Starting phenix.real_space_refine on Fri Aug 22 22:41:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxz_17269/08_2025/8oxz_17269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxz_17269/08_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_17269/08_2025/8oxz_17269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxz_17269/08_2025/8oxz_17269.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxz_17269/08_2025/8oxz_17269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxz_17269/08_2025/8oxz_17269.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN: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: 2.05, per 1000 atoms: 0.25 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: 0.67 Conformation dependent library (CDL) restraints added in 409.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 13.6% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 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: 1.53 Time building geometry restraints manager: 0.87 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: 0.010 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.150 ------------------------------------------------------------------------------- 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 : 15.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG Q 124 TYR 0.018 0.002 TYR P 323 PHE 0.021 0.002 PHE P 528 TRP 0.009 0.002 TRP P 153 HIS 0.004 0.001 HIS Q 321 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8503) covalent geometry : angle 0.81505 (11531) SS BOND : bond 0.00359 ( 15) SS BOND : angle 0.94077 ( 30) hydrogen bonds : bond 0.25492 ( 213) hydrogen bonds : angle 9.62240 ( 546) link_NAG-ASN : bond 0.00927 ( 7) link_NAG-ASN : angle 4.83234 ( 21) *********************** 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 : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 117 GLU cc_start: 0.6447 (mp0) cc_final: 0.5669 (mp0) REVERT: P 196 ARG cc_start: 0.7291 (mtt90) cc_final: 0.6527 (mmt-90) REVERT: P 276 TYR cc_start: 0.6814 (m-80) cc_final: 0.6512 (m-80) REVERT: P 518 ASN cc_start: 0.6903 (p0) cc_final: 0.6688 (p0) REVERT: P 635 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6437 (mt-10) REVERT: P 662 ASP cc_start: 0.7614 (t0) cc_final: 0.7225 (t0) REVERT: P 672 LEU cc_start: 0.7572 (mm) cc_final: 0.7365 (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: 0.6771 (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: 0.6212 (mmp) REVERT: Q 289 LYS cc_start: 0.8421 (tttt) cc_final: 0.8149 (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: 0.6819 (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: 0.6567 (tttt) REVERT: Q 443 GLN cc_start: 0.6602 (mm110) cc_final: 0.6146 (mm-40) outliers start: 11 outliers final: 3 residues processed: 236 average time/residue: 0.1039 time to fit residues: 32.9141 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 : 0.214 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.0010 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 164 GLN P 255 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 161 ASN Q 171 ASN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 342 GLN Q 376 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.156392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131413 restraints weight = 13895.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135577 restraints weight = 7273.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138300 restraints weight = 4549.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140131 restraints weight = 3211.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141174 restraints weight = 2498.711| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8525 Z= 0.188 Angle : 0.786 9.344 11582 Z= 0.393 Chirality : 0.053 0.285 1276 Planarity : 0.006 0.072 1523 Dihedral : 9.424 72.849 1333 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 6.81 % Allowed : 24.55 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.25), residues: 1074 helix: -1.16 (0.48), residues: 105 sheet: -0.83 (0.28), residues: 319 loop : -1.07 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 174 TYR 0.020 0.002 TYR P 415 PHE 0.022 0.002 PHE Q 217 TRP 0.011 0.002 TRP Q 267 HIS 0.008 0.002 HIS Q 321 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8503) covalent geometry : angle 0.77251 (11531) SS BOND : bond 0.00360 ( 15) SS BOND : angle 1.16744 ( 30) hydrogen bonds : bond 0.04473 ( 213) hydrogen bonds : angle 6.84362 ( 546) link_NAG-ASN : bond 0.00832 ( 7) link_NAG-ASN : angle 3.38317 ( 21) *********************** 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 273 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 212 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 166 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.6922 (t70) REVERT: P 196 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7289 (mmt-90) REVERT: P 276 TYR cc_start: 0.7108 (m-80) cc_final: 0.6511 (m-10) REVERT: P 399 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7384 (tp) REVERT: P 594 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: P 635 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6622 (mt-10) REVERT: P 662 ASP cc_start: 0.7967 (t0) cc_final: 0.7413 (t0) REVERT: Q 84 ARG cc_start: 0.5729 (mmm160) cc_final: 0.5392 (mmm160) REVERT: Q 102 MET cc_start: 0.0122 (ttp) cc_final: -0.0193 (ttp) REVERT: Q 149 MET cc_start: 0.6720 (ppp) cc_final: 0.6388 (ppp) REVERT: Q 155 MET cc_start: 0.7320 (mmt) cc_final: 0.6344 (mmp) REVERT: Q 163 LYS cc_start: 0.8408 (pptt) cc_final: 0.7942 (pttm) REVERT: Q 220 LYS cc_start: 0.7520 (ttpt) cc_final: 0.7293 (ttpt) REVERT: Q 256 MET cc_start: 0.6881 (tpp) cc_final: 0.6680 (tpp) REVERT: Q 289 LYS cc_start: 0.8431 (tttt) cc_final: 0.8132 (tttm) REVERT: Q 305 ASN cc_start: 0.6631 (t0) cc_final: 0.6321 (t0) REVERT: Q 307 VAL cc_start: 0.8290 (t) cc_final: 0.7946 (m) REVERT: Q 347 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6474 (mt-10) REVERT: Q 398 LYS cc_start: 0.7547 (mttp) cc_final: 0.7153 (mttp) REVERT: Q 486 GLU cc_start: 0.6299 (pt0) cc_final: 0.4747 (pt0) REVERT: Q 491 ARG cc_start: 0.6963 (ttp-170) cc_final: 0.6200 (ttp-110) outliers start: 61 outliers final: 31 residues processed: 246 average time/residue: 0.1035 time to fit residues: 34.0292 Evaluate side-chains 235 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 403 THR 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 119 LEU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 143 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 290 LEU Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 327 SER Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130317 restraints weight = 13806.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134441 restraints weight = 7334.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137131 restraints weight = 4624.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138781 restraints weight = 3282.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.140012 restraints weight = 2586.835| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8525 Z= 0.198 Angle : 0.727 8.051 11582 Z= 0.369 Chirality : 0.050 0.286 1276 Planarity : 0.006 0.051 1523 Dihedral : 7.932 70.317 1329 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 7.03 % Allowed : 25.33 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.25), residues: 1074 helix: -1.17 (0.49), residues: 102 sheet: -0.71 (0.28), residues: 318 loop : -1.06 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 174 TYR 0.017 0.002 TYR P 349 PHE 0.025 0.002 PHE Q 232 TRP 0.009 0.002 TRP P 211 HIS 0.004 0.002 HIS Q 479 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8503) covalent geometry : angle 0.71527 (11531) SS BOND : bond 0.00393 ( 15) SS BOND : angle 1.12198 ( 30) hydrogen bonds : bond 0.04692 ( 213) hydrogen bonds : angle 6.53366 ( 546) link_NAG-ASN : bond 0.00575 ( 7) link_NAG-ASN : angle 2.99289 ( 21) *********************** 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 287 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 96 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7691 (tt) REVERT: P 196 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7285 (mmt-90) REVERT: P 218 GLN cc_start: 0.7970 (mp10) cc_final: 0.7199 (mp10) REVERT: P 308 GLN cc_start: 0.6656 (pp30) cc_final: 0.6236 (pp30) REVERT: P 323 TYR cc_start: 0.8146 (t80) cc_final: 0.7892 (t80) REVERT: P 331 SER cc_start: 0.7743 (m) cc_final: 0.7393 (t) REVERT: P 399 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7607 (tp) REVERT: P 411 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7415 (m) REVERT: P 437 GLU cc_start: 0.7081 (tp30) cc_final: 0.6853 (tp30) REVERT: P 662 ASP cc_start: 0.8220 (t0) cc_final: 0.6372 (m-30) REVERT: Q 84 ARG cc_start: 0.6009 (mmm160) cc_final: 0.5721 (mmm160) REVERT: Q 102 MET cc_start: 0.0142 (ttp) cc_final: -0.0164 (ttp) REVERT: Q 130 LYS cc_start: 0.7820 (ttmm) cc_final: 0.7610 (ttmm) REVERT: Q 155 MET cc_start: 0.7411 (mmt) cc_final: 0.6466 (mmp) REVERT: Q 163 LYS cc_start: 0.8472 (pptt) cc_final: 0.8146 (ptpp) REVERT: Q 174 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7093 (ttp80) REVERT: Q 220 LYS cc_start: 0.7671 (ttpt) cc_final: 0.7451 (ttpt) REVERT: Q 287 ASP cc_start: 0.6572 (t0) cc_final: 0.6088 (t0) REVERT: Q 289 LYS cc_start: 0.8414 (tttt) cc_final: 0.8178 (tttm) REVERT: Q 307 VAL cc_start: 0.8369 (t) cc_final: 0.7892 (m) REVERT: Q 347 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6413 (mt-10) REVERT: Q 398 LYS cc_start: 0.7809 (mttp) cc_final: 0.7328 (mttp) REVERT: Q 486 GLU cc_start: 0.6391 (pt0) cc_final: 0.4789 (pt0) REVERT: Q 491 ARG cc_start: 0.6942 (ttp-170) cc_final: 0.6102 (ttp-110) outliers start: 63 outliers final: 31 residues processed: 254 average time/residue: 0.1001 time to fit residues: 33.8158 Evaluate side-chains 255 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 LEU 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 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU 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 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 661 LEU Chi-restraints excluded: chain 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 218 SER Chi-restraints excluded: chain Q residue 234 GLU 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 300 GLN Chi-restraints excluded: chain Q residue 340 GLU Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 393 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 458 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 23 optimal weight: 0.0000 chunk 52 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN P 596 GLN Q 117 GLN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 244 ASN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.155870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130522 restraints weight = 14062.