start: 0.0115 (ttp) cc_final: -0.0196 (ttp) REVERT: Q 134 LYS cc_start: 0.8364 (ptmm) cc_final: 0.8066 (ptmm) REVERT: Q 155 MET cc_start: 0.7382 (mmt) cc_final: 0.6489 (mmp) REVERT: Q 163 LYS cc_start: 0.8510 (pptt) cc_final: 0.7930 (ptpp) REVERT: Q 170 MET cc_start: 0.7259 (tpp) cc_final: 0.6858 (tpp) REVERT: Q 174 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7249 (ttp80) REVERT: Q 232 PHE cc_start: 0.7715 (t80) cc_final: 0.7496 (t80) REVERT: Q 268 ARG cc_start: 0.7100 (ttp-170) cc_final: 0.6789 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6681 (t0) cc_final: 0.6260 (t0) REVERT: Q 314 TYR cc_start: 0.8355 (m-10) cc_final: 0.7938 (m-10) REVERT: Q 328 GLU cc_start: 0.7231 (tp30) cc_final: 0.6883 (tp30) REVERT: Q 347 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6433 (mt-10) REVERT: Q 349 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7396 (tptm) REVERT: Q 398 LYS cc_start: 0.7824 (mttp) cc_final: 0.7617 (mttp) REVERT: Q 449 LEU cc_start: 0.7568 (mt) cc_final: 0.7222 (mp) REVERT: Q 454 GLU cc_start: 0.7291 (pm20) cc_final: 0.6804 (pm20) REVERT: Q 486 GLU cc_start: 0.6433 (pt0) cc_final: 0.4959 (pt0) REVERT: Q 491 ARG cc_start: 0.6964 (ttp-170) cc_final: 0.6144 (ttp-110) outliers start: 55 outliers final: 39 residues processed: 251 average time/residue: 0.2394 time to fit residues: 78.8957 Evaluate side-chains 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 277 PHE 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 403 THR Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 445 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 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 661 LEU Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 143 ILE 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 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 49 optimal weight: 0.0040 chunk 73 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 244 ASN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.155817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131336 restraints weight = 13818.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135388 restraints weight = 7250.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138054 restraints weight = 4554.414| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8525 Z= 0.145 Angle : 0.703 11.855 11582 Z= 0.347 Chirality : 0.048 0.353 1276 Planarity : 0.005 0.042 1523 Dihedral : 6.725 56.658 1328 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.69 % Allowed : 27.34 % Favored : 66.96 % 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: -1.39 (0.25), residues: 1074 helix: -1.02 (0.48), residues: 113 sheet: -0.79 (0.27), residues: 321 loop : -0.93 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 267 HIS 0.004 0.001 HIS Q 321 PHE 0.017 0.002 PHE Q 426 TYR 0.013 0.001 TYR Q 141 ARG 0.008 0.001 ARG P 537 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 7) link_NAG-ASN : angle 3.17427 ( 21) hydrogen bonds : bond 0.03555 ( 213) hydrogen bonds : angle 5.99303 ( 546) SS BOND : bond 0.00275 ( 15) SS BOND : angle 0.97803 ( 30) covalent geometry : bond 0.00335 ( 8503) covalent geometry : angle 0.68914 (11531) *********************** 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 270 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 218 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: P 331 SER cc_start: 0.7739 (m) cc_final: 0.7417 (t) REVERT: P 367 SER cc_start: 0.6977 (t) cc_final: 0.6551 (m) REVERT: P 583 LYS cc_start: 0.7408 (ptmm) cc_final: 0.7113 (ptmm) REVERT: Q 71 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.6855 (tptm) REVERT: Q 102 MET cc_start: 0.0088 (ttp) cc_final: -0.0214 (ttp) REVERT: Q 145 LEU cc_start: 0.8438 (tp) cc_final: 0.8164 (tt) REVERT: Q 146 TYR cc_start: 0.7960 (t80) cc_final: 0.7669 (t80) REVERT: Q 155 MET cc_start: 0.7348 (mmt) cc_final: 0.6400 (mmp) REVERT: Q 170 MET cc_start: 0.7247 (tpp) cc_final: 0.6818 (tpp) REVERT: Q 174 ARG cc_start: 0.7344 (ttp80) cc_final: 0.7136 (ttp80) REVERT: Q 232 PHE cc_start: 0.7695 (t80) cc_final: 0.7482 (t80) REVERT: Q 268 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6716 (ttp-110) REVERT: Q 279 ASP cc_start: 0.7609 (m-30) cc_final: 0.7144 (t0) REVERT: Q 287 ASP cc_start: 0.6699 (t0) cc_final: 0.6295 (t0) REVERT: Q 314 TYR cc_start: 0.8354 (m-10) cc_final: 0.7944 (m-10) REVERT: Q 328 GLU cc_start: 