Starting phenix.real_space_refine
on Tue Mar  3 15:31:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v80_31785/03_2026/7v80_31785.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v80_31785/03_2026/7v80_31785.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v80_31785/03_2026/7v80_31785.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v80_31785/03_2026/7v80_31785.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v80_31785/03_2026/7v80_31785.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v80_31785/03_2026/7v80_31785.cif"
  }
  resolution = 3.9
  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=   0.037
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      37      5.16       5
     C    4222      2.51       5
     N    1082      2.21       5
     O    1268      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6609
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1593
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "F"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      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: "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: "A"
      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: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.63, per 1000 atoms: 0.25
  Number of scatterers: 6609
  At special positions: 0
  Unit cell: (74.8, 99, 125.4, 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      37     16.00
     O    1268      8.00
     N    1082      7.00
     C    4222      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 133 " - pdb=" SG  CYS F 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 344 " - pdb=" SG  CYS F 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 530 " - pdb=" SG  CYS F 542 " 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 B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A 331 "
      " NAG A1302 " - " ASN A 343 "
      " NAG B   1 " - " ASN F  90 "
      " NAG C   1 " - " ASN F 103 "
      " NAG D   1 " - " ASN F 546 "
      " NAG F2001 " - " ASN F  53 "
      " NAG F2002 " - " ASN F 322 "
      " NAG F2003 " - " ASN F 432 "
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 248.0 milliseconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 5 sheets defined
      49.2% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.760A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 3.651A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 3.662A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 404 through 408'
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.720A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 53
      removed outlier: 3.714A  pdb=" N   ALA F  25 " --> pdb=" O   ILE F  21 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   LYS F  26 " --> pdb=" O   GLU F  22 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   THR F  27 " --> pdb=" O   GLU F  23 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   PHE F  28 " --> pdb=" O   GLN F  24 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   HIS F  34 " --> pdb=" O   ASP F  30 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLU F  35 " --> pdb=" O   LYS F  31 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASP F  38 " --> pdb=" O   HIS F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 59 through 73
      removed outlier: 3.598A  pdb=" N   LYS F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 80
    Processing helix  chain 'F' and resid 90 through 101
      removed outlier: 3.583A  pdb=" N   ALA F  99 " --> pdb=" O   LEU F  95 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU F 100 " --> pdb=" O   GLN F  96 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 129
    Processing helix  chain 'F' and resid 147 through 152
      removed outlier: 3.802A  pdb=" N   MET F 152 " --> pdb=" O   LEU F 148 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 158 through 172
    Processing helix  chain 'F' and resid 176 through 193
      removed outlier: 3.636A  pdb=" N   GLU F 182 " --> pdb=" O   PRO F 178 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL F 185 " --> pdb=" O   GLU F 181 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 199 through 205
      removed outlier: 3.528A  pdb=" N   TRP F 203 " --> pdb=" O   TYR F 199 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 206 through 208
      No H-bonds generated for 'chain 'F' and resid 206 through 208'
    Processing helix  chain 'F' and resid 218 through 229
      removed outlier: 3.848A  pdb=" N   GLU F 227 " --> pdb=" O   ILE F 223 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 252
      removed outlier: 3.734A  pdb=" N   HIS F 239 " --> pdb=" O   PRO F 235 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LEU F 240 " --> pdb=" O   LEU F 236 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 275 through 279
      removed outlier: 3.927A  pdb=" N   TYR F 279 " --> pdb=" O   THR F 276 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 293 through 300
      removed outlier: 3.990A  pdb=" N   GLN F 300 " --> pdb=" O   ALA F 296 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 303 through 319
