Starting phenix.real_space_refine
on Sun Apr  5 02:29:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mcu_63806/04_2026/9mcu_63806_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mcu_63806/04_2026/9mcu_63806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mcu_63806/04_2026/9mcu_63806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mcu_63806/04_2026/9mcu_63806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mcu_63806/04_2026/9mcu_63806_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mcu_63806/04_2026/9mcu_63806_trim.cif"
  }
  resolution = 2.69
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.134
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    4800      2.51       5
     N    1108      2.21       5
     O    1246      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7184
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 473, 3557
          Classifications: {'peptide': 473}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 450}
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'Y01': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.89, per 1000 atoms: 0.26
  Number of scatterers: 7184
  At special positions: 0
  Unit cell: (73.628, 103.452, 75.492, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1246      8.00
     N    1108      7.00
     C    4800      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 280.3 milliseconds
  

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 0 sheets defined
      76.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 112
      removed outlier: 4.429A  pdb=" N   VAL A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   GLY A 106 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 109 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 135
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 3.674A  pdb=" N   ALA A 148 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE A 150 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR A 158 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 168 through 172
      removed outlier: 3.803A  pdb=" N   THR A 171 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER A 172 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 168 through 172'
    Processing helix  chain 'A' and resid 174 through 191
      removed outlier: 3.669A  pdb=" N   PHE A 183 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 199 through 206
    Processing helix  chain 'A' and resid 229 through 237
      removed outlier: 3.534A  pdb=" N   ALA A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE A 237 " --> pdb=" O   ARG A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 247
      removed outlier: 3.681A  pdb=" N   ILE A 241 " --> pdb=" O   ILE A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 250
      No H-bonds generated for 'chain 'A' and resid 248 through 250'
    Processing helix  chain 'A' and resid 261 through 272
      removed outlier: 3.596A  pdb=" N   GLN A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 283
      removed outlier: 3.621A  pdb=" N   ALA A 283 " --> pdb=" O   PHE A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 280 through 283'
    Processing helix  chain 'A' and resid 284 through 296
      removed outlier: 3.913A  pdb=" N   LEU A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ALA A 294 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLU A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 312
      removed outlier: 3.548A  pdb=" N   ALA A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 321
      removed outlier: 3.848A  pdb=" N   SER A 319 " --> pdb=" O   PRO A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 331
      removed outlier: 3.942A  pdb=" N   LYS A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 352
      removed outlier: 3.511A  pdb=" N   THR A 347 " --> pdb=" O   GLY A 343 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   MET A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 367
      removed outlier: 3.555A  pdb=" N   MET A 362 " --> pdb=" O   ASN A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 375
      removed outlier: 3.581A  pdb=" N   THR A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 380
      removed outlier: 3.587A  pdb=" N   LEU A 379 " --> pdb=" O   CYS A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 397
      removed outlier: 3.886A  pdb=" N   ALA A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 407
      removed outlier: 3.535A  pdb=" N   CYS A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 431
      removed outlier: 3.867A  pdb=" N   TRP A 412 " --> pdb=" O   GLU A 408 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA A 419 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL A 420 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLN A 427 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ASN A 430 " --> pdb=" O   GLY A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 448
      removed outlier: 3.504A  pdb=" N   VAL A 444 " --> pdb=" O   CYS A 440 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLN A 446 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 456
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 474 through 491
      removed outlier: 6.138A  pdb=" N   SER A 482 " --> pdb=" O   GLY A 478 " (cutoff:3.500A)
      removed outlier: 4.891A  pdb=" N   ALA A 483 " --> pdb=" O   ALA A 479 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ALA A 491 " --> pdb=" O   MET A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 500
    Processing helix  chain 'A' and resid 503 through 509
      removed outlier: 3.624A  pdb=" N   PHE A 509 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 526
    Processing helix  chain 'A' and resid 530 through 556
