Starting phenix.real_space_refine
on Wed Feb 12 11:08:37 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/6irt_9722/02_2025/6irt_9722_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6irt_9722/02_2025/6irt_9722.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6irt_9722/02_2025/6irt_9722.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6irt_9722/02_2025/6irt_9722.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6irt_9722/02_2025/6irt_9722_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6irt_9722/02_2025/6irt_9722_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      27      5.16       5
     C    4815      2.51       5
     N    1173      2.21       5
     O    1331      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7348
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446}
    Chain: "B"
      Number of atoms: 3479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3479
          Classifications: {'peptide': 457}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 432}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 31
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 107
          Unusual residues: {'3PH': 2, 'AUU': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 4.79, per 1000 atoms: 0.65
  Number of scatterers: 7348
  At special positions: 0
  Unit cell: (82.916, 84.007, 124.374, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P       2     15.00
     O    1331      8.00
     N    1173      7.00
     C    4815      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS B 164 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 507 "
      " NAG D   1 " - " ASN A 366 "
      " NAG E   1 " - " ASN A 382 "
      " NAG F   1 " - " ASN A 425 "
  Time building additional restraints: 2.00
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 3 sheets defined
      58.4% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 168 through 175
      removed outlier: 3.604A  pdb=" N   LYS A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   VAL A 173 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 185
    Processing helix  chain 'A' and resid 185 through 208
      removed outlier: 3.616A  pdb=" N   PHE A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TRP A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   MET A 197 " --> pdb=" O   GLY A 193 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLY A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ILE A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ILE A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 222
      removed outlier: 3.735A  pdb=" N   HIS A 221 " --> pdb=" O   LYS A 218 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR A 222 " --> pdb=" O   TRP A 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 222'
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 241 through 246
    Processing helix  chain 'A' and resid 248 through 256
      removed outlier: 3.876A  pdb=" N   SER A 254 " --> pdb=" O   ASP A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 301
      removed outlier: 3.866A  pdb=" N   LYS A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 342
      removed outlier: 4.203A  pdb=" N   GLU A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLN A 340 " --> pdb=" O   GLU A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 356 through 370
      removed outlier: 3.768A  pdb=" N   PHE A 360 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   GLU A 363 " --> pdb=" O   SER A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.665A  pdb=" N   LEU A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 428
      removed outlier: 3.787A  pdb=" N   GLN A 422 " --> pdb=" O   SER A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 461
      removed outlier: 3.522A  pdb=" N   GLN A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LEU A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 497
      removed outlier: 4.405A  pdb=" N   PHE A 497 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 519 through 532
      removed outlier: 3.595A  pdb=" N   ARG A 526 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   SER A 532 " --> pdb=" O   SER A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 540
      removed outlier: 3.784A  pdb=" N   HIS A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 63
      removed outlier: 4.369A  pdb=" N   ALA B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ILE B  58 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE B  63 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 74
      removed outlier: 4.759A  pdb=" N   THR B  71 " --> pdb=" O   ILE B  68 " (cutoff:3.500A)
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.607A  pdb=" N   LEU B  86 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   TRP B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY B  93 " --> pdb=" O   TRP B  89 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ILE B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 124