      removed outlier: 3.556A  pdb=" N   PHE F 308 " --> pdb=" O   ALA F 304 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS F 313 " --> pdb=" O   LYS F 309 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE F 315 " --> pdb=" O   ALA F 311 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL F 318 " --> pdb=" O   PHE F 314 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY F 319 " --> pdb=" O   PHE F 315 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 326 through 331
      removed outlier: 3.730A  pdb=" N   SER F 331 " --> pdb=" O   PHE F 327 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 365 through 385
      removed outlier: 3.920A  pdb=" N   TYR F 385 " --> pdb=" O   TYR F 381 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 393
    Processing helix  chain 'F' and resid 399 through 413
      removed outlier: 3.715A  pdb=" N   ALA F 403 " --> pdb=" O   GLY F 399 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   MET F 408 " --> pdb=" O   VAL F 404 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER F 409 " --> pdb=" O   GLY F 405 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA F 413 " --> pdb=" O   SER F 409 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 414 through 421
    Processing helix  chain 'F' and resid 431 through 447
      removed outlier: 3.519A  pdb=" N   GLN F 442 " --> pdb=" O   PHE F 438 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   THR F 445 " --> pdb=" O   LYS F 441 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL F 447 " --> pdb=" O   ALA F 443 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 449 through 466
    Processing helix  chain 'F' and resid 476 through 485
      removed outlier: 4.969A  pdb=" N   GLU F 483 " --> pdb=" O   GLU F 479 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 503 through 508
      removed outlier: 4.117A  pdb=" N   SER F 507 " --> pdb=" O   LEU F 503 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ASN F 508 " --> pdb=" O   PHE F 504 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 503 through 508'
    Processing helix  chain 'F' and resid 513 through 532
      removed outlier: 3.836A  pdb=" N   ARG F 518 " --> pdb=" O   ARG F 514 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   THR F 519 " --> pdb=" O   TYR F 515 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU F 520 " --> pdb=" O   TYR F 516 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE F 523 " --> pdb=" O   THR F 519 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 538 through 542
    Processing helix  chain 'F' and resid 548 through 559
      removed outlier: 3.883A  pdb=" N   GLN F 552 " --> pdb=" O   THR F 548 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   LYS F 553 " --> pdb=" O   GLU F 549 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LEU F 554 " --> pdb=" O   ALA F 550 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   MET F 557 " --> pdb=" O   LYS F 553 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 565 through 570
    Processing helix  chain 'F' and resid 583 through 588
      removed outlier: 3.990A  pdb=" N   PHE F 588 " --> pdb=" O   LEU F 584 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 588 through 596
      removed outlier: 3.703A  pdb=" N   PHE F 592 " --> pdb=" O   PHE F 588 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.712A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'F' and resid 132 through 133
      removed outlier: 3.697A  pdb=" N   VAL F 132 " --> pdb=" O   LEU F 142 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 262 through 263
      removed outlier: 7.017A  pdb=" N   LEU F 262 " --> pdb=" O   VAL F 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 347 through 352
      removed outlier: 5.967A  pdb=" N   ASP F 355 " --> pdb=" O   LEU F 351 " (cutoff:3.500A)

    240 hydrogen bonds defined for protein.
    687 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: 0.87

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2100
        1.34 -     1.46: 1745
        1.46 -     1.58: 2888
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6792
  Sorted by residual:
  bond pdb=" CA  ASP F 350 "
       pdb=" CB  ASP F 350 "
    ideal  model  delta    sigma   weight residual
    1.531  1.666 -0.135 3.28e-02 9.30e+02 1.69e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.04e+00
  bond pdb=" C1  NAG F2003 "
       pdb=" O5  NAG F2003 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.18e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.86e+00
  bond pdb=" CB  PRO F 284 "
       pdb=" CG  PRO F 284 "
    ideal  model  delta    sigma   weight residual
    1.492  1.570 -0.078 5.00e-02 4.00e+02 2.44e+00
  ... (remaining 6787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 9084
        2.19 -     4.38: 118
        4.38 -     6.57: 25
        6.57 -     8.76: 3
        8.76 -    10.95: 1
  Bond angle restraints: 9231
  Sorted by residual:
  angle pdb=" CA  CYS A 432 "
        pdb=" CB  CYS A 432 "
        pdb=" SG  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     114.40  125.35  -10.95 2.30e+00 1.89e-01 2.27e+01
  angle pdb=" N   CYS A 432 "
        pdb=" CA  CYS A 432 "
        pdb=" C   CYS A 432 "
      ideal   model   delta    sigma   weight residual
     107.88  113.57   -5.69 1.41e+00 5.03e-01 1.63e+01
  angle pdb=" N   GLU F 406 "
        pdb=" CA  GLU F 406 "