      removed outlier: 3.955A  pdb=" N   PHE A 535 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LYS A 536 " --> pdb=" O   PRO A 532 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 537 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 553 " --> pdb=" O   TRP A 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 112
      removed outlier: 4.429A  pdb=" N   VAL B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU B 109 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 135
    Processing helix  chain 'B' and resid 143 through 158
      removed outlier: 3.674A  pdb=" N   ALA B 148 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE B 150 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR B 158 " --> pdb=" O   ALA B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 167
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.804A  pdb=" N   THR B 171 " --> pdb=" O   SER B 168 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 169 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 168 through 172'
    Processing helix  chain 'B' and resid 174 through 191
      removed outlier: 3.669A  pdb=" N   PHE B 183 " --> pdb=" O   VAL B 179 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL B 189 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   THR B 191 " --> pdb=" O   GLY B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 197
    Processing helix  chain 'B' and resid 199 through 206
    Processing helix  chain 'B' and resid 229 through 237
      removed outlier: 3.534A  pdb=" N   ALA B 234 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE B 237 " --> pdb=" O   ARG B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 247
      removed outlier: 3.680A  pdb=" N   ILE B 241 " --> pdb=" O   ILE B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 250
      No H-bonds generated for 'chain 'B' and resid 248 through 250'
    Processing helix  chain 'B' and resid 261 through 272
      removed outlier: 3.597A  pdb=" N   GLN B 267 " --> pdb=" O   SER B 263 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   CYS B 272 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 283
      removed outlier: 3.621A  pdb=" N   ALA B 283 " --> pdb=" O   PHE B 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 280 through 283'
    Processing helix  chain 'B' and resid 284 through 296
      removed outlier: 3.913A  pdb=" N   LEU B 288 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU B 291 " --> pdb=" O   ASN B 287 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 294 " --> pdb=" O   CYS B 290 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU B 295 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 312
      removed outlier: 3.549A  pdb=" N   ALA B 311 " --> pdb=" O   SER B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 321
      removed outlier: 3.848A  pdb=" N   SER B 319 " --> pdb=" O   PRO B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 331
      removed outlier: 3.942A  pdb=" N   LYS B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 352
      removed outlier: 3.511A  pdb=" N   THR B 347 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU B 349 " --> pdb=" O   ALA B 345 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   MET B 352 " --> pdb=" O   LYS B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 367
      removed outlier: 3.555A  pdb=" N   MET B 362 " --> pdb=" O   ASN B 358 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 375
      removed outlier: 3.581A  pdb=" N   THR B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 380
      removed outlier: 3.587A  pdb=" N   LEU B 379 " --> pdb=" O   CYS B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 397
      removed outlier: 3.886A  pdb=" N   ALA B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 407
      removed outlier: 3.537A  pdb=" N   CYS B 405 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 431
      removed outlier: 3.868A  pdb=" N   TRP B 412 " --> pdb=" O   GLU B 408 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 419 " --> pdb=" O   LEU B 415 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL B 420 " --> pdb=" O   ALA B 416 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLN B 427 " --> pdb=" O   GLY B 423 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASN B 430 " --> pdb=" O   GLY B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 448
      removed outlier: 3.505A  pdb=" N   VAL B 444 " --> pdb=" O   CYS B 440 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLN B 446 " --> pdb=" O   ALA B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 456
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 466 through 470
    Processing helix  chain 'B' and resid 474 through 491
      removed outlier: 6.139A  pdb=" N   SER B 482 " --> pdb=" O   GLY B 478 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   ALA B 483 " --> pdb=" O   ALA B 479 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA B 491 " --> pdb=" O   MET B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 500
    Processing helix  chain 'B' and resid 503 through 509
      removed outlier: 3.624A  pdb=" N   PHE B 509 " --> pdb=" O   ASN B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 526
    Processing helix  chain 'B' and resid 530 through 556
      removed outlier: 3.955A  pdb=" N   PHE B 535 " --> pdb=" O   LEU B 531 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS B 536 " --> pdb=" O   PRO B 532 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE B 537 " --> pdb=" O   ASP B 533 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY B 553 " --> pdb=" O   TRP B 549 " (cutoff:3.500A)

    370 hydrogen bonds defined for protein.