      removed outlier: 3.569A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 139
    Processing helix  chain 'B' and resid 139 through 158
      removed outlier: 3.581A  pdb=" N   SER B 143 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLN B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ILE B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B 156 " --> pdb=" O   PHE B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 187
      removed outlier: 4.333A  pdb=" N   LEU B 173 " --> pdb=" O   GLU B 169 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   VAL B 174 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA B 175 " --> pdb=" O   ALA B 171 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LEU B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU B 182 " --> pdb=" O   CYS B 178 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 199
      removed outlier: 4.151A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 222
      removed outlier: 3.544A  pdb=" N   LEU B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE B 219 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY B 222 " --> pdb=" O   GLN B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 235
      removed outlier: 4.399A  pdb=" N   GLU B 234 " --> pdb=" O   PHE B 231 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLY B 235 " --> pdb=" O   SER B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 251
      removed outlier: 3.633A  pdb=" N   SER B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 263
      removed outlier: 3.727A  pdb=" N   VAL B 263 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 260 through 263'
    Processing helix  chain 'B' and resid 264 through 269
      removed outlier: 4.079A  pdb=" N   ILE B 268 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 300
      removed outlier: 3.694A  pdb=" N   ALA B 277 " --> pdb=" O   ASN B 273 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE B 279 " --> pdb=" O   PRO B 275 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE B 280 " --> pdb=" O   LEU B 276 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU B 282 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
      removed outlier: 3.730A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 308
    Processing helix  chain 'B' and resid 310 through 320
      removed outlier: 4.029A  pdb=" N   ASP B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   HIS B 319 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 320 " --> pdb=" O   GLY B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 333
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.550A  pdb=" N   VAL B 339 " --> pdb=" O   CYS B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 343
    Processing helix  chain 'B' and resid 344 through 355
      removed outlier: 3.954A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU B 349 " --> pdb=" O   THR B 345 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE B 350 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   VAL B 352 " --> pdb=" O   ARG B 348 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG B 355 " --> pdb=" O   PHE B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 386
      removed outlier: 3.675A  pdb=" N   PHE B 379 " --> pdb=" O   PRO B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 390
    Processing helix  chain 'B' and resid 393 through 421
      removed outlier: 3.509A  pdb=" N   PHE B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   PHE B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE B 412 " --> pdb=" O   VAL B 408 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ARG B 419 " --> pdb=" O   MET B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 453
      removed outlier: 3.808A  pdb=" N   ALA B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   PHE B 445 " --> pdb=" O   LEU B 441 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B 446 " --> pdb=" O   ALA B 442 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE B 447 " --> pdb=" O   CYS B 443 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   PHE B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TRP B 452 " --> pdb=" O   ALA B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 466
      removed outlier: 4.293A  pdb=" N   CYS B 458 " --> pdb=" O   THR B 454 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ILE B 460 " --> pdb=" O   VAL B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 476
    Processing helix  chain 'B' and resid 484 through 501
      removed outlier: 3.950A  pdb=" N   PHE B 490 " --> pdb=" O   LEU B 486 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401
