Starting phenix.real_space_refine on Sun May 11 20:10:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxz_17269/05_2025/8oxz_17269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxz_17269/05_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_17269/05_2025/8oxz_17269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxz_17269/05_2025/8oxz_17269.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxz_17269/05_2025/8oxz_17269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxz_17269/05_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-5687/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: 5.72, per 1000 atoms: 0.69 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.12 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: 2.43 Time building geometry restraints manager: 2.71 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: 5.600 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: 0.420 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 23.580 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.570 ------------------------------------------------------------------------------- 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 : 0.875 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: 0.2202 time to fit residues: 69.1460 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 : 0.853 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131887 restraints weight = 13698.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.135914 restraints weight = 7243.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138594 restraints weight = 4555.138| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 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 7.00514 ( 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 : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 134 LYS cc_start: 0.8259 (tttm) cc_final: 0.7873 (tptm) REVERT: P 166 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6845 (t70) REVERT: P 196 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7437 (mmt-90) REVERT: P 276 TYR cc_start: 0.7048 (m-80) cc_final: 0.6510 (m-80) REVERT: P 399 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7329 (tp) REVERT: P 407 ARG cc_start: 0.7001 (mtm180) cc_final: 0.6768 (ptp-110) REVERT: P 594 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: P 635 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6591 (mt-10) REVERT: P 662 ASP cc_start: 0.7872 (t0) cc_final: 0.7545 (t0) REVERT: Q 84 ARG cc_start: 0.5732 (mmm160) cc_final: 0.5395 (mmm160) REVERT: Q 102 MET cc_start: 0.0074 (ttp) cc_final: -0.0229 (ttp) REVERT: Q 149 MET cc_start: 0.6540 (ppp) cc_final: 0.6183 (ppp) REVERT: Q 155 MET cc_start: 0.7317 (mmt) cc_final: 0.6341 (mmp) REVERT: Q 163 LYS cc_start: 0.8377 (pptt) cc_final: 0.7917 (ptpp) REVERT: Q 174 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7215 (ttp80) REVERT: Q 289 LYS cc_start: 0.8423 (tttt) cc_final: 0.8125 (tttm) REVERT: Q 307 VAL cc_start: 0.8324 (t) cc_final: 0.7978 (m) REVERT: Q 322 LEU cc_start: 0.7968 (tp) cc_final: 0.7294 (tp) REVERT: Q 398 LYS cc_start: 0.7500 (mttp) cc_final: 0.7174 (mttp) REVERT: Q 486 GLU cc_start: 0.6153 (pt0) cc_final: 0.4436 (pt0) REVERT: Q 491 ARG cc_start: 0.6934 (ttp-170) cc_final: 0.6087 (ttp-110) outliers start: 55 outliers final: 28 residues processed: 237 average time/residue: 0.2239 time to fit residues: 71.1714 Evaluate side-chains 230 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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: 0.6980 chunk 97 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 0.0370 chunk 50 optimal weight: 0.0070 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 198 HIS ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 457 ASN Q 117 GLN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 350 ASN Q 460 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.157849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132872 restraints weight = 13836.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137090 restraints weight = 7256.