    1098 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1078
        1.31 -     1.44: 2031
        1.44 -     1.56: 4229
        1.56 -     1.68: 0
        1.68 -     1.81: 48
  Bond restraints: 7386
  Sorted by residual:
  bond pdb=" CAJ Y01 A 601 "
       pdb=" CAO Y01 A 601 "
    ideal  model  delta    sigma   weight residual
    1.526  1.460  0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" CAJ Y01 B 601 "
       pdb=" CAO Y01 B 601 "
    ideal  model  delta    sigma   weight residual
    1.526  1.463  0.063 2.00e-02 2.50e+03 1.01e+01
  bond pdb=" CAJ Y01 A 601 "
       pdb=" CAN Y01 A 601 "
    ideal  model  delta    sigma   weight residual
    1.524  1.485  0.039 2.00e-02 2.50e+03 3.79e+00
  bond pdb=" CAJ Y01 B 601 "
       pdb=" CAN Y01 B 601 "
    ideal  model  delta    sigma   weight residual
    1.524  1.487  0.037 2.00e-02 2.50e+03 3.48e+00
  bond pdb=" C   PHE A 509 "
       pdb=" N   GLY A 510 "
    ideal  model  delta    sigma   weight residual
    1.331  1.308  0.022 1.46e-02 4.69e+03 2.31e+00
  ... (remaining 7381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 9570
        1.82 -     3.64: 447
        3.64 -     5.47: 67
        5.47 -     7.29: 20
        7.29 -     9.11: 8
  Bond angle restraints: 10112
  Sorted by residual:
  angle pdb=" CA  TRP A 452 "
        pdb=" CB  TRP A 452 "
        pdb=" CG  TRP A 452 "
      ideal   model   delta    sigma   weight residual
     113.60  120.78   -7.18 1.90e+00 2.77e-01 1.43e+01
  angle pdb=" CA  TRP B 452 "
        pdb=" CB  TRP B 452 "
        pdb=" CG  TRP B 452 "
      ideal   model   delta    sigma   weight residual
     113.60  120.71   -7.11 1.90e+00 2.77e-01 1.40e+01
  angle pdb=" C   LEU A 508 "
        pdb=" N   PHE A 509 "
        pdb=" CA  PHE A 509 "
      ideal   model   delta    sigma   weight residual
     122.12  115.62    6.50 1.76e+00 3.23e-01 1.36e+01
  angle pdb=" C   LEU B 508 "
        pdb=" N   PHE B 509 "
        pdb=" CA  PHE B 509 "
      ideal   model   delta    sigma   weight residual
     122.12  115.63    6.49 1.76e+00 3.23e-01 1.36e+01
  angle pdb=" N   TYR B 515 "
        pdb=" CA  TYR B 515 "
        pdb=" C   TYR B 515 "
      ideal   model   delta    sigma   weight residual
     112.41  108.03    4.38 1.30e+00 5.92e-01 1.13e+01
  ... (remaining 10107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.00: 4112
       24.00 -    48.01: 182
       48.01 -    72.01: 16
       72.01 -    96.02: 12
       96.02 -   120.02: 4
  Dihedral angle restraints: 4326
    sinusoidal: 1632
      harmonic: 2694
  Sorted by residual:
  dihedral pdb=" CA  ALA A 479 "
           pdb=" C   ALA A 479 "
           pdb=" N   LEU A 480 "
           pdb=" CA  LEU A 480 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.03  -21.97     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  ALA B 479 "
           pdb=" C   ALA B 479 "
           pdb=" N   LEU B 480 "
           pdb=" CA  LEU B 480 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.09  -21.91     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  LEU B 212 "
           pdb=" C   LEU B 212 "
           pdb=" N   SER B 213 "
           pdb=" CA  SER B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.12   21.88     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 4323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 807
       0.045 -    0.090: 321
       0.090 -    0.135: 75
       0.135 -    0.181: 6
       0.181 -    0.226: 5
  Chirality restraints: 1214
  Sorted by residual:
  chirality pdb=" CA  TRP B 452 "
            pdb=" N   TRP B 452 "
            pdb=" C   TRP B 452 "
            pdb=" CB  TRP B 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  TRP A 452 "
            pdb=" N   TRP A 452 "
            pdb=" C   TRP A 452 "
            pdb=" CB  TRP A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL A 384 "
            pdb=" CA  VAL A 384 "
            pdb=" CG1 VAL A 384 "
            pdb=" CG2 VAL A 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.21e-01
  ... (remaining 1211 not shown)

  Planarity restraints: 1208
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 142 "   -0.048 5.00e-02 4.00e+02   7.23e-02 8.37e+00
        pdb=" N   PRO B 143 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO B 143 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 143 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 142 "   -0.048 5.00e-02 4.00e+02   7.20e-02 8.29e+00