      removed outlier: 6.562A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 378 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL A 305 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   GLN A 347 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   LEU A 307 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   TYR A 226 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268
    Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545
      removed outlier: 4.700A  pdb=" N   SER A 553 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ARG A 556 " --> pdb=" O   PHE A 564 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   ARG A 626 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   LEU A 596 " --> pdb=" O   ARG A 626 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    852 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 2.21 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 2069
        1.33 -     1.45: 1333
        1.45 -     1.57: 4077
        1.57 -     1.69: 3
        1.69 -     1.81: 42
  Bond restraints: 7524
  Sorted by residual:
  bond pdb=" C06 AUU B 603 "
       pdb=" C08 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.531  1.707 -0.176 2.00e-02 2.50e+03 7.77e+01
  bond pdb=" C04 AUU B 603 "
       pdb=" C09 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.535  1.362  0.173 2.00e-02 2.50e+03 7.53e+01
  bond pdb=" C04 AUU B 603 "
       pdb=" C08 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.533  1.699 -0.166 2.00e-02 2.50e+03 6.89e+01
  bond pdb=" C06 AUU B 603 "
       pdb=" C07 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.534  1.370  0.164 2.00e-02 2.50e+03 6.71e+01
  bond pdb=" C06 AUU B 603 "
       pdb=" C11 AUU B 603 "
    ideal  model  delta    sigma   weight residual
    1.537  1.383  0.154 2.00e-02 2.50e+03 5.94e+01
  ... (remaining 7519 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 9548
        2.19 -     4.39: 554
        4.39 -     6.58: 79
        6.58 -     8.78: 35
        8.78 -    10.97: 13
  Bond angle restraints: 10229
  Sorted by residual:
  angle pdb=" N   HIS B 319 "
        pdb=" CA  HIS B 319 "
        pdb=" C   HIS B 319 "
      ideal   model   delta    sigma   weight residual
     111.36  122.33  -10.97 1.09e+00 8.42e-01 1.01e+02
  angle pdb=" C   SER A 176 "
        pdb=" N   PRO A 177 "
        pdb=" CA  PRO A 177 "
      ideal   model   delta    sigma   weight residual
     119.84  128.89   -9.05 1.25e+00 6.40e-01 5.24e+01
  angle pdb=" N   LEU B 320 "
        pdb=" CA  LEU B 320 "
        pdb=" C   LEU B 320 "
      ideal   model   delta    sigma   weight residual
     108.34  116.69   -8.35 1.31e+00 5.83e-01 4.07e+01
  angle pdb=" C   PHE B 161 "
        pdb=" N   PRO B 162 "
        pdb=" CD  PRO B 162 "
      ideal   model   delta    sigma   weight residual
     120.60  109.75   10.85 2.20e+00 2.07e-01 2.43e+01
  angle pdb=" CA  LEU B 469 "
        pdb=" C   LEU B 469 "
        pdb=" N   PRO B 470 "
      ideal   model   delta    sigma   weight residual
     120.81  116.58    4.23 8.60e-01 1.35e+00 2.42e+01
  ... (remaining 10224 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.14: 4295
       21.14 -    42.28: 211
       42.28 -    63.42: 34
       63.42 -    84.56: 12
       84.56 -   105.70: 10
  Dihedral angle restraints: 4562
    sinusoidal: 1909
      harmonic: 2653
  Sorted by residual:
  dihedral pdb=" CB  CYS A 211 "
           pdb=" SG  CYS A 211 "
           pdb=" SG  CYS B 164 "
           pdb=" CB  CYS B 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.02   71.02     1      1.00e+01 1.00e-02 6.48e+01
  dihedral pdb=" CA  VAL B 322 "
           pdb=" C   VAL B 322 "
           pdb=" N   MET B 323 "
           pdb=" CA  MET B 323 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.31   26.69     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  GLN A 323 "
           pdb=" C   GLN A 323 "
           pdb=" N   VAL A 324 "
           pdb=" CA  VAL A 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.11  -25.89     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 4559 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.277: 1194
       0.277 -    0.553: 7
       0.553 -    0.830: 0
       0.830 -    1.106: 0
       1.106 -    1.383: 2
  Chirality restraints: 1203
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 507 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.02   -1.38 2.00e-01 2.50e+01 4.78e+01
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A 382 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.10   -1.30 2.00e-01 2.50e+01 4.22e+01
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 366 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.88    0.48 2.00e-01 2.50e+01 5.74e+00
  ... (remaining 1200 not shown)

  Planarity restraints: 1259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 366 "    0.102 2.00e-02 2.50e+03   2.65e-01 8.75e+02