0.7210 (tp30) cc_final: 0.6864 (tp30) REVERT: Q 347 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6424 (mt-10) REVERT: Q 349 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7364 (tptm) REVERT: Q 398 LYS cc_start: 0.7802 (mttp) cc_final: 0.7600 (mttp) REVERT: Q 449 LEU cc_start: 0.7622 (mt) cc_final: 0.7163 (mp) REVERT: Q 454 GLU cc_start: 0.7380 (pm20) cc_final: 0.6936 (pm20) REVERT: Q 491 ARG cc_start: 0.6954 (ttp-170) cc_final: 0.6122 (ttp-110) outliers start: 51 outliers final: 39 residues processed: 241 average time/residue: 0.2383 time to fit residues: 75.3926 Evaluate side-chains 265 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 201 SER 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 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 403 THR Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 445 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 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 661 LEU Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 144 ASP 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 257 GLN Chi-restraints excluded: chain Q residue 268 ARG Chi-restraints excluded: chain Q residue 289 LYS Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 101 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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 257 GLN Q 350 ASN Q 406 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.153957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129321 restraints weight = 13841.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133411 restraints weight = 7259.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136080 restraints weight = 4568.744| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8525 Z= 0.191 Angle : 0.737 13.731 11582 Z= 0.364 Chirality : 0.050 0.424 1276 Planarity : 0.005 0.043 1523 Dihedral : 6.728 53.415 1328 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 6.14 % Allowed : 27.12 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1074 helix: -1.11 (0.47), residues: 113 sheet: -0.75 (0.28), residues: 311 loop : -0.92 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 599 HIS 0.004 0.001 HIS Q 470 PHE 0.024 0.002 PHE Q 426 TYR 0.017 0.002 TYR P 276 ARG 0.010 0.001 ARG P 537 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 7) link_NAG-ASN : angle 3.52026 ( 21) hydrogen bonds : bond 0.03728 ( 213) hydrogen bonds : angle 6.01717 ( 546) SS BOND : bond 0.00380 ( 15) SS BOND : angle 0.96120 ( 30) covalent geometry : bond 0.00435 ( 8503) covalent geometry : angle 0.72130 (11531) *********************** 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 284 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 218 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: P 331 SER cc_start: 0.7795 (m) cc_final: 0.7484 (t) REVERT: P 367 SER cc_start: 0.7057 (t) cc_final: 0.6646 (m) REVERT: P 437 GLU cc_start: 0.7005 (tp30) cc_final: 0.6597 (tp30) REVERT: P 583 LYS cc_start: 0.7425 (ptmm) cc_final: 0.7095 (ptmm) REVERT: Q 71 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7528 (tptt) REVERT: Q 84 ARG cc_start: 0.6962 (mmm-85) cc_final: 0.6727 (mmm-85) REVERT: Q 102 MET cc_start: 0.0095 (ttp) cc_final: -0.0207 (ttp) REVERT: Q 134 LYS cc_start: 0.8434 (ptmm) cc_final: 0.8113 (ptmm) REVERT: Q 155 MET cc_start: 0.7399 (mmt) cc_final: 0.6438 (mmp) REVERT: Q 163 LYS cc_start: 0.8522 (pptt) cc_final: 0.8039 (pttt) REVERT: Q 170 MET cc_start: 0.7258 (tpp) cc_final: 0.6843 (tpp) REVERT: Q 268 ARG cc_start: 0.7183 (ttp-170) cc_final: 0.6861 (ttp-110) REVERT: Q 279 ASP cc_start: 0.7755 (m-30) cc_final: 0.7306 (t0) REVERT: Q 287 ASP cc_start: 0.6819 (t0) cc_final: 0.6337 (t0) REVERT: Q 314 TYR cc_start: 0.8408 (m-10) cc_final: 0.8067 (m-10) REVERT: Q 328 GLU cc_start: 0.7217 (tp30) cc_final: 0.6899 (tp30) REVERT: Q 339 GLU cc_start: 0.7184 (tp30) cc_final: 0.6898 (tp30) REVERT: Q 347 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6511 (mt-10) REVERT: Q 349 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7332 (tptm) REVERT: Q 398 LYS cc_start: 0.7815 (mttp) cc_final: 0.7604 (mttp) REVERT: Q 422 ASP cc_start: 0.6274 (t0) cc_final: 0.5949 (m-30) REVERT: Q 491 ARG cc_start: 0.6853 (ttp-170) cc_final: 0.6096 (ttp-110) outliers start: 55 outliers final: 37 residues processed: 251 average time/residue: 0.2395 time to fit residues: 78.3485 Evaluate side-chains 263 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 277 PHE 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 445 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 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 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 144 ASP Chi-restraints excluded: chain Q residue 173 MET 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 289 LYS Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain Q residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 chunk 104 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130977 restraints weight = 13828.