        pdb=" CB  GLU F 406 "
      ideal   model   delta    sigma   weight residual
     110.41  116.02   -5.61 1.68e+00 3.54e-01 1.11e+01
  angle pdb=" CA  CYS A 379 "
        pdb=" CB  CYS A 379 "
        pdb=" SG  CYS A 379 "
      ideal   model   delta    sigma   weight residual
     114.40  121.52   -7.12 2.30e+00 1.89e-01 9.58e+00
  angle pdb=" C   ASP F 431 "
        pdb=" N   ASN F 432 "
        pdb=" CA  ASN F 432 "
      ideal   model   delta    sigma   weight residual
     121.19  125.95   -4.76 1.59e+00 3.96e-01 8.95e+00
  ... (remaining 9226 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 3685
       18.00 -    36.00: 378
       36.00 -    53.99: 71
       53.99 -    71.99: 8
       71.99 -    89.99: 10
  Dihedral angle restraints: 4152
    sinusoidal: 1813
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.11  -82.89     1      1.00e+01 1.00e-02 8.41e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -9.77  -76.23     1      1.00e+01 1.00e-02 7.31e+01
  dihedral pdb=" CA  CYS A 432 "
           pdb=" C   CYS A 432 "
           pdb=" N   VAL A 433 "
           pdb=" CA  VAL A 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.46  -26.54     0      5.00e+00 4.00e-02 2.82e+01
  ... (remaining 4149 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 952
       0.096 -    0.191: 44
       0.191 -    0.287: 1
       0.287 -    0.382: 0
       0.382 -    0.478: 1
  Chirality restraints: 998
  Sorted by residual:
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN F 546 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.92   -0.48 2.00e-01 2.50e+01 5.71e+00
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 331 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  CYS A 432 "
            pdb=" N   CYS A 432 "
            pdb=" C   CYS A 432 "
            pdb=" CB  CYS A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.59e-01
  ... (remaining 995 not shown)

  Planarity restraints: 1189
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL F 283 "   -0.039 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO F 284 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO F 284 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO F 284 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU F 262 "    0.032 5.00e-02 4.00e+02   4.94e-02 3.91e+00
        pdb=" N   PRO F 263 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO F 263 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 263 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN F 524 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.12e+00
        pdb=" C   GLN F 524 "    0.031 2.00e-02 2.50e+03
        pdb=" O   GLN F 524 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PHE F 525 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1186 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 114
        2.68 -     3.23: 6334
        3.23 -     3.79: 9855
        3.79 -     4.34: 12459
        4.34 -     4.90: 20618
  Nonbonded interactions: 49380
  Sorted by model distance:
  nonbonded pdb=" OG  SER F 109 "
            pdb=" OD1 ASP F 111 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   LEU A 452 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   ILE F 151 "
            pdb=" OG  SER F 155 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" OD1 ASN A 487 "
            pdb=" OH  TYR F  83 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   SER A 530 "
            pdb=" OG  SER A 530 "
     model   vdw
     2.241 3.040
  ... (remaining 49375 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 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             3.760
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.440
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
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      :  0.004   0.135   6810  Z= 0.171
  Angle     :  0.684  10.952   9278  Z= 0.346
  Chirality :  0.046   0.478    998
  Planarity :  0.005   0.058   1181
  Dihedral  : 14.721  89.988   2631
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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: -0.76 (0.31), residues: 793
  helix:  0.30 (0.30), residues: 344
  sheet: -0.70 (0.66), residues: 59
  loop : -1.18 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.010   0.001   TYR A 453 
 PHE   0.009   0.001   PHE F 369 
 TRP   0.024   0.001   TRP F 478 
 HIS   0.004   0.001   HIS F  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6792)
  covalent geometry    : angle       0.64630 ( 9231)
  SS BOND              : bond        0.00285 (    7)
  SS BOND              : angle       4.06508 (   14)
  hydrogen bonds       : bond        0.16892 (  240)
  hydrogen bonds       : angle       5.92475 (  687)
  link_BETA1-4         : bond        0.00435 (    3)
  link_BETA1-4         : angle       1.63141 (    9)
  link_NAG-ASN         : bond        0.00532 (    8)
  link_NAG-ASN         : angle       3.07901 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0765
  time to fit residues: 10.2403
Evaluate side-chains
  79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0050
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
F  81 GLN
** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 401 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.122872 restraints weight = 13400.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.124562 restraints weight = 9963.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.125624 restraints weight = 7011.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.126818 restraints weight = 5386.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.127006 restraints weight = 4547.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.1002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6810  Z= 0.137
  Angle     :  0.645  10.329   9278  Z= 0.324
  Chirality :  0.044   0.340    998
  Planarity :  0.004   0.039   1181
  Dihedral  :  6.344  56.774   1097
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.00 %
    Favored  : 91.14 %
  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 (0.31), residues: 793
  helix:  0.62 (0.30), residues: 343
  sheet: -0.71 (0.65), residues: 59
  loop : -1.26 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 306 
 TYR   0.013   0.001   TYR A 453 
 PHE   0.009   0.001   PHE F 369 
 TRP   0.013   0.001   TRP F 473 
 HIS   0.004   0.001   HIS F 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6792)
  covalent geometry    : angle       0.61326 ( 9231)
  SS BOND              : bond        0.00254 (    7)
  SS BOND              : angle       3.71843 (   14)
  hydrogen bonds       : bond        0.04926 (  240)
  hydrogen bonds       : angle       4.38328 (  687)
  link_BETA1-4         : bond        0.00346 (    3)
  link_BETA1-4         : angle       1.43641 (    9)
  link_NAG-ASN         : bond        0.00599 (    8)
  link_NAG-ASN         : angle       2.73801 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ILE cc_start: 0.8894 (mp) cc_final: 0.8622 (mt)
REVERT: F  600 LYS cc_start: 0.6960 (tppt) cc_final: 0.5704 (tmtt)
  outliers start: 6
  outliers final: 4
  residues processed: 88
  average time/residue: 0.0742
  time to fit residues: 9.2726
Evaluate side-chains
  87 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS
F 524 GLN
F 598 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.125522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.115685 restraints weight = 13738.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.117570 restraints weight = 9427.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.118312 restraints weight = 6525.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.118649 restraints weight = 5144.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.119537 restraints weight = 4515.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   6810  Z= 0.289
  Angle     :  0.825  11.069   9278  Z= 0.414
  Chirality :  0.054   0.468    998
  Planarity :  0.005   0.044   1181
  Dihedral  :  7.149  59.008   1097
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.57 %
    Favored  : 85.14 %
  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: -1.13 (0.30), residues: 793
  helix:  0.19 (0.28), residues: 343
  sheet:  0.11 (0.78), residues: 44
  loop : -1.72 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 169 
 TYR   0.027   0.002   TYR A 453 
 PHE   0.015   0.002   PHE F 369 
 TRP   0.017   0.002   TRP F 473 
 HIS   0.008   0.002   HIS F  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00652 ( 6792)
  covalent geometry    : angle       0.79559 ( 9231)
  SS BOND              : bond        0.00848 (    7)
  SS BOND              : angle       3.65003 (   14)
  hydrogen bonds       : bond        0.06436 (  240)
  hydrogen bonds       : angle       4.74575 (  687)
  link_BETA1-4         : bond        0.00627 (    3)
  link_BETA1-4         : angle       2.24216 (    9)
  link_NAG-ASN         : bond        0.00967 (    8)
  link_NAG-ASN         : angle       3.15968 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.7951 (t0) cc_final: 0.7676 (t0)
REVERT: A  428 ASP cc_start: 0.7084 (p0) cc_final: 0.6792 (p0)
REVERT: F  222 LEU cc_start: 0.8523 (tp) cc_final: 0.8314 (tt)
REVERT: F  376 MET cc_start: 0.8135 (mmm) cc_final: 0.7868 (mmm)
REVERT: F  406 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6768 (mt-10)
REVERT: F  476 LYS cc_start: 0.7393 (pttt) cc_final: 0.7147 (pttt)
  outliers start: 16
  outliers final: 7
  residues processed: 102
  average time/residue: 0.0649
  time to fit residues: 9.6374
Evaluate side-chains
  91 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  544 ILE
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0070
   chunk 70 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
F 378 HIS
F 598 GLN
F 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.129876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.119546 restraints weight = 13617.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.121337 restraints weight = 10238.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.122200 restraints weight = 7080.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.122874 restraints weight = 5408.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.123109 restraints weight = 4739.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6810  Z= 0.128
  Angle     :  0.659   9.365   9278  Z= 0.323
  Chirality :  0.045   0.335    998
  Planarity :  0.004   0.034   1181
  Dihedral  :  6.424  57.465   1097