        pdb=" CG  ASN A 366 "   -0.080 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 366 "    0.153 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 366 "   -0.471 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "    0.296 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 382 "   -0.123 2.00e-02 2.50e+03   2.00e-01 5.00e+02
        pdb=" CG  ASN A 382 "    0.059 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 382 "   -0.058 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 382 "    0.353 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "   -0.231 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 507 "   -0.072 2.00e-02 2.50e+03   8.36e-02 8.74e+01
        pdb=" CG  ASN A 507 "    0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 507 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 507 "    0.139 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.098 2.00e-02 2.50e+03
  ... (remaining 1256 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1762
        2.77 -     3.30: 6596
        3.30 -     3.84: 11683
        3.84 -     4.37: 13661
        4.37 -     4.90: 22977
  Nonbonded interactions: 56679
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 460 "
            pdb=" OH  TYR A 554 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER A 599 "
            pdb=" OE2 GLU A 621 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   ASP A 516 "
            pdb=" OG  SER A 522 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   THR A 460 "
            pdb=" NH1 ARG A 556 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   GLY B 107 "
            pdb=" OG  SER B 111 "
     model   vdw
     2.300 3.040
  ... (remaining 56674 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.160
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
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      :  0.012   0.176   7524  Z= 0.759
  Angle     :  1.234  10.971  10229  Z= 0.644
  Chirality :  0.088   1.383   1203
  Planarity :  0.008   0.063   1255
  Dihedral  : 14.319 105.703   2855
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  9.22 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  :  6.54 %
    Favored  : 90.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.53 (0.19), residues: 922
  helix: -4.19 (0.12), residues: 470
  sheet: -1.95 (0.65), residues: 49
  loop : -3.07 (0.26), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP B 417 
 HIS   0.009   0.004   HIS A 620 
 PHE   0.024   0.003   PHE A 552 
 TYR   0.036   0.004   TYR A 454 
 ARG   0.012   0.001   ARG A 227 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 226
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  534 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7076 (mm-30)
REVERT: B  146 TYR cc_start: 0.8686 (t80) cc_final: 0.8121 (t80)
REVERT: B  195 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7737 (ptt180)
REVERT: B  218 GLN cc_start: 0.8445 (tp40) cc_final: 0.8213 (tp40)
REVERT: B  315 PHE cc_start: 0.8297 (t80) cc_final: 0.8064 (t80)
REVERT: B  419 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7342 (mmp-170)
REVERT: B  440 ILE cc_start: 0.9232 (mt) cc_final: 0.9008 (mt)
REVERT: B  466 LEU cc_start: 0.8515 (mp) cc_final: 0.8275 (tp)
REVERT: B  478 TRP cc_start: 0.6616 (t-100) cc_final: 0.6280 (t-100)
REVERT: B  501 GLN cc_start: 0.8096 (tt0) cc_final: 0.7827 (tm-30)
  outliers start: 23
  outliers final: 5
  residues processed: 234
  average time/residue: 0.2185
  time to fit residues: 66.2354
Evaluate side-chains
  139 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 134
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  490 MET
Chi-restraints excluded: chain B residue   63 ILE
Chi-restraints excluded: chain B residue  131 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
A 221 HIS
A 232 GLN
A 268 ASN
A 388 GLN
A 483 GLN
A 561 ASN
A 620 HIS
B 293 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.122200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.095196 restraints weight = 13335.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.098901 restraints weight = 6844.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101351 restraints weight = 4691.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7524  Z= 0.229
  Angle     :  0.837  12.596  10229  Z= 0.405
  Chirality :  0.051   0.679   1203
  Planarity :  0.006   0.043   1255
  Dihedral  : 12.781  90.249   1274
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.70 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.74 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.02 (0.22), residues: 922
  helix: -2.57 (0.17), residues: 489
  sheet: -1.89 (0.62), residues: 60
  loop : -2.76 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 134 
 HIS   0.005   0.001   HIS B 319 
 PHE   0.021   0.002   PHE B  95 
 TYR   0.013   0.002   TYR B 318 
 ARG   0.010   0.001   ARG B 355 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.7835 (ttp) cc_final: 0.7570 (mmp)
