Starting phenix.real_space_refine
on Tue Mar 11 20:32:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v80_31785/03_2025/7v80_31785.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v80_31785/03_2025/7v80_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_2025/7v80_31785.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v80_31785/03_2025/7v80_31785.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v80_31785/03_2025/7v80_31785.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v80_31785/03_2025/7v80_31785.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.037
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.62, per 1000 atoms: 0.85
  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: 1.71
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.63
  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: 1.64

  Time building geometry restraints manager: 2.00 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:             3.680
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.160
  Find NCS groups from input model:        0.080
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.330
-------------------------------------------------------------------------------
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   6792  Z= 0.264
  Angle     :  0.646  10.952   9231  Z= 0.334
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.024   0.001   TRP F 478 
 HIS   0.004   0.001   HIS F  34 
 PHE   0.009   0.001   PHE F 369 
 TYR   0.010   0.001   TYR A 453 
 ARG   0.005   0.001   ARG A 357 

*********************** 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  : 0.794 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1710
  time to fit residues: 22.5782
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  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    0.1980
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
F  81 GLN
** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 524 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.131973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.120459 restraints weight = 13641.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.122285 restraints weight = 9184.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124180 restraints weight = 6199.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.0982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6792  Z= 0.231
  Angle     :  0.628  10.159   9231  Z= 0.321
  Chirality :  0.045   0.343    998
  Planarity :  0.004   0.040   1181
  Dihedral  :  6.468  57.068   1097
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.86 %
    Favored  : 91.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.31), residues: 793
  helix:  0.60 (0.30), residues: 343
  sheet: -0.73 (0.66), residues: 59
  loop : -1.28 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 473 
 HIS   0.004   0.001   HIS F 401 
 PHE   0.010   0.001   PHE F 369 
 TYR   0.014   0.001   TYR A 453 
 ARG   0.004   0.001   ARG F 306 

*********************** 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  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  332 ILE cc_start: 0.8913 (mp) cc_final: 0.8645 (mt)
REVERT: F  421 ILE cc_start: 0.7571 (pt) cc_final: 0.7314 (tp)
REVERT: F  600 LYS cc_start: 0.6906 (tppt) cc_final: 0.5645 (tmtt)
  outliers start: 6
  outliers final: 4
  residues processed: 88
  average time/residue: 0.1580
  time to fit residues: 19.5719
Evaluate side-chains
  86 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
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 8 optimal weight:    0.0970
   chunk 66 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0170
   chunk 60 optimal weight:    0.0040
   overall best weight:    0.3228

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

Flipped N/Q/H residues before XYZ refinement:
F 378 HIS
F 401 HIS
F 599 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.134738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.123351 restraints weight = 13733.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.125388 restraints weight = 9837.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.126543 restraints weight = 6658.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   6792  Z= 0.156
  Angle     :  0.558   9.972   9231  Z= 0.281
  Chirality :  0.042   0.329    998
  Planarity :  0.004   0.032   1181
  Dihedral  :  5.964  55.270   1097
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.43 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.31), residues: 793
  helix:  0.77 (0.30), residues: 344
  sheet: -0.60 (0.64), residues: 60
  loop : -1.18 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP F 473 
 HIS   0.003   0.001   HIS F 374 
 PHE   0.007   0.001   PHE F 369 
 TYR   0.008   0.001   TYR A 453 
 ARG   0.003   0.000   ARG A 357 

*********************** 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
  101 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  123 MET cc_start: 0.6399 (tpp) cc_final: 0.6111 (tpp)
REVERT: F  222 LEU cc_start: 0.8029 (tp) cc_final: 0.7810 (tt)
REVERT: F  406 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6409 (mt-10)
REVERT: F  449 THR cc_start: 0.7740 (m) cc_final: 0.7482 (t)
REVERT: F  600 LYS cc_start: 0.6995 (tppt) cc_final: 0.5753 (tmtt)
  outliers start: 8
  outliers final: 3
  residues processed: 99
  average time/residue: 0.1597
  time to fit residues: 22.4685
Evaluate side-chains
  91 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain F residue  148 LEU
Chi-restraints excluded: chain F residue  406 GLU
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 66 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0980
   chunk 44 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.129323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.119059 restraints weight = 13782.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.120771 restraints weight = 9614.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.121749 restraints weight = 6607.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6792  Z= 0.283
  Angle     :  0.662   8.885   9231  Z= 0.334
  Chirality :  0.049   0.437    998
  Planarity :  0.004   0.037   1181
  Dihedral  :  6.421  59.371   1097
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 12.71 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.31), residues: 793
  helix:  0.67 (0.29), residues: 342
  sheet: -0.24 (0.74), residues: 50
  loop : -1.42 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP F 478 
 HIS   0.008   0.002   HIS F 265 
 PHE   0.012   0.001   PHE F 369 
 TYR   0.019   0.001   TYR A 453 
 ARG   0.005   0.000   ARG F 169 