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139874 restraints weight = 4525.336| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8525 Z= 0.136 Angle : 0.694 10.733 11582 Z= 0.345 Chirality : 0.049 0.274 1276 Planarity : 0.005 0.046 1523 Dihedral : 8.073 69.707 1329 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 7.03 % Allowed : 24.44 % 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: -1.39 (0.25), residues: 1074 helix: -0.93 (0.49), residues: 103 sheet: -0.69 (0.28), residues: 314 loop : -1.02 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 211 HIS 0.008 0.001 HIS P 584 PHE 0.018 0.002 PHE P 528 TYR 0.013 0.001 TYR P 349 ARG 0.012 0.001 ARG Q 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 7) link_NAG-ASN : angle 3.02319 ( 21) hydrogen bonds : bond 0.04104 ( 213) hydrogen bonds : angle 6.46467 ( 546) SS BOND : bond 0.00320 ( 15) SS BOND : angle 0.91240 ( 30) covalent geometry : bond 0.00305 ( 8503) covalent geometry : angle 0.68175 (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 271 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7793 (mtt90) cc_final: 0.7224 (mmt-90) REVERT: P 276 TYR cc_start: 0.7088 (m-80) cc_final: 0.6677 (m-10) REVERT: P 393 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7655 (mt) REVERT: P 399 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7353 (tp) REVERT: P 411 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7215 (m) REVERT: P 583 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7008 (ptmm) REVERT: P 594 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: P 662 ASP cc_start: 0.8011 (t0) cc_final: 0.7345 (t0) REVERT: Q 84 ARG cc_start: 0.6165 (mmm160) cc_final: 0.5946 (mmm160) REVERT: Q 102 MET cc_start: 0.0058 (ttp) cc_final: -0.0234 (ttp) REVERT: Q 155 MET cc_start: 0.7346 (mmt) cc_final: 0.6384 (mmp) REVERT: Q 163 LYS cc_start: 0.8403 (pptt) cc_final: 0.7971 (ptpp) REVERT: Q 170 MET cc_start: 0.7320 (tpp) cc_final: 0.7093 (tpp) REVERT: Q 256 MET cc_start: 0.6956 (tpp) cc_final: 0.6743 (tpp) REVERT: Q 289 LYS cc_start: 0.8367 (tttt) cc_final: 0.8165 (tttm) REVERT: Q 305 ASN cc_start: 0.6657 (t0) cc_final: 0.6430 (t0) REVERT: Q 307 VAL cc_start: 0.8267 (t) cc_final: 0.7808 (m) REVERT: Q 328 GLU cc_start: 0.7355 (tp30) cc_final: 0.7121 (tp30) REVERT: Q 347 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6290 (mt-10) REVERT: Q 398 LYS cc_start: 0.7644 (mttp) cc_final: 0.7333 (mttp) REVERT: Q 429 SER cc_start: 0.5481 (OUTLIER) cc_final: 0.5268 (p) REVERT: Q 486 GLU cc_start: 0.6249 (pt0) cc_final: 0.4583 (pt0) REVERT: Q 491 ARG cc_start: 0.6959 (ttp-170) cc_final: 0.6131 (ttp-110) outliers start: 63 outliers final: 31 residues processed: 240 average time/residue: 0.2237 time to fit residues: 71.2452 Evaluate side-chains 245 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 496 TRP Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 535 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 594 GLU Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 327 SER Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 596 GLN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 350 ASN Q 406 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129111 restraints weight = 13855.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133362 restraints weight = 7295.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136119 restraints weight = 4591.778| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8525 Z= 0.197 Angle : 0.717 9.539 11582 Z= 0.364 Chirality : 0.050 0.250 1276 Planarity : 0.005 0.045 1523 Dihedral : 7.554 68.010 1329 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 6.25 % Allowed : 26.00 % Favored : 67.75 % 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: -1.48 (0.25), residues: 1074 helix: -1.12 (0.47), residues: 110 sheet: -0.77 (0.28), residues: 318 loop : -1.04 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 599 HIS 0.011 0.002 HIS P 198 PHE 0.020 0.002 PHE Q 461 TYR 0.021 0.002 TYR P 323 ARG 0.008 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 7) link_NAG-ASN : angle 2.83378 ( 21) hydrogen bonds : bond 0.04100 ( 213) hydrogen bonds : angle 6.29420 ( 546) SS BOND : bond 0.00409 ( 15) SS BOND : angle 1.05723 ( 30) covalent geometry : bond 0.00428 ( 8503) covalent geometry : angle 0.70622 (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 281 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7328 (mtt90) REVERT: P 218 GLN cc_start: 0.7963 (mp10) cc_final: 0.7225 (mp10) REVERT: P 231 ASN cc_start: 0.6016 (OUTLIER) cc_final: 0.5815 (t0) REVERT: P 308 GLN cc_start: 0.6689 (pp30) cc_final: 0.6343 (pp30) REVERT: P 331 SER cc_start: 0.7714 (m) cc_final: 0.7276 (t) REVERT: P 399 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7581 (tp) REVERT: P 411 VAL cc_start: 0.7589 (OUTLIER) cc_final: 0.7347 (m) REVERT: P 437 GLU cc_start: 0.7061 (tp30) cc_final: 0.6847 (tp30) REVERT: P 583 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7100 (ptmm) REVERT: P 662 ASP cc_start: 0.8142 (t0) cc_final: 0.6337 (m-30) REVERT: Q 84 ARG cc_start: 0.6462 (mmm160) cc_final: 0.6257 (mmm-85) REVERT: Q 102 MET cc_start: 0.0071 (ttp) cc_final: -0.0219 (ttp) REVERT: Q 130 LYS cc_start: 0.7891 (ttmm) cc_final: 0.7666 (ttmm) REVERT: Q 134 LYS cc_start: 0.8192 (ptmm) cc_final: 0.7455 (ptmm) REVERT: Q 155 MET cc_start: 0.7459 (mmt) cc_final: 0.6532 (mmp) REVERT: Q 163 LYS cc_start: 0.8468 (pptt) cc_final: 0.8042 (ptpp) REVERT: Q 170 MET cc_start: 0.7325 (tpp) cc_final: 0.6988 (tpp) REVERT: Q 174 ARG cc_start: 0.7432 (ttp80) cc_final: 0.7110 (ttp80) REVERT: Q 287 ASP cc_start: 0.6622 (t0) cc_final: 0.6156 (t0) REVERT: Q 289 LYS cc_start: 0.8378 (tttt) cc_final: 0.8175 (tttm) REVERT: Q 305 ASN cc_start: 0.6862 (t0) cc_final: 0.6659 (t0) REVERT: Q 307 VAL cc_start: 0.8289 (t) cc_final: 0.7834 (m) REVERT: Q 314 TYR cc_start: 0.8366 (m-10) cc_final: 0.7965 (m-10) REVERT: Q 328 GLU cc_start: 0.7374 (tp30) cc_final: 0.7171 (tp30) REVERT: Q 347 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6407 (mt-10) REVERT: Q 398 LYS cc_start: 0.7777 (mttp) cc_final: 0.7291 (mttp) REVERT: Q 486 GLU cc_start: 0.6415 (pt0) cc_final: 0.4880 (pt0) REVERT: Q 491 ARG cc_start: 0.6993 (ttp-170) cc_final: 0.6171 (ttp-110) REVERT: Q 500 HIS cc_start: 0.5702 (OUTLIER) cc_final: 0.5480 (m170) outliers start: 56 outliers final: 35 residues processed: 248 average time/residue: 0.2268 time to fit residues: 74.3972 Evaluate side-chains 254 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 418 LEU Chi-restraints excluded: chain P residue 444 SER Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 294 VAL 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 Chi-restraints excluded: chain Q residue 500 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 104 optimal weight: 0.0030 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 311 GLN Q 239 GLN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 443 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132561 restraints weight = 13676.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136677 restraints weight = 7205.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139317 restraints weight = 4546.518| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8525 Z= 0.150 Angle : 0.682 9.034 11582 Z= 0.343 Chirality : 0.048 0.235 1276 Planarity : 0.005 0.042 1523 Dihedral : 7.168 64.341 1329 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 6.25 % Allowed : 27.12 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.25), residues: 1074 helix: -1.12 (0.47), residues: 113 sheet: -0.72 (0.28), residues: 317 loop : -1.01 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP Q 267 HIS 0.005 0.001 HIS P 198 PHE 0.022 0.002 PHE Q 426 TYR 0.018 0.001 TYR P 323 ARG 0.006 0.000 ARG P 537 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 7) link_NAG-ASN : angle 2.65566 ( 21) hydrogen bonds : bond 0.03637 ( 213) hydrogen bonds : angle 6.12244 ( 546) SS BOND : bond 0.00329 ( 15) SS BOND : angle 0.94766 ( 30) covalent geometry : bond 0.00344 ( 8503) covalent geometry : angle 0.67198 (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 266 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 196 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7441 (mmt-90) REVERT: P 218 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7204 (mp10) REVERT: P 224 THR cc_start: 0.7902 (p) cc_final: 0.7688 (p) REVERT: P 231 ASN cc_start: 0.5981 (OUTLIER) cc_final: 0.5738 (t0) REVERT: P 308 GLN cc_start: 0.6778 (pp30) cc_final: 0.6465 (pp30) REVERT: P 331 SER cc_start: 0.7750 (m) cc_final: 0.7401 (t) REVERT: P 399 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7634 (tp) REVERT: P 411 VAL cc_start: 0.7512 (OUTLIER) cc_final: 0.7285 (m) REVERT: P 583 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7035 (ptmm) REVERT: Q 71 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7151 (tptt) REVERT: Q 102 MET cc_start: 0.0082 (ttp) cc_final: -0.0219 (ttp) REVERT: Q 130 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7731 (ttmm) REVERT: Q 134 LYS cc_start: 0.8225 (ptmm) cc_final: 0.7416 (ptmm) REVERT: Q 155 MET cc_start: 0.7363 (mmt) cc_final: 0.6423 (mmp) REVERT: Q 163 LYS cc_start: 0.8499 (pptt) cc_final: 0.8093 (ptpp) REVERT: Q 170 MET cc_start: 0.7256 (tpp) cc_final: 0.6895 (tpp) REVERT: Q 174 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6186 (ttp80) REVERT: Q 287 ASP cc_start: 0.6627 (t0) cc_final: 0.6204 (t0) REVERT: Q 314 TYR cc_start: 0.8348 (m-10) cc_final: 0.7822 (m-10) REVERT: Q 347 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6307 (mt-10) REVERT: Q 349 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7447 (tptm) REVERT: Q 398 LYS cc_start: 0.7814 (mttp) cc_final: 0.7358 (mttp) REVERT: Q 486 GLU cc_start: 0.6401 (pt0) cc_final: 0.4875 (pt0) REVERT: Q 491 ARG cc_start: 0.6936 (ttp-170) cc_final: 0.6132 (ttp-110) REVERT: Q 500 HIS cc_start: 0.5669 (OUTLIER) cc_final: 0.5453 (m90) outliers start: 56 outliers final: 32 residues processed: 236 average time/residue: 0.2275 time to fit residues: 71.4270 Evaluate side-chains 257 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 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 257 GLN Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN 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 452 THR Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 462 ILE Chi-restraints excluded: chain Q residue 500 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 479 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.156583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131823 restraints weight = 13642.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135933 restraints weight = 7199.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138595 restraints weight = 4541.386| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8525 Z= 0.164 Angle : 0.705 13.852 11582 Z= 0.350 Chirality : 0.048 0.227 1276 Planarity : 0.005 0.047 1523 Dihedral : 6.961 60.913 1329 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 7.14 % Allowed : 26.67 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.25), residues: 1074 helix: -1.13 (0.47), residues: 113 sheet: -0.73 (0.28), residues: 325 loop : -0.99 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 267 HIS 0.004 0.001 HIS Q 321 PHE 0.020 0.002 PHE Q 426 TYR 0.014 0.001 TYR Q 308 ARG 0.008 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 7) link_NAG-ASN : angle 2.65833 ( 21) hydrogen bonds : bond 0.03623 ( 213) hydrogen bonds : angle 6.00412 ( 546) SS BOND : bond 0.00316 ( 15) SS BOND : angle 1.03149 ( 30) covalent geometry : bond 0.00375 ( 8503) covalent geometry : angle 0.69545 (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 277 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 218 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: P 231 ASN cc_start: 0.6003 (OUTLIER) cc_final: 0.5771 (t0) REVERT: P 264 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7931 (mtmm) REVERT: P 308 GLN cc_start: 0.6929 (pp30) cc_final: 0.6628 (pp30) REVERT: P 331 SER cc_start: 0.7771 (m) cc_final: 0.7442 (t) REVERT: P 399 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7648 (tp) REVERT: P 411 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7313 (m) REVERT: P 437 GLU cc_start: 0.7091 (tp30) cc_final: 0.6827 (tp30) REVERT: P 583 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7007 (ptmm) REVERT: Q 71 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7484 (tptt) REVERT: Q 84 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6673 (mmm-85) REVERT: Q 102 MET cc_start: 0.0129 (ttp) cc_final: -0.0185 (ttp) REVERT: Q 124 ARG cc_start: 0.5457 (OUTLIER) cc_final: 0.5026 (mtm180) REVERT: Q 130 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7704 (ttmm) REVERT: Q 134 LYS cc_start: 0.8327 (ptmm) cc_final: 0.7954 (ptmm) REVERT: Q 155 MET cc_start: 0.7331 (mmt) cc_final: 0.6494 (mmp) REVERT: Q 163 LYS cc_start: 0.8471 (pptt) cc_final: 0.8014 (ptpp) REVERT: Q 170 MET cc_start: 0.7257 (tpp) cc_final: 0.6864 (tpp) REVERT: Q 268 ARG cc_start: 0.7045 (ttp-170) cc_final: 0.6585 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6665 (t0) cc_final: 0.6256 (t0) REVERT: Q 314 TYR cc_start: 0.8352 (m-10) cc_final: 0.7874 (m-10) REVERT: Q 341 PHE cc_start: 0.6737 (m-80) cc_final: 0.6437 (m-80) REVERT: Q 347 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6301 (mt-10) REVERT: Q 349 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7442 (tptm) REVERT: Q 429 SER cc_start: 0.5723 (OUTLIER) cc_final: 0.5244 (p) REVERT: Q 449 LEU cc_start: 0.7683 (mt) cc_final: 0.7262 (mp) REVERT: Q 454 GLU cc_start: 0.7400 (pm20) cc_final: 0.7064 (pm20) REVERT: Q 491 ARG cc_start: 0.6964 (ttp-170) cc_final: 0.6114 (ttp-110) outliers start: 64 outliers final: 35 residues processed: 245 average time/residue: 0.2160 time to fit