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135143 restraints weight = 7255.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137881 restraints weight = 4536.454| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8525 Z= 0.149 Angle : 0.735 13.327 11582 Z= 0.364 Chirality : 0.048 0.372 1276 Planarity : 0.005 0.042 1523 Dihedral : 6.486 49.968 1328 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.02 % Allowed : 28.24 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1074 helix: -1.10 (0.47), residues: 113 sheet: -0.70 (0.28), residues: 311 loop : -0.90 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 153 HIS 0.004 0.001 HIS Q 321 PHE 0.026 0.002 PHE Q 232 TYR 0.010 0.001 TYR P 415 ARG 0.012 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 7) link_NAG-ASN : angle 3.19350 ( 21) hydrogen bonds : bond 0.03465 ( 213) hydrogen bonds : angle 5.93631 ( 546) SS BOND : bond 0.00304 ( 15) SS BOND : angle 2.02492 ( 30) covalent geometry : bond 0.00340 ( 8503) covalent geometry : angle 0.71670 (11531) *********************** 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 271 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8502 (mp10) cc_final: 0.8222 (mp10) REVERT: P 196 ARG cc_start: 0.7780 (mmt-90) cc_final: 0.7560 (mmt-90) REVERT: P 218 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: P 331 SER cc_start: 0.7771 (m) cc_final: 0.7470 (t) REVERT: P 367 SER cc_start: 0.7132 (t) cc_final: 0.6671 (m) REVERT: P 437 GLU cc_start: 0.7012 (tp30) cc_final: 0.6605 (tp30) REVERT: P 583 LYS cc_start: 0.7428 (ptmm) cc_final: 0.7154 (ptmm) REVERT: Q 102 MET cc_start: 0.0076 (ttp) cc_final: -0.0232 (ttp) REVERT: Q 134 LYS cc_start: 0.8457 (ptmm) cc_final: 0.8109 (ptmm) REVERT: Q 146 TYR cc_start: 0.8023 (t80) cc_final: 0.7763 (t80) REVERT: Q 155 MET cc_start: 0.7363 (mmt) cc_final: 0.6455 (mmp) REVERT: Q 163 LYS cc_start: 0.8520 (pptt) cc_final: 0.8018 (pttt) REVERT: Q 170 MET cc_start: 0.7271 (tpp) cc_final: 0.6854 (tpp) REVERT: Q 268 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6947 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6804 (t0) cc_final: 0.6296 (t0) REVERT: Q 314 TYR cc_start: 0.8390 (m-10) cc_final: 0.8023 (m-10) REVERT: Q 339 GLU cc_start: 0.7223 (tp30) cc_final: 0.6961 (tp30) REVERT: Q 347 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6482 (mt-10) REVERT: Q 349 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7329 (tptm) REVERT: Q 398 LYS cc_start: 0.7799 (mttp) cc_final: 0.7583 (mttp) REVERT: Q 422 ASP cc_start: 0.6340 (t0) cc_final: 0.5977 (m-30) REVERT: Q 449 LEU cc_start: 0.7334 (mp) cc_final: 0.6841 (mp) REVERT: Q 454 GLU cc_start: 0.7000 (pp20) cc_final: 0.6788 (pp20) REVERT: Q 491 ARG cc_start: 0.6867 (ttp-170) cc_final: 0.6130 (ttp-110) outliers start: 45 outliers final: 35 residues processed: 243 average time/residue: 0.2414 time to fit residues: 77.1653 Evaluate side-chains 262 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 277 PHE 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 445 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 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 144 ASP Chi-restraints excluded: chain Q residue 173 MET 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 268 ARG 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 367 VAL Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 GLN ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.156410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131561 restraints weight = 13861.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135712 restraints weight = 7232.