        pdb=" N   PRO A 143 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A 143 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 143 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 239 "    0.043 5.00e-02 4.00e+02   6.42e-02 6.60e+00
        pdb=" N   PRO A 240 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 240 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 240 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1205 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2352
        2.82 -     3.34: 6522
        3.34 -     3.86: 12123
        3.86 -     4.38: 15506
        4.38 -     4.90: 25015
  Nonbonded interactions: 61518
  Sorted by model distance:
  nonbonded pdb=" CG2 THR B 230 "
            pdb=" OE1 GLN B 519 "
     model   vdw
     2.297 3.460
  nonbonded pdb=" CG2 THR A 230 "
            pdb=" OE1 GLN A 519 "
     model   vdw
     2.298 3.460
  nonbonded pdb=" O   TYR B 468 "
            pdb=" OH  TYR B 515 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   TYR A 468 "
            pdb=" OH  TYR A 515 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   THR B 338 "
            pdb=" OG1 THR B 338 "
     model   vdw
     2.341 3.040
  ... (remaining 61513 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
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:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.900
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
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      :  0.007   0.066   7386  Z= 0.307
  Angle     :  0.911   9.112  10112  Z= 0.487
  Chirality :  0.050   0.226   1214
  Planarity :  0.008   0.072   1208
  Dihedral  : 15.020 120.024   2602
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.91 (0.14), residues: 942
  helix: -4.65 (0.07), residues: 748
  sheet:  None (None), residues: 0
  loop : -2.73 (0.37), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 259 
 TYR   0.010   0.002   TYR A 214 
 PHE   0.027   0.002   PHE B 509 
 TRP   0.018   0.002   TRP B 176 
 HIS   0.006   0.002   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00723 ( 7386)
  covalent geometry    : angle       0.91144 (10112)
  hydrogen bonds       : bond        0.30887 (  370)
  hydrogen bonds       : angle      11.24919 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  536 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7398 (ttpt)
REVERT: B  195 ASP cc_start: 0.7244 (t0) cc_final: 0.7025 (t0)
REVERT: B  536 LYS cc_start: 0.7714 (mtmt) cc_final: 0.7481 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.3290
  time to fit residues: 57.7001
Evaluate side-chains
  103 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 122 GLN
A 269 GLN
A 287 ASN
B  92 GLN
B 122 GLN
B 287 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.155508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.142879 restraints weight = 8089.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.35
r_work: 0.3514 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7386  Z= 0.133
  Angle     :  0.624   9.767  10112  Z= 0.317
  Chirality :  0.039   0.139   1214
  Planarity :  0.006   0.050   1208
  Dihedral  :  7.979  49.911   1124
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 10.03 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.04 (0.22), residues: 942
  helix: -2.68 (0.14), residues: 742
  sheet:  None (None), residues: 0
  loop : -1.56 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 233 
 TYR   0.006   0.001   TYR B 523 
 PHE   0.028   0.002   PHE B 509 
 TRP   0.023   0.002   TRP A 417 
 HIS   0.003   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7386)
  covalent geometry    : angle       0.62425 (10112)
  hydrogen bonds       : bond        0.04146 (  370)
  hydrogen bonds       : angle       5.32555 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8060 (mt)
REVERT: A  350 LYS cc_start: 0.6722 (mmtt) cc_final: 0.6301 (mtmt)
REVERT: A  401 ASN cc_start: 0.8632 (p0) cc_final: 0.8353 (p0)
REVERT: B  195 ASP cc_start: 0.7885 (t0) cc_final: 0.7582 (t0)
REVERT: B  314 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8046 (mt)
REVERT: B  350 LYS cc_start: 0.6682 (mmtt) cc_final: 0.6274 (mtmt)
REVERT: B  401 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8332 (p0)
  outliers start: 19
  outliers final: 7
  residues processed: 122