*********************** 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: 16
    poor density    : 91
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  406 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6582 (mt-10)
REVERT: F  512 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7368 (t80)
REVERT: F  600 LYS cc_start: 0.7132 (tppt) cc_final: 0.5753 (tmtt)
  outliers start: 16
  outliers final: 8
  residues processed: 103
  average time/residue: 0.1517
  time to fit residues: 22.4427
Evaluate side-chains
  95 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
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  378 HIS
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  407 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.131050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.120679 restraints weight = 13738.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.122647 restraints weight = 9640.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.123791 restraints weight = 6387.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6792  Z= 0.221
  Angle     :  0.634   9.585   9231  Z= 0.316
  Chirality :  0.047   0.420    998
  Planarity :  0.004   0.036   1181
  Dihedral  :  6.196  58.191   1097
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.00 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.31), residues: 793
  helix:  0.73 (0.30), residues: 339
  sheet: -0.26 (0.73), residues: 50
  loop : -1.37 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP F 478 
 HIS   0.006   0.001   HIS F 378 
 PHE   0.010   0.001   PHE F 369 
 TYR   0.014   0.001   TYR A 453 
 ARG   0.004   0.000   ARG F 169 

*********************** 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
  105 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5472 (tt)
REVERT: F  406 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6538 (mt-10)
REVERT: F  512 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7322 (t80)
REVERT: F  600 LYS cc_start: 0.7120 (tppt) cc_final: 0.5781 (tmtt)
  outliers start: 18
  outliers final: 9
  residues processed: 100
  average time/residue: 0.1597
  time to fit residues: 22.4865
Evaluate side-chains
  96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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  378 HIS
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  407 ILE
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 9 optimal weight:    0.0060
   chunk 54 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0570
   chunk 22 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0970
   chunk 35 optimal weight:    0.0770
   chunk 61 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.1870

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.121850 restraints weight = 13812.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.123847 restraints weight = 9675.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.125185 restraints weight = 6552.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6792  Z= 0.162
  Angle     :  0.590  10.304   9231  Z= 0.294
  Chirality :  0.044   0.393    998
  Planarity :  0.004   0.031   1181
  Dihedral  :  5.867  56.349   1097
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.86 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.31), residues: 793
  helix:  0.86 (0.30), residues: 340
  sheet: -0.14 (0.74), residues: 50
  loop : -1.24 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP F 478 
 HIS   0.008   0.001   HIS F 378 
 PHE   0.013   0.001   PHE F 504 
 TYR   0.009   0.001   TYR F  41 
 ARG   0.006   0.000   ARG A 357 

*********************** 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
  102 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.5354 (tt)
REVERT: F  222 LEU cc_start: 0.8081 (tp) cc_final: 0.7838 (tt)
REVERT: F  379 ILE cc_start: 0.8897 (mm) cc_final: 0.8687 (mt)
REVERT: F  406 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6441 (mt-10)
REVERT: F  449 THR cc_start: 0.7877 (m) cc_final: 0.7639 (t)
REVERT: F  512 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7144 (t80)
REVERT: F  600 LYS cc_start: 0.7052 (tppt) cc_final: 0.5787 (tmtt)
  outliers start: 12
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1776
  time to fit residues: 24.1384
Evaluate side-chains
  96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 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  406 GLU
Chi-restraints excluded: chain F residue  407 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 54 optimal weight:    0.0870
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0670
   chunk 43 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 53 optimal weight:    0.3980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.134670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.124196 restraints weight = 13450.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.125802 restraints weight = 9936.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.126885 restraints weight = 6955.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6792  Z= 0.168
  Angle     :  0.589  10.268   9231  Z= 0.292
  Chirality :  0.044   0.379    998
  Planarity :  0.003   0.030   1181
  Dihedral  :  5.604  55.937   1097
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.57 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.31), residues: 793
  helix:  0.93 (0.30), residues: 341
  sheet: -0.07 (0.75), residues: 50
  loop : -1.20 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 478 
 HIS   0.009   0.001   HIS F 378 
 PHE   0.007   0.001   PHE F 369 
 TYR   0.009   0.001   TYR A 453 
 ARG   0.005   0.000   ARG F 393 

*********************** 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
  100 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5425 (tt)
REVERT: F  222 LEU cc_start: 0.8087 (tp) cc_final: 0.7857 (tt)
REVERT: F  406 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6468 (mt-10)
REVERT: F  449 THR cc_start: 0.7631 (m) cc_final: 0.7407 (t)
REVERT: F  512 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6769 (t80)
REVERT: F  600 LYS cc_start: 0.6939 (tppt) cc_final: 0.5734 (tmtt)
  outliers start: 12
  outliers final: 7
  residues processed: 97
  average time/residue: 0.1668
  time to fit residues: 22.4458
Evaluate side-chains
  94 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 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  378 HIS
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  407 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0370
   chunk 14 optimal weight:    0.0470
   chunk 42 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 75 optimal weight:    0.3980
   chunk 54 optimal weight:    0.0870
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.2534