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.43 %
    Favored  : 82.86 %
  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: -0.77 (0.30), residues: 793
  helix:  0.55 (0.30), residues: 338
  sheet: -0.24 (0.73), residues: 50
  loop : -1.49 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 169 
 TYR   0.017   0.001   TYR F 183 
 PHE   0.009   0.001   PHE F 369 
 TRP   0.020   0.001   TRP F 478 
 HIS   0.003   0.001   HIS F  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6792)
  covalent geometry    : angle       0.63100 ( 9231)
  SS BOND              : bond        0.00344 (    7)
  SS BOND              : angle       3.43479 (   14)
  hydrogen bonds       : bond        0.04532 (  240)
  hydrogen bonds       : angle       4.25350 (  687)
  link_BETA1-4         : bond        0.00504 (    3)
  link_BETA1-4         : angle       1.68679 (    9)
  link_NAG-ASN         : bond        0.00524 (    8)
  link_NAG-ASN         : angle       2.57518 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ASP cc_start: 0.7134 (p0) cc_final: 0.6841 (p0)
REVERT: F  222 LEU cc_start: 0.8070 (tp) cc_final: 0.7859 (tt)
REVERT: F  406 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6660 (mt-10)
REVERT: F  512 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7371 (t80)
REVERT: F  600 LYS cc_start: 0.7331 (tppt) cc_final: 0.5918 (tmtt)
  outliers start: 19
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0677
  time to fit residues: 9.9649
Evaluate side-chains
  91 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  378 HIS
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  473 TRP
Chi-restraints excluded: chain F residue  512 PHE
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 67 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS
F 598 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.125813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.115658 restraints weight = 13912.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.117356 restraints weight = 9715.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.118258 restraints weight = 6860.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.118748 restraints weight = 5214.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.119354 restraints weight = 4555.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   6810  Z= 0.285
  Angle     :  0.850  15.970   9278  Z= 0.411
  Chirality :  0.054   0.586    998
  Planarity :  0.005   0.043   1181
  Dihedral  :  7.022  58.671   1097
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 15.14 %
    Favored  : 81.57 %
  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: -1.15 (0.30), residues: 793
  helix:  0.33 (0.29), residues: 339
  sheet: -0.04 (0.75), residues: 44
  loop : -1.85 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 169 
 TYR   0.024   0.002   TYR A 453 
 PHE   0.014   0.002   PHE F 369 
 TRP   0.022   0.002   TRP F 478 
 HIS   0.021   0.003   HIS F 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00645 ( 6792)
  covalent geometry    : angle       0.78809 ( 9231)
  SS BOND              : bond        0.00589 (    7)
  SS BOND              : angle       3.75931 (   14)
  hydrogen bonds       : bond        0.05808 (  240)
  hydrogen bonds       : angle       4.58569 (  687)
  link_BETA1-4         : bond        0.01101 (    3)
  link_BETA1-4         : angle       2.09579 (    9)
  link_NAG-ASN         : bond        0.00970 (    8)
  link_NAG-ASN         : angle       5.51352 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ASP cc_start: 0.7208 (p0) cc_final: 0.6829 (p0)
REVERT: A  472 ILE cc_start: 0.7633 (mm) cc_final: 0.7424 (mm)
REVERT: A  518 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5614 (tt)
REVERT: F  142 LEU cc_start: 0.6593 (mt) cc_final: 0.6370 (mp)
REVERT: F  162 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5934 (tp)
REVERT: F  406 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6845 (mt-10)
REVERT: F  476 LYS cc_start: 0.7312 (pttt) cc_final: 0.7047 (pttt)
REVERT: F  512 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7393 (t80)
REVERT: F  600 LYS cc_start: 0.7445 (tppt) cc_final: 0.6028 (tmtt)
  outliers start: 23
  outliers final: 14
  residues processed: 104
  average time/residue: 0.0667
  time to fit residues: 10.0565
Evaluate side-chains
  101 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  162 LEU
Chi-restraints excluded: chain F residue  244 VAL
Chi-restraints excluded: chain F residue  252 TYR
Chi-restraints excluded: chain F residue  339 VAL
Chi-restraints excluded: chain F residue  347 THR
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  473 TRP
Chi-restraints excluded: chain F residue  512 PHE
Chi-restraints excluded: chain F residue  544 ILE
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 44 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
F 493 HIS
F 598 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.130350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.118945 restraints weight = 14016.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.121164 restraints weight = 9486.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.122248 restraints weight = 6236.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.122786 restraints weight = 4812.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.123122 restraints weight = 4345.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6810  Z= 0.123