  average time/residue: 0.3688
  time to fit residues: 48.3240
Evaluate side-chains
  102 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
B  92 GLN
B 122 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.143659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.130719 restraints weight = 8051.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.35
r_work: 0.3375 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7386  Z= 0.161
  Angle     :  0.640   9.267  10112  Z= 0.318
  Chirality :  0.041   0.151   1214
  Planarity :  0.005   0.043   1208
  Dihedral  :  8.073  59.924   1124
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 11.63 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.25), residues: 942
  helix: -1.49 (0.17), residues: 762
  sheet:  None (None), residues: 0
  loop : -0.88 (0.47), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 233 
 TYR   0.012   0.002   TYR A 524 
 PHE   0.033   0.002   PHE B 509 
 TRP   0.022   0.002   TRP B 417 
 HIS   0.004   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 7386)
  covalent geometry    : angle       0.64018 (10112)
  hydrogen bonds       : bond        0.04009 (  370)
  hydrogen bonds       : angle       4.86486 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  186 ARG cc_start: 0.8253 (tpp-160) cc_final: 0.7835 (tpp80)
REVERT: A  314 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8012 (mm)
REVERT: A  350 LYS cc_start: 0.7055 (mmtt) cc_final: 0.6547 (mtmt)
REVERT: A  401 ASN cc_start: 0.8773 (p0) cc_final: 0.8538 (p0)
REVERT: A  404 ASP cc_start: 0.8333 (m-30) cc_final: 0.8126 (m-30)
REVERT: A  536 LYS cc_start: 0.7708 (mtmt) cc_final: 0.7261 (tttp)
REVERT: B  195 ASP cc_start: 0.8004 (t0) cc_final: 0.7721 (t0)
REVERT: B  314 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7976 (mm)
REVERT: B  350 LYS cc_start: 0.7038 (mmtt) cc_final: 0.6578 (mtmt)
REVERT: B  388 MET cc_start: 0.8836 (mtm) cc_final: 0.8473 (mtp)
REVERT: B  401 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8398 (p0)
REVERT: B  536 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7325 (tttp)
  outliers start: 25
  outliers final: 8
  residues processed: 110
  average time/residue: 0.4022
  time to fit residues: 47.5205
Evaluate side-chains
  96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue  222 LEU
Chi-restraints excluded: chain B residue  297 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.136369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.123117 restraints weight = 8285.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.42
r_work: 0.3284 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7386  Z= 0.158
  Angle     :  0.605   8.469  10112  Z= 0.298
  Chirality :  0.041   0.134   1214
  Planarity :  0.004   0.040   1208
  Dihedral  :  8.023  59.971   1124
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 12.97 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.27), residues: 942
  helix: -0.83 (0.18), residues: 762
  sheet:  None (None), residues: 0
  loop : -0.69 (0.47), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 186 
 TYR   0.012   0.002   TYR B 524 
 PHE   0.031   0.002   PHE A 509 
 TRP   0.021   0.002   TRP B 417 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7386)
  covalent geometry    : angle       0.60508 (10112)
  hydrogen bonds       : bond        0.03625 (  370)
  hydrogen bonds       : angle       4.71031 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8093 (mm)
REVERT: A  330 LEU cc_start: 0.7941 (tt) cc_final: 0.7236 (mp)
REVERT: A  350 LYS cc_start: 0.7016 (mmtt) cc_final: 0.6475 (mtmt)
REVERT: A  401 ASN cc_start: 0.8665 (p0) cc_final: 0.8427 (p0)
REVERT: A  536 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7346 (tttp)
REVERT: B  195 ASP cc_start: 0.7988 (t0) cc_final: 0.7726 (t0)
REVERT: B  314 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8077 (mm)
REVERT: B  350 LYS cc_start: 0.7057 (mmtt) cc_final: 0.6520 (mtmt)
REVERT: B  388 MET cc_start: 0.8843 (mtm) cc_final: 0.8602 (mtp)
REVERT: B  401 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8426 (p0)
REVERT: B  536 LYS cc_start: 0.7902 (mtmt) cc_final: 0.7354 (tttp)
  outliers start: 22
  outliers final: 4
  residues processed: 92
  average time/residue: 0.3845
  time to fit residues: 38.0905
Evaluate side-chains