residues: 70.1151 Evaluate side-chains 260 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 264 LYS Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 144 ASP Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 222 VAL Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 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 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 453 GLU 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: 0.1980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.0060 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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** Q 244 ASN 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 = 0.4026 r_free = 0.4026 target = 0.156687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132176 restraints weight = 13769.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136184 restraints weight = 7294.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138746 restraints weight = 4633.324| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8525 Z= 0.146 Angle : 0.691 14.383 11582 Z= 0.345 Chirality : 0.048 0.216 1276 Planarity : 0.005 0.043 1523 Dihedral : 6.719 57.426 1329 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 6.25 % Allowed : 27.46 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.25), residues: 1074 helix: -1.06 (0.48), residues: 112 sheet: -0.68 (0.28), residues: 323 loop : -0.87 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 267 HIS 0.004 0.001 HIS Q 321 PHE 0.017 0.002 PHE Q 426 TYR 0.018 0.001 TYR Q 308 ARG 0.010 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 7) link_NAG-ASN : angle 2.64681 ( 21) hydrogen bonds : bond 0.03581 ( 213) hydrogen bonds : angle 5.93068 ( 546) SS BOND : bond 0.00284 ( 15) SS BOND : angle 0.96580 ( 30) covalent geometry : bond 0.00340 ( 8503) covalent geometry : angle 0.68158 (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 261 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 218 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: P 231 ASN cc_start: 0.5993 (OUTLIER) cc_final: 0.5756 (t0) REVERT: P 264 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7940 (mtmm) REVERT: P 308 GLN cc_start: 0.6961 (pp30) cc_final: 0.6622 (pp30) REVERT: P 331 SER cc_start: 0.7729 (m) cc_final: 0.7416 (t) REVERT: P 367 SER cc_start: 0.6944 (t) cc_final: 0.6483 (m) REVERT: P 411 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7272 (m) REVERT: P 437 GLU cc_start: 0.7096 (tp30) cc_final: 0.6741 (tp30) REVERT: P 528 PHE cc_start: 0.8225 (p90) cc_final: 0.7960 (p90) REVERT: P 583 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7027 (ptmm) REVERT: Q 71 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7129 (tppt) REVERT: Q 102 MET cc_start: 0.0073 (ttp) cc_final: -0.0229 (ttp) REVERT: Q 124 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.5117 (mtm180) REVERT: Q 155 MET cc_start: 0.7361 (mmt) cc_final: 0.6487 (mmp) REVERT: Q 163 LYS cc_start: 0.8471 (pptt) cc_final: 0.7973 (ptpp) REVERT: Q 170 MET cc_start: 0.7243 (tpp) cc_final: 0.6850 (tpp) REVERT: Q 174 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6940 (ttp80) REVERT: Q 268 ARG cc_start: 0.7101 (ttp-170) cc_final: 0.6828 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6636 (t0) cc_final: 0.6251 (t0) REVERT: Q 314 TYR cc_start: 0.8328 (m-10) cc_final: 0.7922 (m-10) REVERT: Q 341 PHE cc_start: 0.6793 (m-80) cc_final: 0.6471 (m-80) REVERT: Q 347 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6270 (mt-10) REVERT: Q 349 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7411 (tptm) REVERT: Q 449 LEU cc_start: 0.7649 (mt) cc_final: 0.7218 (mp) REVERT: Q 454 GLU cc_start: 0.7358 (pm20) cc_final: 0.7019 (pm20) REVERT: Q 491 ARG cc_start: 0.6954 (ttp-170) cc_final: 0.6120 (ttp-110) outliers start: 56 outliers final: 36 residues processed: 230 average time/residue: 0.2136 time to fit residues: 66.0064 Evaluate side-chains 253 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 264 LYS Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 527 SER Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 623 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 124 ARG Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 222 VAL Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 257 GLN 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 = 0.3971 r_free = 0.3971 target = 0.152972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128722 restraints weight = 13876.