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134742 restraints weight = 7388.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137515 restraints weight = 4612.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139373 restraints weight = 3278.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140600 restraints weight = 2542.434| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8525 Z= 0.138 Angle : 0.675 7.477 11582 Z= 0.343 Chirality : 0.048 0.241 1276 Planarity : 0.005 0.045 1523 Dihedral : 7.390 66.728 1329 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 7.37 % Allowed : 25.45 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.25), residues: 1074 helix: -0.97 (0.49), residues: 107 sheet: -0.69 (0.28), residues: 323 loop : -0.99 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 124 TYR 0.013 0.001 TYR Q 308 PHE 0.018 0.002 PHE P 528 TRP 0.010 0.001 TRP P 599 HIS 0.006 0.001 HIS P 584 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8503) covalent geometry : angle 0.66440 (11531) SS BOND : bond 0.00310 ( 15) SS BOND : angle 0.94539 ( 30) hydrogen bonds : bond 0.03671 ( 213) hydrogen bonds : angle 6.21031 ( 546) link_NAG-ASN : bond 0.00591 ( 7) link_NAG-ASN : angle 2.81233 ( 21) *********************** 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 277 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 211 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 96 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7688 (tt) REVERT: P 196 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7252 (mmt-90) REVERT: P 218 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: P 231 ASN cc_start: 0.5948 (OUTLIER) cc_final: 0.5719 (t0) REVERT: P 308 GLN cc_start: 0.6770 (pp30) cc_final: 0.6345 (pp30) REVERT: P 331 SER cc_start: 0.7744 (m) cc_final: 0.7372 (t) REVERT: P 399 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7524 (tp) REVERT: P 411 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7305 (m) REVERT: P 437 GLU cc_start: 0.7071 (tp30) cc_final: 0.6728 (tp30) REVERT: P 520 TYR cc_start: 0.7332 (m-80) cc_final: 0.7096 (m-80) REVERT: P 522 ASP cc_start: 0.7141 (m-30) cc_final: 0.6932 (m-30) REVERT: P 583 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7132 (ptmm) REVERT: Q 35 CYS cc_start: 0.4289 (OUTLIER) cc_final: 0.3023 (t) REVERT: Q 71 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7236 (tptt) REVERT: Q 84 ARG cc_start: 0.6435 (mmm160) cc_final: 0.6220 (mmm-85) REVERT: Q 102 MET cc_start: 0.0126 (ttp) cc_final: -0.0180 (ttp) REVERT: Q 130 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7692 (ttmm) REVERT: Q 134 LYS cc_start: 0.8200 (ptmm) cc_final: 0.7390 (ptmm) REVERT: Q 143 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7717 (mt) REVERT: Q 145 LEU cc_start: 0.8360 (tp) cc_final: 0.8105 (tt) REVERT: Q 155 MET cc_start: 0.7358 (mmt) cc_final: 0.6411 (mmp) REVERT: Q 163 LYS cc_start: 0.8495 (pptt) cc_final: 0.8088 (ptpp) REVERT: Q 287 ASP cc_start: 0.6563 (t0) cc_final: 0.6131 (t0) REVERT: Q 314 TYR cc_start: 0.8343 (m-10) cc_final: 0.7845 (m-10) REVERT: Q 328 GLU cc_start: 0.7266 (tp30) cc_final: 0.6870 (tp30) REVERT: Q 347 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6294 (mt-10) REVERT: Q 349 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7330 (tptm) REVERT: Q 398 LYS cc_start: 0.7824 (mttp) cc_final: 0.7319 (mttp) REVERT: Q 454 GLU cc_start: 0.6848 (pp20) cc_final: 0.6520 (pp20) REVERT: Q 455 VAL cc_start: 0.6012 (OUTLIER) cc_final: 0.5415 (p) REVERT: Q 486 GLU cc_start: 0.6420 (pt0) cc_final: 0.4875 (pt0) REVERT: Q 491 ARG cc_start: 0.6926 (ttp-170) cc_final: 0.6097 (ttp-110) outliers start: 66 outliers final: 32 residues processed: 245 average time/residue: 0.1019 time to fit residues: 33.1225 Evaluate side-chains 256 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 196 ARG Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 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 476 ILE Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 661 LEU Chi-restraints excluded: chain P residue 667 MET Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain Q residue 35 CYS Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 71 LYS Chi-restraints excluded: chain Q residue 117 GLN Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 175 ARG 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 340 GLU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 401 CYS Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN P 311 GLN Q 239 GLN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 443 GLN Q 479 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.156034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131206 restraints weight = 13904.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135347 restraints weight = 7186.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138028 restraints weight = 4478.