  80 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.137097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.123791 restraints weight = 8276.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.42
r_work: 0.3305 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.4369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7386  Z= 0.128
  Angle     :  0.571   9.063  10112  Z= 0.281
  Chirality :  0.040   0.133   1214
  Planarity :  0.004   0.037   1208
  Dihedral  :  7.922  59.942   1124
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.44 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.27), residues: 942
  helix: -0.29 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -0.61 (0.46), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 186 
 TYR   0.010   0.001   TYR B 524 
 PHE   0.027   0.001   PHE A 509 
 TRP   0.020   0.001   TRP A 417 
 HIS   0.002   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7386)
  covalent geometry    : angle       0.57134 (10112)
  hydrogen bonds       : bond        0.03326 (  370)
  hydrogen bonds       : angle       4.58117 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8164 (mt)
REVERT: A  330 LEU cc_start: 0.7866 (tt) cc_final: 0.7301 (mp)
REVERT: A  401 ASN cc_start: 0.8724 (p0) cc_final: 0.8435 (p0)
REVERT: A  536 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7294 (tttp)
REVERT: B  195 ASP cc_start: 0.7939 (t0) cc_final: 0.7655 (t0)
REVERT: B  330 LEU cc_start: 0.7773 (tp) cc_final: 0.7232 (mp)
REVERT: B  388 MET cc_start: 0.8841 (mtm) cc_final: 0.8585 (mtp)
REVERT: B  401 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8442 (p0)
REVERT: B  536 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7297 (tttp)
  outliers start: 16
  outliers final: 5
  residues processed: 84
  average time/residue: 0.3912
  time to fit residues: 35.4227
Evaluate side-chains
  82 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 78 optimal weight:    0.4980
   chunk 69 optimal weight:    0.0670
   chunk 80 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.139149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.126280 restraints weight = 8189.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.35
r_work: 0.3356 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7386  Z= 0.110
  Angle     :  0.545   7.675  10112  Z= 0.269
  Chirality :  0.039   0.131   1214
  Planarity :  0.004   0.035   1208
  Dihedral  :  7.830  59.752   1124
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 13.90 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.28), residues: 942
  helix:  0.13 (0.19), residues: 766
  sheet:  None (None), residues: 0
  loop : -0.37 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 186 
 TYR   0.010   0.001   TYR A 524 
 PHE   0.025   0.001   PHE A 509 
 TRP   0.021   0.001   TRP B 417 
 HIS   0.001   0.001   HIS A 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7386)
  covalent geometry    : angle       0.54454 (10112)
  hydrogen bonds       : bond        0.03118 (  370)
  hydrogen bonds       : angle       4.45627 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  231 THR cc_start: 0.9088 (t) cc_final: 0.8621 (m)
REVERT: A  330 LEU cc_start: 0.7851 (tp) cc_final: 0.7400 (mp)
REVERT: A  401 ASN cc_start: 0.8650 (p0) cc_final: 0.8421 (p0)
REVERT: A  536 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7340 (tttp)
REVERT: B  195 ASP cc_start: 0.8015 (t0) cc_final: 0.7804 (t0)
REVERT: B  231 THR cc_start: 0.9042 (t) cc_final: 0.8675 (m)
REVERT: B  330 LEU cc_start: 0.7805 (tp) cc_final: 0.7328 (mp)
REVERT: B  388 MET cc_start: 0.8857 (mtm) cc_final: 0.8623 (mtp)
REVERT: B  536 LYS cc_start: 0.7856 (mtmt) cc_final: 0.7389 (tttp)
  outliers start: 19
  outliers final: 7
  residues processed: 89
  average time/residue: 0.3659
  time to fit residues: 35.2194
Evaluate side-chains
  81 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue  291 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    0.4980
   chunk 64 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   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  92 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.137079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.123775 restraints weight = 8208.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.41
r_work: 0.3320 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7386  Z= 0.125
  Angle     :  0.549   6.782  10112  Z= 0.273
  Chirality :  0.039   0.131   1214