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132736 restraints weight = 7329.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135412 restraints weight = 4616.584| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8525 Z= 0.187 Angle : 0.723 14.663 11582 Z= 0.361 Chirality : 0.049 0.203 1276 Planarity : 0.005 0.063 1523 Dihedral : 6.613 52.215 1329 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 6.03 % Allowed : 26.90 % 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: -1.37 (0.25), residues: 1074 helix: -1.12 (0.49), residues: 112 sheet: -0.69 (0.28), residues: 324 loop : -0.96 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 496 HIS 0.004 0.001 HIS Q 470 PHE 0.024 0.002 PHE Q 426 TYR 0.024 0.002 TYR P 276 ARG 0.010 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 7) link_NAG-ASN : angle 2.61356 ( 21) hydrogen bonds : bond 0.03731 ( 213) hydrogen bonds : angle 6.04416 ( 546) SS BOND : bond 0.00357 ( 15) SS BOND : angle 1.09532 ( 30) covalent geometry : bond 0.00431 ( 8503) covalent geometry : angle 0.71418 (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 285 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 168 LYS cc_start: 0.7841 (mttt) cc_final: 0.7597 (mmtt) REVERT: P 196 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7170 (mmt-90) REVERT: P 218 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: P 308 GLN cc_start: 0.7110 (pp30) cc_final: 0.6771 (pp30) REVERT: P 331 SER cc_start: 0.7842 (m) cc_final: 0.7492 (t) REVERT: P 367 SER cc_start: 0.7064 (t) cc_final: 0.6661 (m) REVERT: P 411 VAL cc_start: 0.7523 (OUTLIER) cc_final: 0.7282 (m) REVERT: P 437 GLU cc_start: 0.7122 (tp30) cc_final: 0.6626 (tp30) REVERT: P 583 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7102 (ptmm) REVERT: Q 71 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7517 (tptt) REVERT: Q 102 MET cc_start: 0.0095 (ttp) cc_final: -0.0217 (ttp) REVERT: Q 112 THR cc_start: 0.7369 (p) cc_final: 0.7137 (p) REVERT: Q 124 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5356 (mtm180) REVERT: Q 130 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7654 (ttmm) REVERT: Q 134 LYS cc_start: 0.8453 (ptmm) cc_final: 0.8087 (ptmm) REVERT: Q 155 MET cc_start: 0.7423 (mmt) cc_final: 0.6548 (mmp) REVERT: Q 163 LYS cc_start: 0.8478 (pptt) cc_final: 0.7998 (pttt) REVERT: Q 170 MET cc_start: 0.7280 (tpp) cc_final: 0.6876 (tpp) REVERT: Q 174 ARG cc_start: 0.7222 (ttp80) cc_final: 0.7002 (ttp80) REVERT: Q 268 ARG cc_start: 0.7214 (ttp-170) cc_final: 0.6854 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6808 (t0) cc_final: 0.6317 (t0) REVERT: Q 314 TYR cc_start: 0.8390 (m-10) cc_final: 0.7975 (m-10) REVERT: Q 339 GLU cc_start: 0.6934 (tp30) cc_final: 0.6671 (tp30) REVERT: Q 341 PHE cc_start: 0.6958 (m-80) cc_final: 0.6503 (m-80) REVERT: Q 347 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6492 (mt-10) REVERT: Q 349 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7370 (tptm) REVERT: Q 422 ASP cc_start: 0.6300 (t0) cc_final: 0.6009 (m-30) REVERT: Q 454 GLU cc_start: 0.7442 (pm20) cc_final: 0.7036 (pm20) REVERT: Q 491 ARG cc_start: 0.6966 (ttp-170) cc_final: 0.6144 (ttp-110) outliers start: 54 outliers final: 37 residues processed: 253 average time/residue: 0.2447 time to fit residues: 81.8232 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 : 0.895 ------------------------------------------------------------------------------- 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 286 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 411 VAL Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 623 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR 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: 6.9990 chunk 32 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 chunk 40 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 0.0030 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.3928 ------------------------------------------------------------------------------- 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 257 GLN 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 = 0.156184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131421 restraints weight = 13854.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135592 restraints weight = 7286.