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139808 restraints weight = 3178.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140834 restraints weight = 2476.946| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8525 Z= 0.151 Angle : 0.666 8.101 11582 Z= 0.337 Chirality : 0.048 0.235 1276 Planarity : 0.005 0.046 1523 Dihedral : 7.118 63.883 1329 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 7.25 % Allowed : 25.22 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.25), residues: 1074 helix: -1.12 (0.47), residues: 113 sheet: -0.70 (0.28), residues: 317 loop : -1.00 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 174 TYR 0.013 0.001 TYR P 349 PHE 0.018 0.002 PHE P 528 TRP 0.006 0.002 TRP P 211 HIS 0.004 0.001 HIS P 584 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8503) covalent geometry : angle 0.65547 (11531) SS BOND : bond 0.00308 ( 15) SS BOND : angle 0.90749 ( 30) hydrogen bonds : bond 0.03637 ( 213) hydrogen bonds : angle 6.16415 ( 546) link_NAG-ASN : bond 0.00541 ( 7) link_NAG-ASN : angle 2.70655 ( 21) *********************** 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 284 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 96 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7722 (tt) REVERT: P 218 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: P 231 ASN cc_start: 0.5954 (OUTLIER) cc_final: 0.5701 (t0) REVERT: P 308 GLN cc_start: 0.6882 (pp30) cc_final: 0.6530 (pp30) REVERT: P 331 SER cc_start: 0.7727 (m) cc_final: 0.7404 (t) REVERT: P 399 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7572 (tp) REVERT: P 437 GLU cc_start: 0.7042 (tp30) cc_final: 0.6730 (tp30) REVERT: P 583 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7061 (ptmm) REVERT: P 634 ARG cc_start: 0.6097 (mtm110) cc_final: 0.5516 (mtp180) REVERT: Q 63 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.5227 (mmm160) REVERT: Q 102 MET cc_start: 0.0187 (ttp) cc_final: -0.0135 (ttp) REVERT: Q 130 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7747 (ttmm) REVERT: Q 134 LYS cc_start: 0.8279 (ptmm) cc_final: 0.7971 (ptmm) REVERT: Q 143 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7723 (mt) REVERT: Q 155 MET cc_start: 0.7268 (mmt) cc_final: 0.6374 (mmp) REVERT: Q 163 LYS cc_start: 0.8486 (pptt) cc_final: 0.8074 (ptpp) REVERT: Q 174 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6709 (ttp80) REVERT: Q 287 ASP cc_start: 0.6589 (t0) cc_final: 0.6195 (t0) REVERT: Q 314 TYR cc_start: 0.8342 (m-10) cc_final: 0.7843 (m-10) REVERT: Q 328 GLU cc_start: 0.7232 (tp30) cc_final: 0.6859 (tp30) REVERT: Q 347 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6265 (mt-10) REVERT: Q 349 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7416 (tptm) REVERT: Q 375 TYR cc_start: 0.7379 (t80) cc_final: 0.7033 (t80) REVERT: Q 398 LYS cc_start: 0.7824 (mttp) cc_final: 0.7302 (mttp) REVERT: Q 449 LEU cc_start: 0.7606 (mt) cc_final: 0.7191 (mp) REVERT: Q 491 ARG cc_start: 0.6904 (ttp-170) cc_final: 0.6076 (ttp-110) outliers start: 65 outliers final: 43 residues processed: 250 average time/residue: 0.1017 time to fit residues: 33.8086 Evaluate side-chains 268 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 399 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 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 667 MET Chi-restraints excluded: chain P residue 670 HIS Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain P residue 676 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 188 VAL Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 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 429 SER Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 458 VAL Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 80 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 104 optimal weight: 0.0670 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 Q 117 GLN Q 257 GLN Q 332 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131267 restraints weight = 13595.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135348 restraints weight = 7127.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138020 restraints weight = 4489.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139602 restraints weight = 3196.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140845 restraints weight = 2537.228| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8525 Z= 0.154 Angle : 0.686 8.774 11582 Z= 0.346 Chirality : 0.048 0.226 1276 Planarity : 0.005 0.045 1523 Dihedral : 6.931 60.218 1329 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 7.14 % Allowed : 26.79 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.25), residues: 1074 helix: -1.15 (0.47), residues: 113 sheet: -0.71 (0.28), residues: 314 loop : -0.96 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 196 TYR 0.012 0.001 TYR P 349 PHE 0.019 0.002 PHE Q 426 TRP 0.007 0.001 TRP Q 267 HIS 0.004 0.001 HIS Q 321 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8503) covalent geometry : angle 0.67582 (11531) SS BOND : bond 0.00307 ( 15) SS BOND : angle 0.98872 ( 30) hydrogen bonds : bond 0.03591 ( 213) hydrogen bonds : angle 6.04165 ( 546) link_NAG-ASN : bond 0.00536 ( 7) link_NAG-ASN : angle 2.70563 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 207 