REVERT: A  279 LEU cc_start: 0.8087 (pp) cc_final: 0.7799 (pp)
REVERT: B  120 MET cc_start: 0.9081 (tpp) cc_final: 0.8822 (tpp)
REVERT: B  146 TYR cc_start: 0.8627 (t80) cc_final: 0.8118 (t80)
REVERT: B  195 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7756 (ptt180)
REVERT: B  218 GLN cc_start: 0.8691 (tp40) cc_final: 0.8415 (tp-100)
REVERT: B  254 TYR cc_start: 0.8739 (m-80) cc_final: 0.8297 (m-80)
REVERT: B  352 VAL cc_start: 0.9387 (t) cc_final: 0.9067 (t)
REVERT: B  466 LEU cc_start: 0.8632 (mp) cc_final: 0.8302 (tp)
REVERT: B  478 TRP cc_start: 0.6522 (t-100) cc_final: 0.6235 (t-100)
REVERT: B  499 LEU cc_start: 0.9123 (tt) cc_final: 0.8887 (tt)
  outliers start: 20
  outliers final: 10
  residues processed: 185
  average time/residue: 0.1651
  time to fit residues: 42.6402
Evaluate side-chains
  151 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  393 ILE
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 30 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 317 ASN
B 497 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.117679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.090683 restraints weight = 13923.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.094201 restraints weight = 7371.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.096448 restraints weight = 5134.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7524  Z= 0.257
  Angle     :  0.755  10.592  10229  Z= 0.367
  Chirality :  0.047   0.430   1203
  Planarity :  0.005   0.040   1255
  Dihedral  : 10.966  89.919   1267
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.70 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 14.79 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.25), residues: 922
  helix: -1.35 (0.21), residues: 491
  sheet: -1.19 (0.67), residues: 54
  loop : -2.55 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.023   0.002   PHE B  95 
 TYR   0.017   0.002   TYR B 119 
 ARG   0.005   0.001   ARG B 272 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 151
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.7849 (ttp) cc_final: 0.7627 (mmp)
REVERT: A  534 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6438 (mt-10)
REVERT: B  146 TYR cc_start: 0.8688 (t80) cc_final: 0.8191 (t80)
REVERT: B  195 ARG cc_start: 0.7997 (mtm110) cc_final: 0.7718 (ptt180)
REVERT: B  218 GLN cc_start: 0.8786 (tp40) cc_final: 0.8492 (tp-100)
REVERT: B  254 TYR cc_start: 0.8782 (m-80) cc_final: 0.8187 (m-80)
REVERT: B  318 TYR cc_start: 0.6896 (t80) cc_final: 0.6608 (t80)
REVERT: B  352 VAL cc_start: 0.9257 (t) cc_final: 0.8376 (t)
REVERT: B  466 LEU cc_start: 0.8664 (mp) cc_final: 0.8343 (tp)
REVERT: B  499 LEU cc_start: 0.9029 (tt) cc_final: 0.8819 (tt)
  outliers start: 35
  outliers final: 18
  residues processed: 169
  average time/residue: 0.1521
  time to fit residues: 36.9230
Evaluate side-chains
  152 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  427 ARG
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 24 optimal weight:    0.2980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 317 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.121415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.093952 restraints weight = 13590.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.097672 restraints weight = 6943.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.100079 restraints weight = 4757.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7524  Z= 0.284
  Angle     :  0.736   9.717  10229  Z= 0.360
  Chirality :  0.048   0.409   1203
  Planarity :  0.005   0.041   1255
  Dihedral  : 10.168  86.066   1264
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.81 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.49 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.26), residues: 922
  helix: -0.88 (0.22), residues: 504
  sheet: -1.06 (0.68), residues: 54
  loop : -2.41 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 405 
 HIS   0.006   0.002   HIS B 367 
 PHE   0.024   0.002   PHE B  95 
 TYR   0.017   0.002   TYR A 405 
 ARG   0.004   0.000   ARG B 272 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 137
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  146 TYR cc_start: 0.8652 (t80) cc_final: 0.8253 (t80)
REVERT: B  195 ARG cc_start: 0.7977 (mtm110) cc_final: 0.7757 (ptt180)
REVERT: B  466 LEU cc_start: 0.8676 (mp) cc_final: 0.8348 (tp)
  outliers start: 27
  outliers final: 22
  residues processed: 150
  average time/residue: 0.1536
  time to fit residues: 33.2471
Evaluate side-chains
  150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  414 GLU
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  320 LEU
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  432 ASN
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 53 optimal weight:    0.0770
   chunk 74 optimal weight:    0.0870
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.4516