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138076 restraints weight = 4576.055| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8525 Z= 0.140 Angle : 0.718 15.508 11582 Z= 0.356 Chirality : 0.049 0.442 1276 Planarity : 0.004 0.041 1523 Dihedral : 6.416 48.638 1329 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.91 % Allowed : 29.13 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1074 helix: -1.06 (0.48), residues: 112 sheet: -0.71 (0.28), residues: 323 loop : -0.89 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Q 267 HIS 0.004 0.001 HIS Q 321 PHE 0.016 0.002 PHE Q 426 TYR 0.016 0.001 TYR Q 308 ARG 0.007 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 7) link_NAG-ASN : angle 3.30387 ( 21) hydrogen bonds : bond 0.03453 ( 213) hydrogen bonds : angle 5.90159 ( 546) SS BOND : bond 0.00309 ( 15) SS BOND : angle 0.92437 ( 30) covalent geometry : bond 0.00326 ( 8503) covalent geometry : angle 0.70439 (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 269 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8427 (mp10) cc_final: 0.8166 (mp10) REVERT: P 168 LYS cc_start: 0.7782 (mttt) cc_final: 0.7530 (mmtt) REVERT: P 196 ARG cc_start: 0.7599 (mtt90) cc_final: 0.7200 (mmt-90) REVERT: P 218 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: P 308 GLN cc_start: 0.7067 (pp30) cc_final: 0.6739 (pp30) REVERT: P 331 SER cc_start: 0.7792 (m) cc_final: 0.7463 (t) REVERT: P 367 SER cc_start: 0.7093 (t) cc_final: 0.6671 (m) REVERT: P 393 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7752 (mp) REVERT: P 411 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7234 (m) REVERT: P 437 GLU cc_start: 0.7089 (tp30) cc_final: 0.6673 (tp30) REVERT: P 583 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7080 (ptmm) REVERT: P 677 HIS cc_start: 0.7871 (t-90) cc_final: 0.7555 (t-90) REVERT: Q 71 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7464 (tppt) REVERT: Q 102 MET cc_start: 0.0070 (ttp) cc_final: -0.0233 (ttp) REVERT: Q 112 THR cc_start: 0.7326 (p) cc_final: 0.7105 (p) REVERT: Q 124 ARG cc_start: 0.5655 (OUTLIER) cc_final: 0.5220 (mtm180) REVERT: Q 130 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7799 (ttmm) REVERT: Q 136 LYS cc_start: 0.8487 (pttt) cc_final: 0.8053 (ptmt) REVERT: Q 146 TYR cc_start: 0.8014 (t80) cc_final: 0.7808 (t80) REVERT: Q 155 MET cc_start: 0.7337 (mmt) cc_final: 0.6463 (mmp) REVERT: Q 163 LYS cc_start: 0.8465 (pptt) cc_final: 0.8010 (pttt) REVERT: Q 170 MET cc_start: 0.7238 (tpp) cc_final: 0.6841 (tpp) REVERT: Q 174 ARG cc_start: 0.7157 (ttp80) cc_final: 0.6957 (ttp80) REVERT: Q 268 ARG cc_start: 0.7117 (ttp-170) cc_final: 0.6814 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6692 (t0) cc_final: 0.6268 (t0) REVERT: Q 314 TYR cc_start: 0.8355 (m-10) cc_final: 0.7986 (m-10) REVERT: Q 339 GLU cc_start: 0.6988 (tp30) cc_final: 0.6671 (tp30) REVERT: Q 341 PHE cc_start: 0.6870 (m-80) cc_final: 0.6471 (m-80) REVERT: Q 347 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6365 (mt-10) REVERT: Q 349 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7303 (tptm) REVERT: Q 422 ASP cc_start: 0.6278 (t0) cc_final: 0.5925 (m-30) REVERT: Q 449 LEU cc_start: 0.7346 (mp) cc_final: 0.6857 (mp) REVERT: Q 491 ARG cc_start: 0.6832 (ttp-170) cc_final: 0.6124 (ttp-110) outliers start: 44 outliers final: 29 residues processed: 244 average time/residue: 0.2267 time to fit residues: 72.9506 Evaluate side-chains 260 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 124 ARG Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 0.6980 chunk 12 optimal weight: 0.0970 chunk 76 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 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 = 0.4014 r_free = 0.4014 target = 0.155911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131134 restraints weight = 13895.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135263 restraints weight = 7302.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137935 restraints weight = 4599.903| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8525 Z= 0.154 Angle : 0.733 16.161 11582 Z= 0.362 Chirality : 0.049 0.382 1276 Planarity : 0.004 0.042 1523 Dihedral : 6.310 45.734 1328 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.02 % Allowed : 30.69 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.25), residues: 1074 helix: -1.03 (0.48), residues: 112 sheet: -0.71 (0.28), residues: 318 loop : -0.90 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 496 HIS 0.004 0.001 HIS Q 321 PHE 0.017 0.002 PHE Q 426 TYR 0.012 0.001 TYR P 374 ARG 0.007 0.001 ARG P 537 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 7) link_NAG-ASN : angle 