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 96 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7671 (tt) REVERT: P 218 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: P 231 ASN cc_start: 0.5943 (OUTLIER) cc_final: 0.5693 (t0) REVERT: P 308 GLN cc_start: 0.6979 (pp30) cc_final: 0.6656 (pp30) REVERT: P 331 SER cc_start: 0.7710 (m) cc_final: 0.7402 (t) REVERT: P 367 SER cc_start: 0.7057 (t) cc_final: 0.6591 (m) REVERT: P 437 GLU cc_start: 0.7022 (tp30) cc_final: 0.6756 (tp30) REVERT: P 583 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7067 (ptmm) REVERT: P 623 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7436 (pt) REVERT: P 634 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.5542 (mtp180) REVERT: P 677 HIS cc_start: 0.7772 (t-90) cc_final: 0.7484 (t-90) REVERT: Q 63 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5152 (mmm160) REVERT: Q 102 MET cc_start: 0.0195 (ttp) cc_final: -0.0129 (ttp) REVERT: Q 124 ARG cc_start: 0.5369 (mtt180) cc_final: 0.5044 (mtm180) REVERT: Q 143 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7848 (mt) REVERT: Q 155 MET cc_start: 0.7302 (mmt) cc_final: 0.6461 (mmp) REVERT: Q 163 LYS cc_start: 0.8483 (pptt) cc_final: 0.7996 (ptpp) REVERT: Q 174 ARG cc_start: 0.7179 (ttp80) cc_final: 0.6952 (ttp80) REVERT: Q 287 ASP cc_start: 0.6675 (t0) cc_final: 0.6296 (t0) REVERT: Q 314 TYR cc_start: 0.8345 (m-10) cc_final: 0.7931 (m-10) REVERT: Q 328 GLU cc_start: 0.7207 (tp30) cc_final: 0.6871 (tp30) REVERT: Q 347 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6312 (mt-10) REVERT: Q 349 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7424 (tptm) REVERT: Q 429 SER cc_start: 0.5650 (OUTLIER) cc_final: 0.5231 (p) REVERT: Q 445 LYS cc_start: 0.6817 (mttt) cc_final: 0.6439 (mttt) REVERT: Q 449 LEU cc_start: 0.7636 (mt) cc_final: 0.7220 (mp) REVERT: Q 491 ARG cc_start: 0.6938 (ttp-170) cc_final: 0.6107 (ttp-110) outliers start: 64 outliers final: 36 residues processed: 239 average time/residue: 0.0983 time to fit residues: 31.7883 Evaluate side-chains 256 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 623 LEU Chi-restraints excluded: chain P residue 634 ARG 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 63 ARG Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 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 429 SER Chi-restraints excluded: chain Q residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN Q 117 GLN Q 257 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.154203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130308 restraints weight = 13802.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134277 restraints weight = 7286.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136893 restraints weight = 4554.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.138456 restraints weight = 3210.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139653 restraints weight = 2516.610| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8525 Z= 0.186 Angle : 0.706 10.157 11582 Z= 0.356 Chirality : 0.048 0.216 1276 Planarity : 0.005 0.043 1523 Dihedral : 6.849 56.939 1329 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 6.36 % Allowed : 27.57 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.25), residues: 1074 helix: -1.19 (0.48), residues: 112 sheet: -0.65 (0.29), residues: 314 loop : -0.93 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 196 TYR 0.020 0.002 TYR P 276 PHE 0.021 0.002 PHE Q 426 TRP 0.009 0.002 TRP P 496 HIS 0.004 0.001 HIS Q 321 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8503) covalent geometry : angle 0.69609 (11531) SS BOND : bond 0.00440 ( 15) SS BOND : angle 1.03227 ( 30) hydrogen bonds : bond 0.03718 ( 213) hydrogen bonds : angle 6.13719 ( 546) link_NAG-ASN : bond 0.00490 ( 7) link_NAG-ASN : angle 2.74521 ( 21) *********************** 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 281 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 96 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7766 (tt) REVERT: P 218 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: P 231 ASN cc_start: 0.6011 (OUTLIER) cc_final: 0.5764 (t0) REVERT: P 308 GLN cc_start: 0.7077 (pp30) cc_final: 0.6722 (pp30) REVERT: P 331 SER cc_start: 0.7853 (m) cc_final: 0.7554 (t) REVERT: P 367 SER cc_start: 0.7135 (t) cc_final: 0.6678 (m) REVERT: P 393 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7630 (mp) REVERT: P 509 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8021 (pp) REVERT: P 583 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7074 (ptmm) REVERT: P 634 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5660 (mtp180) REVERT: P 677 HIS cc_start: 0.7973 (t-90) cc_final: 0.7565 (t-90) REVERT: Q 102 MET cc_start: 0.0211 (ttp) cc_final: -0.0117 (ttp) REVERT: Q 112 THR cc_start: 0.7315 (p) cc_final: 0.7062 (p) REVERT: Q 122 LYS cc_start: 0.7583 (ptmt) cc_final: 0.7150 (ptmt) REVERT: Q 124 ARG cc_start: 0.5602 (mtt180) cc_final: 0.5239 (mtt180) REVERT: Q 130 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7597 (ttmm) REVERT: Q 134 LYS cc_start: 0.8403 (ptmm) cc_final: 0.8108 (ptmm) REVERT: Q 145 LEU cc_start: 0.8378 (tp) cc_final: 0.8126 (tt) REVERT: Q 155 MET cc_start: 0.7348 (mmt) cc_final: 