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.138431 restraints weight = 4541.028| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8525 Z= 0.139 Angle : 0.732 15.453 11582 Z= 0.360 Chirality : 0.048 0.337 1276 Planarity : 0.005 0.041 1523 Dihedral : 6.289 46.313 1328 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % 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: -1.26 (0.25), residues: 1074 helix: -0.96 (0.48), residues: 113 sheet: -0.61 (0.28), residues: 308 loop : -0.89 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 267 HIS 0.004 0.001 HIS Q 321 PHE 0.022 0.002 PHE Q 232 TYR 0.017 0.001 TYR Q 308 ARG 0.011 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 7) link_NAG-ASN : angle 3.03680 ( 21) hydrogen bonds : bond 0.03423 ( 213) hydrogen bonds : angle 5.84848 ( 546) SS BOND : bond 0.00280 ( 15) SS BOND : angle 1.75592 ( 30) covalent geometry : bond 0.00320 ( 8503) covalent geometry : angle 0.71625 (11531) ********************** 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 270 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8515 (mp10) cc_final: 0.8211 (mp10) REVERT: P 218 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: P 331 SER cc_start: 0.7731 (m) cc_final: 0.7490 (t) REVERT: P 437 GLU cc_start: 0.7002 (tp30) cc_final: 0.6632 (tp30) REVERT: P 583 LYS cc_start: 0.7430 (ptmm) cc_final: 0.7173 (ptmm) REVERT: Q 102 MET cc_start: 0.0058 (ttp) cc_final: -0.0244 (ttp) REVERT: Q 146 TYR cc_start: 0.8031 (t80) cc_final: 0.7807 (t80) REVERT: Q 155 MET cc_start: 0.7306 (mmt) cc_final: 0.6411 (mmp) REVERT: Q 170 MET cc_start: 0.7255 (tpp) cc_final: 0.6836 (tpp) REVERT: Q 257 GLN cc_start: 0.7931 (tp40) cc_final: 0.7725 (tt0) REVERT: Q 268 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6828 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6741 (t0) cc_final: 0.6268 (t0) REVERT: Q 314 TYR cc_start: 0.8413 (m-10) cc_final: 0.8051 (m-10) REVERT: Q 339 GLU cc_start: 0.7202 (tp30) cc_final: 0.6950 (tp30) REVERT: Q 347 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6449 (mt-10) REVERT: Q 349 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7313 (tptm) REVERT: Q 398 LYS cc_start: 0.7792 (mttp) cc_final: 0.7576 (mttp) REVERT: Q 422 ASP cc_start: 0.6349 (t0) cc_final: 0.5979 (m-30) REVERT: Q 454 GLU cc_start: 0.7099 (pp20) cc_final: 0.6622 (pp20) REVERT: Q 491 ARG cc_start: 0.6852 (ttp-170) cc_final: 0.6140 (ttp-110) outliers start: 40 outliers final: 34 residues processed: 244 average time/residue: 0.2352 time to fit residues: 76.4001 Evaluate side-chains 262 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 277 PHE 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 445 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 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 144 ASP Chi-restraints excluded: chain Q residue 173 MET Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 268 ARG Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 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 444 LEU Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 61 optimal weight: 0.0010 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN ** Q 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.157706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132838 restraints weight = 13945.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136938 restraints weight = 7355.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.139656 restraints weight = 4656.099| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8525 Z= 0.128 Angle : 0.718 15.486 11582 Z= 0.353 Chirality : 0.047 0.300 1276 Planarity : 0.004 0.041 1523 Dihedral : 5.980 42.395 1328 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.13 % Allowed : 30.25 % 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: -1.27 (0.25), residues: 1074 helix: -0.89 (0.48), residues: 113 sheet: -0.59 (0.29), residues: 310 loop : -0.93 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 153 HIS 0.003 0.001 HIS Q 321 PHE 0.020 0.002 PHE Q 232 TYR 0.013 0.001 TYR Q 308 ARG 0.009 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 7) link_NAG-ASN : angle 2.80088 ( 21) hydrogen bonds : bond 0.03284 ( 213) hydrogen bonds : angle 5.87295 ( 546) SS BOND : bond 0.00269 ( 15) SS BOND : angle 1.45715 ( 30) covalent geometry : bond 0.00295 ( 8503) covalent geometry : angle 0.70518 (11531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3626.75 seconds wall clock time: 64 minutes 50.91 seconds (3890.91 seconds total)