3.12918 ( 21) hydrogen bonds : bond 0.03571 ( 213) hydrogen bonds : angle 5.86804 ( 546) SS BOND : bond 0.00343 ( 15) SS BOND : angle 2.01228 ( 30) covalent geometry : bond 0.00357 ( 8503) covalent geometry : angle 0.71470 (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 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 144 GLN cc_start: 0.8476 (mp10) cc_final: 0.8178 (mp10) REVERT: P 168 LYS cc_start: 0.7781 (mttt) cc_final: 0.7530 (mmtt) REVERT: P 196 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7172 (mmt-90) REVERT: P 218 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: P 308 GLN cc_start: 0.7079 (pp30) cc_final: 0.6740 (pp30) REVERT: P 331 SER cc_start: 0.7793 (m) cc_final: 0.7504 (t) REVERT: P 393 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7757 (mp) REVERT: P 411 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7251 (m) REVERT: P 437 GLU cc_start: 0.7086 (tp30) cc_final: 0.6671 (tp30) REVERT: P 583 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7072 (ptmm) REVERT: P 634 ARG cc_start: 0.6349 (mtp-110) cc_final: 0.6141 (mtp180) REVERT: P 677 HIS cc_start: 0.7904 (t-90) cc_final: 0.7543 (t-90) REVERT: Q 71 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7454 (tppt) REVERT: Q 84 ARG cc_start: 0.6930 (mmm-85) cc_final: 0.6458 (mmm-85) REVERT: Q 102 MET cc_start: 0.0098 (ttp) cc_final: -0.0212 (ttp) REVERT: Q 124 ARG cc_start: 0.5626 (OUTLIER) cc_final: 0.5231 (mtm180) REVERT: Q 130 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7799 (ttmm) REVERT: Q 136 LYS cc_start: 0.8493 (pttt) cc_final: 0.8085 (ptmt) REVERT: Q 146 TYR cc_start: 0.8025 (t80) cc_final: 0.7811 (t80) REVERT: Q 155 MET cc_start: 0.7335 (mmt) cc_final: 0.6479 (mmp) REVERT: Q 163 LYS cc_start: 0.8512 (pptt) cc_final: 0.8041 (pttt) REVERT: Q 170 MET cc_start: 0.7243 (tpp) cc_final: 0.6848 (tpp) REVERT: Q 174 ARG cc_start: 0.7181 (ttp80) cc_final: 0.6974 (ttp80) REVERT: Q 268 ARG cc_start: 0.7151 (ttp-170) cc_final: 0.6839 (ttp-110) REVERT: Q 287 ASP cc_start: 0.6757 (t0) cc_final: 0.6312 (t0) REVERT: Q 314 TYR cc_start: 0.8399 (m-10) cc_final: 0.8052 (m-10) REVERT: Q 339 GLU cc_start: 0.7025 (tp30) cc_final: 0.6740 (tp30) REVERT: Q 341 PHE cc_start: 0.6914 (m-80) cc_final: 0.6483 (m-80) REVERT: Q 347 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6414 (mt-10) REVERT: Q 349 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7323 (tptm) REVERT: Q 422 ASP cc_start: 0.6351 (t0) cc_final: 0.5990 (m-30) REVERT: Q 454 GLU cc_start: 0.7053 (pp20) cc_final: 0.6816 (pp20) REVERT: Q 491 ARG cc_start: 0.6836 (ttp-170) cc_final: 0.6134 (ttp-110) outliers start: 36 outliers final: 27 residues processed: 243 average time/residue: 0.2338 time to fit residues: 74.9573 Evaluate side-chains 254 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 264 LYS Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 411 VAL Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 124 ARG 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 322 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 306 GLN ** P 490 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 = 0.3968 r_free = 0.3968 target = 0.152755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128578 restraints weight = 13902.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.132692 restraints weight = 7333.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135345 restraints weight = 4577.595| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8525 Z= 0.200 Angle : 0.763 16.113 11582 Z= 0.377 Chirality : 0.050 0.323 1276 Planarity : 0.005 0.043 1523 Dihedral : 6.382 48.295 1328 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.35 % Allowed : 31.03 % Favored : 64.62 % 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: -1.42 (0.25), residues: 1074 helix: -1.00 (0.49), residues: 112 sheet: -0.80 (0.28), residues: 318 loop : -0.97 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 599 HIS 0.004 0.001 HIS Q 470 PHE 0.025 0.002 PHE Q 426 TYR 0.028 0.002 TYR P 276 ARG 0.006 0.001 ARG Q 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 7) link_NAG-ASN : angle 3.07510 ( 21) hydrogen bonds : bond 0.03843 ( 213) hydrogen bonds : angle 6.02389 ( 546) SS BOND : bond 0.00367 ( 15) SS BOND : angle 2.01287 ( 30) covalent geometry : bond 0.00457 ( 8503) covalent geometry : angle 0.74601 (11531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3288.81 seconds wall clock time: 58 minutes 20.63 seconds (3500.63 seconds total)