  Angle     :  0.692  10.977   9278  Z= 0.333
  Chirality :  0.045   0.328    998
  Planarity :  0.004   0.033   1181
  Dihedral  :  6.588  59.948   1097
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.57 %
    Favored  : 80.71 %
  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: -0.78 (0.30), residues: 793
  helix:  0.66 (0.30), residues: 331
  sheet: -0.46 (0.71), residues: 50
  loop : -1.57 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.011   0.001   TYR F 183 
 PHE   0.010   0.001   PHE F 327 
 TRP   0.027   0.001   TRP F 478 
 HIS   0.003   0.001   HIS F  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6792)
  covalent geometry    : angle       0.64930 ( 9231)
  SS BOND              : bond        0.00614 (    7)
  SS BOND              : angle       3.57366 (   14)
  hydrogen bonds       : bond        0.04335 (  240)
  hydrogen bonds       : angle       4.20531 (  687)
  link_BETA1-4         : bond        0.00699 (    3)
  link_BETA1-4         : angle       1.62602 (    9)
  link_NAG-ASN         : bond        0.00463 (    8)
  link_NAG-ASN         : angle       3.80195 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ASP cc_start: 0.7172 (p0) cc_final: 0.6831 (p0)
REVERT: A  518 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5457 (tt)
REVERT: F   42 GLN cc_start: 0.8614 (pp30) cc_final: 0.8386 (pp30)
REVERT: F  406 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6680 (mt-10)
REVERT: F  512 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7312 (t80)
REVERT: F  534 LYS cc_start: 0.6144 (pttp) cc_final: 0.5906 (ptpp)
REVERT: F  600 LYS cc_start: 0.7431 (tppt) cc_final: 0.6093 (tmtt)
  outliers start: 19
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0700
  time to fit residues: 9.9923
Evaluate side-chains
  95 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  378 HIS
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  468 ILE
Chi-restraints excluded: chain F residue  473 TRP
Chi-restraints excluded: chain F residue  512 PHE
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0010
   chunk 74 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.5786

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.130340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.120076 restraints weight = 13575.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.121560 restraints weight = 10210.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.122418 restraints weight = 7280.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.123383 restraints weight = 5739.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.123581 restraints weight = 4829.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6810  Z= 0.122
  Angle     :  0.673   9.999   9278  Z= 0.324
  Chirality :  0.044   0.310    998
  Planarity :  0.004   0.033   1181
  Dihedral  :  6.208  59.905   1097
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.14 %
    Favored  : 80.29 %
  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 (0.30), residues: 793
  helix:  0.78 (0.30), residues: 331
  sheet: -0.20 (0.73), residues: 50
  loop : -1.41 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 306 
 TYR   0.015   0.001   TYR F 202 
 PHE   0.014   0.001   PHE F 504 
 TRP   0.032   0.001   TRP F 478 
 HIS   0.004   0.001   HIS F 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6792)
  covalent geometry    : angle       0.63561 ( 9231)
  SS BOND              : bond        0.00436 (    7)
  SS BOND              : angle       3.71430 (   14)
  hydrogen bonds       : bond        0.04063 (  240)
  hydrogen bonds       : angle       4.13529 (  687)
  link_BETA1-4         : bond        0.00627 (    3)
  link_BETA1-4         : angle       1.51349 (    9)
  link_NAG-ASN         : bond        0.00516 (    8)
  link_NAG-ASN         : angle       3.31759 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ASP cc_start: 0.7114 (p0) cc_final: 0.6769 (p0)
REVERT: A  518 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.5277 (tt)
REVERT: F   42 GLN cc_start: 0.8669 (pp30) cc_final: 0.8436 (pp30)
REVERT: F  222 LEU cc_start: 0.8120 (tp) cc_final: 0.7738 (tt)
REVERT: F  393 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7381 (mtp85)
REVERT: F  406 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6699 (mt-10)
REVERT: F  512 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6740 (t80)
REVERT: F  600 LYS cc_start: 0.7338 (tppt) cc_final: 0.6013 (tmtt)
  outliers start: 18
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0719
  time to fit residues: 10.2462
Evaluate side-chains
  96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  339 VAL
Chi-restraints excluded: chain F residue  347 THR
Chi-restraints excluded: chain F residue  378 HIS
Chi-restraints excluded: chain F residue  393 ARG
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  473 TRP
Chi-restraints excluded: chain F residue  512 PHE
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    0.3980