0.6427 (mmp) REVERT: Q 163 LYS cc_start: 0.8492 (pptt) cc_final: 0.8089 (pttt) REVERT: Q 287 ASP cc_start: 0.6761 (t0) cc_final: 0.6327 (t0) REVERT: Q 314 TYR cc_start: 0.8375 (m-10) cc_final: 0.7985 (m-10) REVERT: Q 328 GLU cc_start: 0.7220 (tp30) cc_final: 0.6890 (tp30) REVERT: Q 339 GLU cc_start: 0.7108 (tp30) cc_final: 0.6822 (tp30) REVERT: Q 347 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6401 (mt-10) REVERT: Q 349 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7405 (tptm) REVERT: Q 491 ARG cc_start: 0.6945 (ttp-170) cc_final: 0.6132 (ttp-110) outliers start: 57 outliers final: 38 residues processed: 250 average time/residue: 0.0914 time to fit residues: 30.7466 Evaluate side-chains 264 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 531 ASP Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 623 LEU Chi-restraints excluded: chain P residue 634 ARG Chi-restraints excluded: chain P residue 672 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 271 THR 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 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 31 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.129349 restraints weight = 13655.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133321 restraints weight = 7295.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135889 restraints weight = 4604.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137615 restraints weight = 3267.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138701 restraints weight = 2532.768| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8525 Z= 0.173 Angle : 0.706 9.488 11582 Z= 0.357 Chirality : 0.047 0.205 1276 Planarity : 0.005 0.043 1523 Dihedral : 6.703 53.282 1329 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 6.03 % Allowed : 28.91 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.25), residues: 1074 helix: -1.26 (0.47), residues: 113 sheet: -0.70 (0.29), residues: 313 loop : -0.97 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 174 TYR 0.016 0.001 TYR P 276 PHE 0.021 0.002 PHE Q 426 TRP 0.022 0.002 TRP Q 267 HIS 0.004 0.001 HIS Q 321 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8503) covalent geometry : angle 0.69603 (11531) SS BOND : bond 0.00274 ( 15) SS BOND : angle 1.01030 ( 30) hydrogen bonds : bond 0.03590 ( 213) hydrogen bonds : angle 6.12405 ( 546) link_NAG-ASN : bond 0.00499 ( 7) link_NAG-ASN : angle 2.74737 ( 21) *********************** 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 280 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: P 96 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7752 (tt) REVERT: P 144 GLN cc_start: 0.8508 (mp10) cc_final: 0.8195 (mp10) REVERT: P 218 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: P 231 ASN cc_start: 0.6028 (OUTLIER) cc_final: 0.5769 (t0) REVERT: P 308 GLN cc_start: 0.7091 (pp30) cc_final: 0.6750 (pp30) REVERT: P 331 SER cc_start: 0.7812 (m) cc_final: 0.7507 (t) REVERT: P 367 SER cc_start: 0.7107 (t) cc_final: 0.6659 (m) REVERT: P 393 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7648 (mp) REVERT: P 437 GLU cc_start: 0.6984 (tp30) cc_final: 0.6621 (tp30) REVERT: P 583 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7106 (ptmm) REVERT: P 634 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5696 (mtp180) REVERT: P 677 HIS cc_start: 0.7996 (t-90) cc_final: 0.7570 (t-90) REVERT: Q 102 MET cc_start: 0.0190 (ttp) cc_final: -0.0137 (ttp) REVERT: Q 130 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7602 (ttmm) REVERT: Q 134 LYS cc_start: 0.8447 (ptmm) cc_final: 0.8136 (ptmm) REVERT: Q 146 TYR cc_start: 0.7953 (t80) cc_final: 0.7687 (t80) REVERT: Q 155 MET cc_start: 0.7338 (mmt) cc_final: 0.6460 (mmp) REVERT: Q 163 LYS cc_start: 0.8514 (pptt) cc_final: 0.7996 (pttt) REVERT: Q 287 ASP cc_start: 0.6766 (t0) cc_final: 0.6287 (t0) REVERT: Q 314 TYR cc_start: 0.8381 (m-10) cc_final: 0.8014 (m-10) REVERT: Q 328 GLU cc_start: 0.7194 (tp30) cc_final: 0.6897 (tp30) REVERT: Q 339 GLU cc_start: 0.7138 (tp30) cc_final: 0.6869 (tp30) REVERT: Q 347 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6452 (mt-10) REVERT: Q 349 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7360 (tptm) REVERT: Q 422 ASP cc_start: 0.6181 (t0) cc_final: 0.5848 (m-30) REVERT: Q 491 ARG cc_start: 0.6820 (ttp-170) cc_final: 0.6058 (ttp-110) outliers start: 54 outliers final: 39 residues processed: 249 average time/residue: 0.1047 time to fit residues: 34.9478 Evaluate side-chains 270 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 445 LEU Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 623 LEU Chi-restraints excluded: chain P residue 634 ARG Chi-restraints excluded: chain P residue 676 LEU Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 257 GLN Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 294 VAL 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 424 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 0.0000 chunk 81 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN Q 117 GLN 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 = 0.3984 r_free = 0.3984 target = 0.154080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129797 restraints weight = 13698.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133872 restraints weight = 7240.