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.125235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.098104 restraints weight = 13109.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.102024 restraints weight = 6593.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.104567 restraints weight = 4458.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7524  Z= 0.171
  Angle     :  0.697   9.679  10229  Z= 0.331
  Chirality :  0.045   0.428   1203
  Planarity :  0.004   0.038   1255
  Dihedral  :  9.355  86.767   1264
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  7.16 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.06 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.27), residues: 922
  helix: -0.34 (0.23), residues: 499
  sheet: -0.63 (0.69), residues: 55
  loop : -2.34 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 405 
 HIS   0.007   0.001   HIS B 367 
 PHE   0.022   0.001   PHE B  95 
 TYR   0.015   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 146
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  469 TYR cc_start: 0.9199 (p90) cc_final: 0.8973 (p90)
REVERT: B  120 MET cc_start: 0.9081 (tpp) cc_final: 0.8734 (tpp)
REVERT: B  146 TYR cc_start: 0.8656 (t80) cc_final: 0.8228 (t80)
REVERT: B  195 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7697 (ptt180)
REVERT: B  254 TYR cc_start: 0.8752 (m-80) cc_final: 0.8290 (m-80)
REVERT: B  265 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7067 (tm-30)
REVERT: B  438 PHE cc_start: 0.8059 (t80) cc_final: 0.7788 (t80)
REVERT: B  453 LYS cc_start: 0.8431 (tppt) cc_final: 0.7938 (mmtt)
REVERT: B  466 LEU cc_start: 0.8625 (mp) cc_final: 0.8316 (tp)
  outliers start: 23
  outliers final: 14
  residues processed: 156
  average time/residue: 0.1655
  time to fit residues: 38.0255
Evaluate side-chains
  148 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 54 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.124658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.097169 restraints weight = 13236.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101011 restraints weight = 6597.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.103483 restraints weight = 4492.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7524  Z= 0.193
  Angle     :  0.694   9.017  10229  Z= 0.333
  Chirality :  0.046   0.410   1203
  Planarity :  0.004   0.039   1255
  Dihedral  :  8.891  86.222   1262
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.81 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 17.80 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.27), residues: 922
  helix: -0.10 (0.23), residues: 501
  sheet: -0.45 (0.69), residues: 55
  loop : -2.33 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.026   0.001   PHE B  95 
 TYR   0.017   0.001   TYR A 405 
 ARG   0.004   0.000   ARG A 227 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 LEU cc_start: 0.9253 (mt) cc_final: 0.8944 (mt)
REVERT: A  272 ASP cc_start: 0.7875 (t0) cc_final: 0.7665 (p0)
REVERT: A  469 TYR cc_start: 0.9185 (p90) cc_final: 0.8940 (p90)
REVERT: B  146 TYR cc_start: 0.8664 (t80) cc_final: 0.8278 (t80)
REVERT: B  195 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7721 (ptt180)
REVERT: B  254 TYR cc_start: 0.8792 (m-80) cc_final: 0.8266 (m-80)
REVERT: B  438 PHE cc_start: 0.8156 (t80) cc_final: 0.7738 (t80)
REVERT: B  453 LYS cc_start: 0.8431 (tppt) cc_final: 0.7918 (mmtt)
REVERT: B  466 LEU cc_start: 0.8619 (mp) cc_final: 0.8326 (tp)
REVERT: B  501 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8083 (tm-30)
  outliers start: 29
  outliers final: 23
  residues processed: 156
  average time/residue: 0.1560
  time to fit residues: 34.9781
Evaluate side-chains
  159 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 136
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  413 ILE
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  467 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 72 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.124823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.097054 restraints weight = 13342.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.100942 restraints weight = 6646.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.103492 restraints weight = 4545.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.4573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7524  Z= 0.195
  Angle     :  0.691   8.494  10229  Z= 0.329
  Chirality :  0.045   0.407   1203
  Planarity :  0.004   0.040   1255
  Dihedral  :  8.590  86.210   1262
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.81 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.37 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.28), residues: 922
  helix:  0.08 (0.24), residues: 499
  sheet: -0.18 (0.68), residues: 62
  loop : -2.29 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 319 