   chunk 40 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.130705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.119467 restraints weight = 13916.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.121515 restraints weight = 9329.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.122548 restraints weight = 6295.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.123217 restraints weight = 4841.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.123471 restraints weight = 4345.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6810  Z= 0.138
  Angle     :  0.764  25.100   9278  Z= 0.351
  Chirality :  0.052   0.807    998
  Planarity :  0.004   0.036   1181
  Dihedral  :  6.475  59.550   1097
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.86 %
    Favored  : 79.86 %
  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: -0.56 (0.30), residues: 793
  helix:  0.80 (0.30), residues: 331
  sheet: -0.27 (0.72), residues: 50
  loop : -1.40 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 169 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.009   0.001   PHE F 327 
 TRP   0.031   0.001   TRP F 478 
 HIS   0.003   0.001   HIS F  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6792)
  covalent geometry    : angle       0.66655 ( 9231)
  SS BOND              : bond        0.00325 (    7)
  SS BOND              : angle       3.91950 (   14)
  hydrogen bonds       : bond        0.04184 (  240)
  hydrogen bonds       : angle       4.11875 (  687)
  link_BETA1-4         : bond        0.00569 (    3)
  link_BETA1-4         : angle       1.73605 (    9)
  link_NAG-ASN         : bond        0.00797 (    8)
  link_NAG-ASN         : angle       6.70468 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ASP cc_start: 0.7103 (p0) cc_final: 0.6802 (p0)
REVERT: A  518 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5338 (tt)
REVERT: F  123 MET cc_start: 0.6276 (tpp) cc_final: 0.5987 (tpp)
REVERT: F  222 LEU cc_start: 0.8222 (tp) cc_final: 0.7890 (tt)
REVERT: F  393 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7826 (mtt90)
REVERT: F  406 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6808 (mt-10)
REVERT: F  512 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6661 (t80)
REVERT: F  600 LYS cc_start: 0.7373 (tppt) cc_final: 0.6070 (tmtt)
  outliers start: 16
  outliers final: 9
  residues processed: 99
  average time/residue: 0.0729
  time to fit residues: 10.2429
Evaluate side-chains
  97 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  347 THR
Chi-restraints excluded: chain F residue  378 HIS
Chi-restraints excluded: chain F residue  393 ARG
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  473 TRP
Chi-restraints excluded: chain F residue  512 PHE
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0570
   chunk 2 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0470
   chunk 25 optimal weight:    0.8980
   chunk 46 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.4396

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.131997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.121311 restraints weight = 13719.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.122877 restraints weight = 10318.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.123822 restraints weight = 7326.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.125024 restraints weight = 5582.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.125212 restraints weight = 4537.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   6810  Z= 0.120
  Angle     :  0.757  22.462   9278  Z= 0.351
  Chirality :  0.049   0.691    998
  Planarity :  0.004   0.032   1181
  Dihedral  :  6.347  57.925   1097
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 18.86 %
    Favored  : 79.43 %
  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: -0.43 (0.31), residues: 793
  helix:  0.88 (0.30), residues: 332
  sheet: -0.48 (0.65), residues: 60
  loop : -1.27 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 169 
 TYR   0.011   0.001   TYR F 183 
 PHE   0.017   0.001   PHE F 504 
 TRP   0.028   0.001   TRP F 478 
 HIS   0.006   0.001   HIS F 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6792)
  covalent geometry    : angle       0.67088 ( 9231)
  SS BOND              : bond        0.00272 (    7)
  SS BOND              : angle       3.78999 (   14)
  hydrogen bonds       : bond        0.03833 (  240)
  hydrogen bonds       : angle       4.06929 (  687)
  link_BETA1-4         : bond        0.00521 (    3)
  link_BETA1-4         : angle       1.83338 (    9)
  link_NAG-ASN         : bond        0.00919 (    8)
  link_NAG-ASN         : angle       6.20372 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ASP cc_start: 0.6977 (p0) cc_final: 0.6692 (p0)
REVERT: A  518 LEU cc_start: 0.5693 (OUTLIER) cc_final: 0.5421 (tt)
REVERT: F   42 GLN cc_start: 0.8685 (pp30) cc_final: 0.8475 (pp30)
REVERT: F  123 MET cc_start: 0.6321 (tpp) cc_final: 0.6015 (tpp)
REVERT: F  190 MET cc_start: 0.8400 (tmm) cc_final: 0.8097 (tmm)
REVERT: F  222 LEU cc_start: 0.8167 (tp) cc_final: 0.7821 (tt)
REVERT: F  393 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7299 (mtp85)
REVERT: F  406 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6644 (mt-10)
REVERT: F  512 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6636 (t80)