  Planarity :  0.004   0.035   1208
  Dihedral  :  7.827  59.706   1124
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.51 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.28), residues: 942
  helix:  0.34 (0.20), residues: 764
  sheet:  None (None), residues: 0
  loop : -0.26 (0.46), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 186 
 TYR   0.016   0.001   TYR A 563 
 PHE   0.028   0.001   PHE A 509 
 TRP   0.020   0.001   TRP A 417 
 HIS   0.002   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7386)
  covalent geometry    : angle       0.54902 (10112)
  hydrogen bonds       : bond        0.03256 (  370)
  hydrogen bonds       : angle       4.49359 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  231 THR cc_start: 0.9067 (t) cc_final: 0.8612 (m)
REVERT: A  330 LEU cc_start: 0.7799 (tp) cc_final: 0.7339 (mp)
REVERT: A  401 ASN cc_start: 0.8651 (p0) cc_final: 0.8404 (p0)
REVERT: A  536 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7324 (tttp)
REVERT: B  195 ASP cc_start: 0.8024 (t0) cc_final: 0.7810 (t0)
REVERT: B  231 THR cc_start: 0.9004 (t) cc_final: 0.8663 (m)
REVERT: B  330 LEU cc_start: 0.7797 (tp) cc_final: 0.7361 (mp)
REVERT: B  388 MET cc_start: 0.8845 (mtm) cc_final: 0.8618 (mtp)
REVERT: B  536 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7303 (tttp)
  outliers start: 11
  outliers final: 4
  residues processed: 85
  average time/residue: 0.3870
  time to fit residues: 35.4659
Evaluate side-chains
  79 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 90 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.135617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122343 restraints weight = 8364.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.42
r_work: 0.3301 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7386  Z= 0.128
  Angle     :  0.551   6.880  10112  Z= 0.274
  Chirality :  0.040   0.132   1214
  Planarity :  0.004   0.035   1208
  Dihedral  :  7.821  59.879   1124
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.04 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.28), residues: 942
  helix:  0.47 (0.20), residues: 766
  sheet:  None (None), residues: 0
  loop : -0.13 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 186 
 TYR   0.014   0.001   TYR A 563 
 PHE   0.028   0.001   PHE A 509 
 TRP   0.021   0.001   TRP B 417 
 HIS   0.002   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7386)
  covalent geometry    : angle       0.55134 (10112)
  hydrogen bonds       : bond        0.03282 (  370)
  hydrogen bonds       : angle       4.49602 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  231 THR cc_start: 0.9064 (t) cc_final: 0.8606 (m)
REVERT: A  330 LEU cc_start: 0.7784 (tp) cc_final: 0.7358 (mp)
REVERT: A  350 LYS cc_start: 0.6818 (mmtm) cc_final: 0.6319 (tttm)
REVERT: A  401 ASN cc_start: 0.8742 (p0) cc_final: 0.8468 (p0)
REVERT: A  536 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7335 (tttp)
REVERT: B  195 ASP cc_start: 0.8063 (t0) cc_final: 0.7834 (t0)
REVERT: B  231 THR cc_start: 0.9007 (t) cc_final: 0.8673 (m)
REVERT: B  330 LEU cc_start: 0.7802 (tp) cc_final: 0.7372 (mp)
REVERT: B  388 MET cc_start: 0.8867 (mtm) cc_final: 0.8649 (mtp)
REVERT: B  536 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7379 (tttp)
REVERT: B  541 MET cc_start: 0.8497 (tpt) cc_final: 0.8179 (mmp)
  outliers start: 10
  outliers final: 5
  residues processed: 81
  average time/residue: 0.4146
  time to fit residues: 36.0732
Evaluate side-chains
  78 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0270
   chunk 73 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.137124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.124023 restraints weight = 8214.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.40
r_work: 0.3321 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7386  Z= 0.118
  Angle     :  0.540   6.693  10112  Z= 0.269
  Chirality :  0.039   0.132   1214
  Planarity :  0.004   0.034   1208
  Dihedral  :  7.768  59.518   1124
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 16.04 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.28), residues: 942
  helix:  0.60 (0.20), residues: 766
  sheet:  None (None), residues: 0
  loop : -0.08 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 186 
 TYR   0.019   0.001   TYR A 563 
 PHE   0.027   0.001   PHE A 509 
 TRP   0.021   0.001   TRP B 417 