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136553 restraints weight = 4529.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138309 restraints weight = 3191.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139325 restraints weight = 2472.069| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8525 Z= 0.156 Angle : 0.718 13.006 11582 Z= 0.359 Chirality : 0.047 0.197 1276 Planarity : 0.005 0.042 1523 Dihedral : 6.494 49.981 1329 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.69 % Allowed : 29.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.25), residues: 1074 helix: -1.22 (0.47), residues: 113 sheet: -0.67 (0.29), residues: 314 loop : -0.97 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 174 TYR 0.013 0.001 TYR P 276 PHE 0.019 0.002 PHE Q 426 TRP 0.007 0.002 TRP P 496 HIS 0.004 0.001 HIS Q 321 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8503) covalent geometry : angle 0.70879 (11531) SS BOND : bond 0.00300 ( 15) SS BOND : angle 1.02468 ( 30) hydrogen bonds : bond 0.03478 ( 213) hydrogen bonds : angle 6.04161 ( 546) link_NAG-ASN : bond 0.00451 ( 7) link_NAG-ASN : angle 2.68352 ( 21) *********************** 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 274 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 96 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7778 (tt) REVERT: P 144 GLN cc_start: 0.8536 (mp10) cc_final: 0.8167 (mp10) REVERT: P 218 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: P 231 ASN cc_start: 0.6026 (OUTLIER) cc_final: 0.5766 (t0) REVERT: P 308 GLN cc_start: 0.7160 (pp30) cc_final: 0.6821 (pp30) REVERT: P 331 SER cc_start: 0.7824 (m) cc_final: 0.7503 (t) REVERT: P 367 SER cc_start: 0.7241 (t) cc_final: 0.6760 (m) REVERT: P 393 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7659 (mp) REVERT: P 437 GLU cc_start: 0.6991 (tp30) cc_final: 0.6632 (tp30) REVERT: P 583 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7110 (ptmm) REVERT: P 634 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5747 (mtp180) REVERT: P 677 HIS cc_start: 0.7962 (t-90) cc_final: 0.7556 (t-90) REVERT: Q 102 MET cc_start: 0.0176 (ttp) cc_final: -0.0147 (ttp) REVERT: Q 136 LYS cc_start: 0.8472 (pttt) cc_final: 0.8014 (ptmt) REVERT: Q 146 TYR cc_start: 0.7980 (t80) cc_final: 0.7769 (t80) REVERT: Q 155 MET cc_start: 0.7348 (mmt) cc_final: 0.6485 (mmp) REVERT: Q 163 LYS cc_start: 0.8504 (pptt) cc_final: 0.8024 (pttt) REVERT: Q 287 ASP cc_start: 0.6761 (t0) cc_final: 0.6290 (t0) REVERT: Q 314 TYR cc_start: 0.8407 (m-10) cc_final: 0.7974 (m-10) REVERT: Q 339 GLU cc_start: 0.7170 (tp30) cc_final: 0.6919 (tp30) REVERT: Q 347 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6504 (mt-10) REVERT: Q 349 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7304 (tptm) REVERT: Q 422 ASP cc_start: 0.6169 (t0) cc_final: 0.5866 (m-30) REVERT: Q 491 ARG cc_start: 0.6836 (ttp-170) cc_final: 0.6068 (ttp-110) outliers start: 51 outliers final: 35 residues processed: 245 average time/residue: 0.0868 time to fit residues: 28.8851 Evaluate side-chains 271 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 187 SER Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE Chi-restraints excluded: chain P residue 530 VAL Chi-restraints excluded: chain P residue 554 MET Chi-restraints excluded: chain P residue 583 LYS Chi-restraints excluded: chain P residue 589 ILE Chi-restraints excluded: chain P residue 634 ARG Chi-restraints excluded: chain Q residue 51 THR Chi-restraints excluded: chain Q residue 63 ARG Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 143 ILE Chi-restraints excluded: chain Q residue 218 SER Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 289 LYS Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 300 GLN Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 367 VAL Chi-restraints excluded: chain Q residue 382 VAL Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.0050 chunk 33 optimal weight: 0.0000 chunk 61 optimal weight: 0.2980 chunk 75 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 255 GLN Q 117 GLN ** Q 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 332 GLN Q 350 ASN ** Q 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.155067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131040 restraints weight = 13717.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135031 restraints weight = 7287.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137670 restraints weight = 4573.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139351 restraints weight = 3227.