REVERT: F  600 LYS cc_start: 0.7249 (tppt) cc_final: 0.6032 (tmtt)
  outliers start: 12
  outliers final: 7
  residues processed: 100
  average time/residue: 0.0719
  time to fit residues: 10.1784
Evaluate side-chains
  97 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  378 HIS
Chi-restraints excluded: chain F residue  393 ARG
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  473 TRP
Chi-restraints excluded: chain F residue  512 PHE
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.131368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.121308 restraints weight = 13738.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.122935 restraints weight = 9668.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.123950 restraints weight = 6770.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124309 restraints weight = 5300.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.124630 restraints weight = 4825.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6810  Z= 0.140
  Angle     :  0.766  21.920   9278  Z= 0.353
  Chirality :  0.050   0.653    998
  Planarity :  0.004   0.034   1181
  Dihedral  :  6.407  58.447   1097
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.00 %
    Favored  : 79.14 %
  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: -0.46 (0.31), residues: 793
  helix:  0.85 (0.30), residues: 332
  sheet: -0.11 (0.74), residues: 50
  loop : -1.33 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 169 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.008   0.001   PHE F 327 
 TRP   0.026   0.001   TRP F 478 
 HIS   0.003   0.001   HIS F  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6792)
  covalent geometry    : angle       0.68364 ( 9231)
  SS BOND              : bond        0.00341 (    7)
  SS BOND              : angle       3.75505 (   14)
  hydrogen bonds       : bond        0.04059 (  240)
  hydrogen bonds       : angle       4.07805 (  687)
  link_BETA1-4         : bond        0.00590 (    3)
  link_BETA1-4         : angle       1.95267 (    9)
  link_NAG-ASN         : bond        0.00932 (    8)
  link_NAG-ASN         : angle       6.10317 (   24)

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ASP cc_start: 0.7154 (p0) cc_final: 0.6866 (p0)
REVERT: A  518 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5318 (tt)
REVERT: F  123 MET cc_start: 0.6383 (tpp) cc_final: 0.6059 (tpp)
REVERT: F  222 LEU cc_start: 0.8211 (tp) cc_final: 0.7893 (tt)
REVERT: F  393 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7340 (mtp85)
REVERT: F  406 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6765 (mt-10)
REVERT: F  512 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6427 (t80)
REVERT: F  600 LYS cc_start: 0.7405 (tppt) cc_final: 0.6186 (tmtt)
  outliers start: 13
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0716
  time to fit residues: 9.7935
Evaluate side-chains
  98 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  432 CYS
Chi-restraints excluded: chain A residue  518 LEU
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  339 VAL
Chi-restraints excluded: chain F residue  347 THR
Chi-restraints excluded: chain F residue  378 HIS
Chi-restraints excluded: chain F residue  393 ARG
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  473 TRP
Chi-restraints excluded: chain F residue  512 PHE
Chi-restraints excluded: chain F residue  604 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 6 optimal weight:    0.1980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.132499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.122715 restraints weight = 13670.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.123663 restraints weight = 9649.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.124545 restraints weight = 8048.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.124800 restraints weight = 6398.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.125001 restraints weight = 5652.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6810  Z= 0.131
  Angle     :  0.753  21.371   9278  Z= 0.346
  Chirality :  0.049   0.628    998
  Planarity :  0.004   0.030   1181
  Dihedral  :  6.378  58.172   1097
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.14 %
    Favored  : 79.00 %
  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: -0.42 (0.31), residues: 793
  helix:  0.85 (0.30), residues: 333
  sheet: -0.08 (0.74), residues: 50
  loop : -1.29 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 169 
 TYR   0.012   0.001   TYR A 453 
 PHE   0.017   0.001   PHE F 504 
 TRP   0.034   0.001   TRP F 478 
 HIS   0.002   0.001   HIS F  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6792)
  covalent geometry    : angle       0.67418 ( 9231)
  SS BOND              : bond        0.00289 (    7)
  SS BOND              : angle       3.58900 (   14)
  hydrogen bonds       : bond        0.03968 (  240)
  hydrogen bonds       : angle       4.06462 (  687)
  link_BETA1-4         : bond        0.00547 (    3)
  link_BETA1-4         : angle       1.98504 (    9)
  link_NAG-ASN         : bond        0.00880 (    8)
  link_NAG-ASN         : angle       5.93034 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1107.70 seconds
wall clock time: 19 minutes 50.48 seconds (1190.48 seconds total)