 PHE   0.024   0.002   PHE B  95 
 TYR   0.016   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 LEU cc_start: 0.9230 (mt) cc_final: 0.8937 (mt)
REVERT: A  272 ASP cc_start: 0.7899 (t0) cc_final: 0.7663 (p0)
REVERT: A  469 TYR cc_start: 0.9169 (p90) cc_final: 0.8902 (p90)
REVERT: B  120 MET cc_start: 0.9101 (tpp) cc_final: 0.8862 (mmm)
REVERT: B  146 TYR cc_start: 0.8674 (t80) cc_final: 0.8292 (t80)
REVERT: B  195 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7736 (ptt180)
REVERT: B  206 LEU cc_start: 0.9009 (tt) cc_final: 0.8809 (pp)
REVERT: B  254 TYR cc_start: 0.8812 (m-80) cc_final: 0.8271 (m-80)
REVERT: B  265 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7104 (tm-30)
REVERT: B  318 TYR cc_start: 0.7292 (t80) cc_final: 0.6995 (t80)
REVERT: B  438 PHE cc_start: 0.8146 (t80) cc_final: 0.7848 (t80)
REVERT: B  453 LYS cc_start: 0.8465 (tppt) cc_final: 0.7925 (mmtt)
REVERT: B  466 LEU cc_start: 0.8588 (mp) cc_final: 0.8320 (tp)
REVERT: B  501 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8026 (tm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 155
  average time/residue: 0.1577
  time to fit residues: 35.4135
Evaluate side-chains
  154 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  205 ILE
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  467 SER
Chi-restraints excluded: chain B residue  480 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0170
   chunk 35 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 71 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.6418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.125497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.097913 restraints weight = 13440.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.101801 restraints weight = 6831.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.104331 restraints weight = 4697.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.4705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7524  Z= 0.187
  Angle     :  0.711   8.463  10229  Z= 0.336
  Chirality :  0.045   0.409   1203
  Planarity :  0.004   0.040   1255
  Dihedral  :  8.359  86.824   1262
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.94 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.34 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.27), residues: 922
  helix:  0.09 (0.24), residues: 498
  sheet: -0.15 (0.68), residues: 62
  loop : -2.25 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B  95 
 TYR   0.015   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 LEU cc_start: 0.9200 (mt) cc_final: 0.8919 (mt)
REVERT: A  272 ASP cc_start: 0.7874 (t0) cc_final: 0.7595 (p0)
REVERT: A  469 TYR cc_start: 0.9153 (p90) cc_final: 0.8902 (p90)
REVERT: B  120 MET cc_start: 0.9083 (tpp) cc_final: 0.8846 (mmm)
REVERT: B  146 TYR cc_start: 0.8664 (t80) cc_final: 0.8311 (t80)
REVERT: B  195 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7633 (ptt180)
REVERT: B  254 TYR cc_start: 0.8801 (m-80) cc_final: 0.8261 (m-80)
REVERT: B  265 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7063 (tm-30)
REVERT: B  318 TYR cc_start: 0.7402 (t80) cc_final: 0.7093 (t80)
REVERT: B  438 PHE cc_start: 0.8078 (t80) cc_final: 0.7828 (t80)
REVERT: B  453 LYS cc_start: 0.8469 (tppt) cc_final: 0.7941 (mmtt)
REVERT: B  466 LEU cc_start: 0.8632 (mp) cc_final: 0.8383 (tp)
REVERT: B  501 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8327 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 151
  average time/residue: 0.1482
  time to fit residues: 32.3943
Evaluate side-chains
  146 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  416 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0020
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0060
   overall best weight:    0.6408

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.126127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.097758 restraints weight = 13421.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.101719 restraints weight = 6758.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.104288 restraints weight = 4677.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.4822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7524  Z= 0.189
  Angle     :  0.723  12.983  10229  Z= 0.339
  Chirality :  0.045   0.407   1203
  Planarity :  0.004   0.041   1255
  Dihedral  :  8.138  87.419   1262
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.05 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.94 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.27), residues: 922
  helix:  0.18 (0.24), residues: 499
  sheet: -0.26 (0.66), residues: 62
  loop : -2.26 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 405 
 HIS   0.002   0.001   HIS B 319 
 PHE   0.024   0.002   PHE B  95 
 TYR   0.016   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 LEU cc_start: 0.9192 (mt) cc_final: 0.8904 (mt)