 HIS   0.002   0.001   HIS B 488 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7386)
  covalent geometry    : angle       0.53990 (10112)
  hydrogen bonds       : bond        0.03178 (  370)
  hydrogen bonds       : angle       4.45852 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  231 THR cc_start: 0.9065 (t) cc_final: 0.8611 (m)
REVERT: A  330 LEU cc_start: 0.7793 (tp) cc_final: 0.7402 (mp)
REVERT: A  350 LYS cc_start: 0.6821 (mmtm) cc_final: 0.6328 (tttm)
REVERT: A  401 ASN cc_start: 0.8750 (p0) cc_final: 0.8495 (p0)
REVERT: A  536 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7377 (tttp)
REVERT: B  231 THR cc_start: 0.9013 (t) cc_final: 0.8674 (m)
REVERT: B  330 LEU cc_start: 0.7804 (tp) cc_final: 0.7396 (mp)
REVERT: B  350 LYS cc_start: 0.6853 (mmtm) cc_final: 0.6336 (tttm)
REVERT: B  388 MET cc_start: 0.8867 (mtm) cc_final: 0.8651 (mtp)
REVERT: B  536 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7395 (tttp)
REVERT: B  541 MET cc_start: 0.8500 (tpt) cc_final: 0.8202 (mmp)
  outliers start: 10
  outliers final: 4
  residues processed: 85
  average time/residue: 0.4037
  time to fit residues: 36.8654
Evaluate side-chains
  77 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.136396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.123181 restraints weight = 8252.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.40
r_work: 0.3312 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7386  Z= 0.128
  Angle     :  0.554   6.936  10112  Z= 0.276
  Chirality :  0.040   0.132   1214
  Planarity :  0.004   0.035   1208
  Dihedral  :  7.805  59.935   1124
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 16.98 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.28), residues: 942
  helix:  0.60 (0.20), residues: 766
  sheet:  None (None), residues: 0
  loop : -0.02 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 186 
 TYR   0.021   0.001   TYR A 563 
 PHE   0.028   0.001   PHE A 509 
 TRP   0.021   0.001   TRP B 417 
 HIS   0.002   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7386)
  covalent geometry    : angle       0.55449 (10112)
  hydrogen bonds       : bond        0.03274 (  370)
  hydrogen bonds       : angle       4.53246 ( 1098)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  231 THR cc_start: 0.9069 (t) cc_final: 0.8616 (m)
REVERT: A  330 LEU cc_start: 0.7791 (tp) cc_final: 0.7384 (mp)
REVERT: A  350 LYS cc_start: 0.6834 (mmtm) cc_final: 0.6339 (tttm)
REVERT: A  401 ASN cc_start: 0.8735 (p0) cc_final: 0.8484 (p0)
REVERT: A  536 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7370 (tttp)
REVERT: B  231 THR cc_start: 0.9007 (t) cc_final: 0.8671 (m)
REVERT: B  330 LEU cc_start: 0.7822 (tp) cc_final: 0.7403 (mp)
REVERT: B  350 LYS cc_start: 0.6894 (mmtm) cc_final: 0.6373 (tttm)
REVERT: B  388 MET cc_start: 0.8859 (mtm) cc_final: 0.8648 (mtp)
REVERT: B  536 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7378 (tttp)
REVERT: B  541 MET cc_start: 0.8490 (tpt) cc_final: 0.8181 (mmp)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 0.4396
  time to fit residues: 35.3590
Evaluate side-chains
  78 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0050
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.136739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.123517 restraints weight = 8311.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.41
r_work: 0.3317 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7386  Z= 0.121
  Angle     :  0.545   6.802  10112  Z= 0.272
  Chirality :  0.039   0.132   1214
  Planarity :  0.004   0.034   1208
  Dihedral  :  7.735  58.822   1124
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 16.44 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.29), residues: 942
  helix:  0.68 (0.20), residues: 766
  sheet:  None (None), residues: 0
  loop :  0.02 (0.47), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 186 
 TYR   0.022   0.001   TYR A 563 
 PHE   0.027   0.001   PHE A 509 
 TRP   0.021   0.001   TRP B 417 
 HIS   0.001   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7386)
  covalent geometry    : angle       0.54539 (10112)
  hydrogen bonds       : bond        0.03200 (  370)
  hydrogen bonds       : angle       4.49990 ( 1098)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1892.08 seconds
wall clock time: 33 minutes 7.30 seconds (1987.30 seconds total)