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.135542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.124895 restraints weight = 13506.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.126666 restraints weight = 9983.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.127669 restraints weight = 6759.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   6792  Z= 0.162
  Angle     :  0.603  10.401   9231  Z= 0.298
  Chirality :  0.043   0.371    998
  Planarity :  0.003   0.028   1181
  Dihedral  :  5.474  55.474   1097
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.71 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.31), residues: 793
  helix:  1.01 (0.30), residues: 335
  sheet: -0.07 (0.75), residues: 50
  loop : -1.13 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP F 478 
 HIS   0.013   0.001   HIS F 378 
 PHE   0.014   0.001   PHE F 504 
 TYR   0.007   0.001   TYR F  41 
 ARG   0.004   0.000   ARG F 393 

*********************** 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
  101 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5371 (tt)
REVERT: F  222 LEU cc_start: 0.7952 (tp) cc_final: 0.7738 (tt)
REVERT: F  378 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.7816 (t70)
REVERT: F  406 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6463 (mt-10)
REVERT: F  512 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6709 (t80)
REVERT: F  600 LYS cc_start: 0.7093 (tppt) cc_final: 0.5842 (tmtt)
  outliers start: 14
  outliers final: 6
  residues processed: 98
  average time/residue: 0.1604
  time to fit residues: 21.9555
Evaluate side-chains
  94 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 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  378 HIS
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  407 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.132413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.121815 restraints weight = 13778.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.123437 restraints weight = 10596.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.124364 restraints weight = 7184.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   6792  Z= 0.210
  Angle     :  0.624  10.426   9231  Z= 0.310
  Chirality :  0.045   0.373    998
  Planarity :  0.004   0.033   1181
  Dihedral  :  5.465  56.073   1097
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 16.57 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.31), residues: 793
  helix:  0.92 (0.30), residues: 341
  sheet: -0.12 (0.75), residues: 50
  loop : -1.20 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP F 478 
 HIS   0.009   0.001   HIS F 378 
 PHE   0.007   0.001   PHE F 369 
 TYR   0.012   0.001   TYR A 453 
 ARG   0.004   0.000   ARG A 357 

*********************** 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
  100 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5505 (tt)
REVERT: F  222 LEU cc_start: 0.8059 (tp) cc_final: 0.7843 (tt)
REVERT: F  378 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.7931 (t70)
REVERT: F  406 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6516 (mt-10)
REVERT: F  512 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6537 (t80)
REVERT: F  600 LYS cc_start: 0.7015 (tppt) cc_final: 0.5719 (tmtt)
  outliers start: 15
  outliers final: 7
  residues processed: 96
  average time/residue: 0.1540
  time to fit residues: 21.0119
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  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 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  339 VAL
Chi-restraints excluded: chain F residue  378 HIS
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  407 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 32 optimal weight:    0.0010
   chunk 57 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0270
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6048

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.132809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.121961 restraints weight = 13759.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.123672 restraints weight = 10412.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.124979 restraints weight = 6985.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6792  Z= 0.197
  Angle     :  0.630  10.302   9231  Z= 0.312
  Chirality :  0.044   0.372    998
  Planarity :  0.004   0.032   1181
  Dihedral  :  5.489  56.071   1097
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.29 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.31), residues: 793
  helix:  0.92 (0.30), residues: 341
  sheet: -0.13 (0.76), residues: 50
  loop : -1.21 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP F 478 
 HIS   0.005   0.001   HIS F 378 
 PHE   0.016   0.001   PHE F 504 
 TYR   0.011   0.001   TYR A 453 
 ARG   0.004   0.000   ARG A 357 

********************** 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
  97 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
REVERT: A  518 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5475 (tt)
REVERT: F  222 LEU cc_start: 0.8048 (tp) cc_final: 0.7835 (tt)
REVERT: F  378 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.7999 (t70)
REVERT: F  406 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6523 (mt-10)
REVERT: F  512 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6598 (t80)
REVERT: F  600 LYS cc_start: 0.7147 (tppt) cc_final: 0.5876 (tmtt)
  outliers start: 12
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1533
  time to fit residues: 21.0550
Evaluate side-chains
  96 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 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  339 VAL
Chi-restraints excluded: chain F residue  378 HIS
Chi-restraints excluded: chain F residue  406 GLU
Chi-restraints excluded: chain F residue  407 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0470
   chunk 53 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.132248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.121381 restraints weight = 13838.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.123201 restraints weight = 10440.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.124365 restraints weight = 6899.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6792  Z= 0.204
  Angle     :  0.627  10.476   9231  Z= 0.311
  Chirality :  0.045   0.370    998
  Planarity :  0.004   0.033   1181
  Dihedral  :  5.466  56.191   1097
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.14 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.31), residues: 793
  helix:  0.90 (0.30), residues: 341
  sheet: -0.14 (0.76), residues: 50
  loop : -1.22 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP F 478 
 HIS   0.010   0.001   HIS F 378 
 PHE   0.007   0.001   PHE F 369 
 TYR   0.012   0.001   TYR A 453 
 ARG   0.004   0.000   ARG A 357 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2090.13 seconds
wall clock time: 37 minutes 5.91 seconds (2225.91 seconds total)