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140532 restraints weight = 2509.667| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.5513 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= 0.134 Angle : 0.714 15.079 11582 Z= 0.355 Chirality : 0.047 0.199 1276 Planarity : 0.005 0.041 1523 Dihedral : 6.134 44.860 1329 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.80 % Allowed : 29.58 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.25), residues: 1074 helix: -1.24 (0.46), residues: 113 sheet: -0.61 (0.28), residues: 320 loop : -0.94 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 174 TYR 0.019 0.001 TYR Q 308 PHE 0.015 0.002 PHE Q 426 TRP 0.007 0.001 TRP P 496 HIS 0.005 0.001 HIS Q 321 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8503) covalent geometry : angle 0.70596 (11531) SS BOND : bond 0.00252 ( 15) SS BOND : angle 0.91304 ( 30) hydrogen bonds : bond 0.03329 ( 213) hydrogen bonds : angle 5.94353 ( 546) link_NAG-ASN : bond 0.00447 ( 7) link_NAG-ASN : angle 2.57103 ( 21) ********************** 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: 43 poor density : 221 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 96 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7759 (tt) REVERT: P 144 GLN cc_start: 0.8509 (mp10) cc_final: 0.8230 (mp10) REVERT: P 218 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: P 231 ASN cc_start: 0.5977 (OUTLIER) cc_final: 0.5702 (t0) REVERT: P 308 GLN cc_start: 0.7162 (pp30) cc_final: 0.6841 (pp30) REVERT: P 331 SER cc_start: 0.7742 (m) cc_final: 0.7474 (t) REVERT: P 367 SER cc_start: 0.7106 (t) cc_final: 0.6770 (m) REVERT: P 393 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7674 (mp) REVERT: P 437 GLU cc_start: 0.6973 (tp30) cc_final: 0.6606 (tp30) REVERT: P 583 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7098 (ptmm) REVERT: P 677 HIS cc_start: 0.7905 (t-90) cc_final: 0.7510 (t-90) REVERT: Q 63 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5891 (mmt180) REVERT: Q 84 ARG cc_start: 0.6842 (mmm160) cc_final: 0.6613 (mmm-85) REVERT: Q 102 MET cc_start: 0.0179 (ttp) cc_final: -0.0147 (ttp) REVERT: Q 146 TYR cc_start: 0.7987 (t80) cc_final: 0.7779 (t80) REVERT: Q 155 MET cc_start: 0.7284 (mmt) cc_final: 0.6402 (mmp) REVERT: Q 163 LYS cc_start: 0.8539 (pptt) cc_final: 0.8065 (pttt) REVERT: Q 174 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6801 (ttp80) REVERT: Q 257 GLN cc_start: 0.7968 (tp40) cc_final: 0.7752 (tt0) REVERT: Q 287 ASP cc_start: 0.6717 (t0) cc_final: 0.6309 (t0) REVERT: Q 314 TYR cc_start: 0.8373 (m-10) cc_final: 0.8004 (m-10) REVERT: Q 339 GLU cc_start: 0.7148 (tp30) cc_final: 0.6880 (tp30) REVERT: Q 347 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6435 (mt-10) REVERT: Q 349 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7273 (tptm) REVERT: Q 422 ASP cc_start: 0.6201 (t0) cc_final: 0.5900 (m-30) REVERT: Q 491 ARG cc_start: 0.6838 (ttp-170) cc_final: 0.6074 (ttp-110) outliers start: 43 outliers final: 28 residues processed: 244 average time/residue: 0.0920 time to fit residues: 30.5454 Evaluate side-chains 261 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 115 SER Chi-restraints excluded: chain P residue 189 GLN Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 202 ILE Chi-restraints excluded: chain P residue 218 GLN Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 277 PHE Chi-restraints excluded: chain P residue 289 GLN Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 374 TYR Chi-restraints excluded: chain P residue 382 THR Chi-restraints excluded: chain P residue 393 LEU Chi-restraints excluded: chain P residue 398 LEU Chi-restraints excluded: chain P residue 403 THR Chi-restraints excluded: chain P residue 468 GLU Chi-restraints excluded: chain P residue 476 ILE 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 63 ARG Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 238 GLN Chi-restraints excluded: chain Q residue 241 ILE Chi-restraints excluded: chain Q residue 271 THR Chi-restraints excluded: chain Q residue 294 VAL Chi-restraints excluded: chain Q residue 322 LEU Chi-restraints excluded: chain Q residue 349 LYS Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain Q residue 452 THR Chi-restraints excluded: chain Q residue 462 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 104 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN ** 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 = 0.3982 r_free = 0.3982 target = 0.154066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129886 restraints weight = 13672.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133908 restraints weight = 7263.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136563 restraints weight = 4564.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138324 restraints weight = 3222.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139359 restraints weight = 2486.334| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8525 Z= 0.156 Angle : 0.725 14.739 11582 Z= 0.359 Chirality : 0.047 0.192 1276 Planarity : 0.005 0.048 1523 Dihedral : 6.043 44.824 1329 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.13 % Allowed : 30.25 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.25), residues: 1074 helix: -1.19 (0.47), residues: 113 sheet: -0.60 (0.28), residues: 321 loop : -0.94 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 174 TYR 0.017 0.001 TYR P 276 PHE 0.019 0.002 PHE Q 426 TRP 0.009 0.001 TRP P 496 HIS 0.006 0.001 HIS Q 321 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8503) covalent geometry : angle 0.71681 (11531) SS BOND : bond 0.00245 ( 15) SS BOND : angle 0.94826 ( 30) hydrogen bonds : bond 0.03447 ( 213) hydrogen bonds : angle 5.89624 ( 546) link_NAG-ASN : bond 0.00430 ( 7) link_NAG-ASN : angle 2.57067 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.70 seconds wall clock time: 30 minutes 0.70 seconds (1800.70 seconds total)