REVERT: A  469 TYR cc_start: 0.9131 (p90) cc_final: 0.8843 (p90)
REVERT: A  486 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8079 (mp0)
REVERT: B  120 MET cc_start: 0.9081 (tpp) cc_final: 0.8838 (mmm)
REVERT: B  146 TYR cc_start: 0.8674 (t80) cc_final: 0.8342 (t80)
REVERT: B  195 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7627 (ptt180)
REVERT: B  254 TYR cc_start: 0.8801 (m-80) cc_final: 0.8313 (m-80)
REVERT: B  265 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7111 (tm-30)
REVERT: B  318 TYR cc_start: 0.7393 (t80) cc_final: 0.7085 (t80)
REVERT: B  438 PHE cc_start: 0.8085 (t80) cc_final: 0.7865 (t80)
REVERT: B  453 LYS cc_start: 0.8471 (tppt) cc_final: 0.7945 (mmtt)
REVERT: B  466 LEU cc_start: 0.8752 (mp) cc_final: 0.8473 (tp)
REVERT: B  501 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8281 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 143
  average time/residue: 0.1539
  time to fit residues: 31.7033
Evaluate side-chains
  151 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  486 GLU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  416 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0670
   chunk 53 optimal weight:    0.0980
   chunk 49 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0970
   chunk 89 optimal weight:    0.0070
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.1934

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 293 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.128076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.100135 restraints weight = 13434.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.104345 restraints weight = 6566.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.107001 restraints weight = 4409.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.4972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7524  Z= 0.166
  Angle     :  0.707   9.566  10229  Z= 0.333
  Chirality :  0.045   0.413   1203
  Planarity :  0.004   0.041   1255
  Dihedral  :  7.870  88.809   1262
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  7.48 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 21.47 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.27), residues: 922
  helix:  0.22 (0.24), residues: 497
  sheet: -0.26 (0.65), residues: 62
  loop : -2.23 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 405 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.023   0.001   PHE B  95 
 TYR   0.017   0.001   TYR A 405 
 ARG   0.003   0.000   ARG A 227 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 LEU cc_start: 0.9181 (mt) cc_final: 0.8879 (mt)
REVERT: A  272 ASP cc_start: 0.7972 (t0) cc_final: 0.7721 (p0)
REVERT: A  469 TYR cc_start: 0.9086 (p90) cc_final: 0.8752 (p90)
REVERT: A  554 TYR cc_start: 0.9262 (p90) cc_final: 0.8967 (p90)
REVERT: B  105 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8646 (tp30)
REVERT: B  146 TYR cc_start: 0.8684 (t80) cc_final: 0.8320 (t80)
REVERT: B  195 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7530 (ptt180)
REVERT: B  254 TYR cc_start: 0.8764 (m-80) cc_final: 0.8355 (m-80)
REVERT: B  318 TYR cc_start: 0.7444 (t80) cc_final: 0.7192 (t80)
REVERT: B  453 LYS cc_start: 0.8393 (tppt) cc_final: 0.7898 (mmtt)
REVERT: B  466 LEU cc_start: 0.8708 (mp) cc_final: 0.8455 (tp)
REVERT: B  501 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8269 (tm-30)
  outliers start: 20
  outliers final: 15
  residues processed: 158
  average time/residue: 0.1550
  time to fit residues: 34.9792
Evaluate side-chains
  153 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  213 LEU
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  359 LEU
Chi-restraints excluded: chain B residue  416 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0670
   chunk 90 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.126906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098565 restraints weight = 13350.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.102556 restraints weight = 6771.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.105160 restraints weight = 4676.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7524  Z= 0.192
  Angle     :  0.733   9.275  10229  Z= 0.345
  Chirality :  0.045   0.405   1203
  Planarity :  0.004   0.039   1255
  Dihedral  :  7.760  88.622   1262
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.72 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 21.86 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.27), residues: 922
  helix:  0.19 (0.23), residues: 502
  sheet: -0.22 (0.65), residues: 62
  loop : -2.30 (0.30), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 405 
 HIS   0.005   0.001   HIS B 367 
 PHE   0.042   0.002   PHE B 438 
 TYR   0.018   0.002   TYR A 405 
 ARG   0.003   0.000   ARG A 227 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2433.52 seconds
wall clock time: 44 minutes 25.30 seconds (2665.30 seconds total)