Starting phenix.real_space_refine
on Tue Feb 11 23:23:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v8b_31796/02_2025/7v8b_31796.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v8b_31796/02_2025/7v8b_31796.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v8b_31796/02_2025/7v8b_31796.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v8b_31796/02_2025/7v8b_31796.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v8b_31796/02_2025/7v8b_31796.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v8b_31796/02_2025/7v8b_31796.cif"
  }
  resolution = 3.2
  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=   0.032
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    4242      2.51       5
     N    1088      2.21       5
     O    1283      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6650
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1595
          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: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      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: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.86, per 1000 atoms: 0.73
  Number of scatterers: 6650
  At special positions: 0
  Unit cell: (79.2, 105.6, 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    1283      8.00
     N    1088      7.00
     C    4242      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=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    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=2.02
    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 B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A 331 "
      " NAG B   1 " - " ASN A 343 "
      " NAG C   1 " - " ASN F  90 "
      " NAG D   1 " - " ASN F 103 "
      " NAG E   1 " - " ASN F 322 "
      " NAG F2001 " - " ASN F  53 "
      " NAG F2002 " - " ASN F 432 "
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 894.1 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:
      40 helices and 4 sheets defined
      55.3% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.667A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 385 through 389
      removed outlier: 3.835A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 501 through 506
      removed outlier: 3.987A  pdb=" N   TYR A 505 " --> pdb=" O   ASN A 501 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 20 through 53
      removed outlier: 3.797A  pdb=" N   GLN F  24 " --> pdb=" O   THR F  20 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   HIS F  34 " --> pdb=" O   ASP F  30 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLU F  35 " --> pdb=" O   LYS F  31 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ASP F  38 " --> pdb=" O   HIS F  34 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU F  39 " --> pdb=" O   GLU F  35 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 55 through 58
    Processing helix  chain 'F' and resid 59 through 80
      removed outlier: 4.515A  pdb=" N   LYS F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLU F  75 " --> pdb=" O   ALA F  71 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN F  76 " --> pdb=" O   PHE F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 101
      removed outlier: 3.765A  pdb=" N   ALA F  99 " --> pdb=" O   LEU F  95 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   LEU F 100 " --> pdb=" O   GLN F  96 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 103 through 108
      removed outlier: 3.877A  pdb=" N   VAL F 107 " --> pdb=" O   GLY F 104 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 129
      removed outlier: 3.812A  pdb=" N   ARG F 115 " --> pdb=" O   ASP F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 147 through 154
    Processing helix  chain 'F' and resid 157 through 172
    Processing helix  chain 'F' and resid 175 through 194
      removed outlier: 4.361A  pdb=" N   LEU F 179 " --> pdb=" O   GLN F 175 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL F 185 " --> pdb=" O   GLU F 181 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 198 through 205
      removed outlier: 3.513A  pdb=" N   TYR F 202 " --> pdb=" O   ASP F 198 " (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 220 through 231
      removed outlier: 3.890A  pdb=" N   GLU F 224 " --> pdb=" O   GLY F 220 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU F 227 " --> pdb=" O   ILE F 223 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   HIS F 228 " --> pdb=" O   GLU F 224 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 233 through 252
      removed outlier: 3.635A  pdb=" N   HIS F 239 " --> pdb=" O   PRO F 235 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU F 240 " --> pdb=" O   LEU F 236 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 275 through 281
      removed outlier: 4.182A  pdb=" N   SER F 280 " --> pdb=" O   ASN F 277 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 293 through 300
    Processing helix  chain 'F' and resid 303 through 319
      removed outlier: 3.532A  pdb=" N   GLU F 312 " --> pdb=" O   PHE F 308 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   PHE F 314 " --> pdb=" O   GLU F 310 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   PHE F 315 " --> pdb=" O   ALA F 311 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 326 through 331
    Processing helix  chain 'F' and resid 365 through 385
      removed outlier: 3.956A  pdb=" N   TYR F 385 " --> pdb=" O   TYR F 381 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 389 through 393
      removed outlier: 3.645A  pdb=" N   ARG F 393 " --> pdb=" O   PHE F 390 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 399 through 412
      removed outlier: 3.509A  pdb=" N   ALA F 403 " --> pdb=" O   GLY F 399 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   MET F 408 " --> pdb=" O   VAL F 404 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   SER F 409 " --> pdb=" O   GLY F 405 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 414 through 421
    Processing helix  chain 'F' and resid 431 through 447
      removed outlier: 3.757A  pdb=" N   GLU F 435 " --> pdb=" O   ASP F 431 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR F 445 " --> pdb=" O   LYS F 441 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 449 through 466
    Processing helix  chain 'F' and resid 473 through 485
      removed outlier: 3.790A  pdb=" N   TRP F 478 " --> pdb=" O   MET F 474 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG F 482 " --> pdb=" O   TRP F 478 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU F 483 " --> pdb=" O   GLU F 479 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 503 through 508
    Processing helix  chain 'F' and resid 513 through 532
      removed outlier: 3.560A  pdb=" N   THR F 517 " --> pdb=" O   ILE F 513 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   THR F 519 " --> pdb=" O   TYR F 515 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LEU F 520 " --> pdb=" O   TYR F 516 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 538 through 542
    Processing helix  chain 'F' and resid 547 through 559
      removed outlier: 3.785A  pdb=" N   MET F 557 " --> pdb=" O   LYS F 553 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 560 through 564
      removed outlier: 4.468A  pdb=" N   GLU F 564 " --> pdb=" O   GLY F 561 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 565 through 570
    Processing helix  chain 'F' and resid 581 through 588
    Processing helix  chain 'F' and resid 588 through 599
      removed outlier: 3.950A  pdb=" N   ASP F 597 " --> pdb=" O   THR F 593 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASN F 599 " --> pdb=" O   LEU F 595 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    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
    Processing sheet with id=AA4, first strand: chain 'F' and resid 347 through 350

    281 hydrogen bonds defined for protein.
    786 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: 1.60

  Time building geometry restraints manager: 2.14 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: 2109
        1.34 -     1.46: 1732
        1.46 -     1.58: 2933
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6832
  Sorted by residual:
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.30e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 2.99e+00
  bond pdb=" C1  NAG F2001 "
       pdb=" O5  NAG F2001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.92e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.84e+00
  ... (remaining 6827 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 9056
        1.66 -     3.31: 194
        3.31 -     4.97: 23
        4.97 -     6.63: 6
        6.63 -     8.28: 3
  Bond angle restraints: 9282
  Sorted by residual:
  angle pdb=" CA  CYS A 391 "
        pdb=" CB  CYS A 391 "
        pdb=" SG  CYS A 391 "
      ideal   model   delta    sigma   weight residual
     114.40  122.68   -8.28 2.30e+00 1.89e-01 1.30e+01
  angle pdb=" CB  ARG F 192 "
        pdb=" CG  ARG F 192 "
        pdb=" CD  ARG F 192 "
      ideal   model   delta    sigma   weight residual
     111.30  118.38   -7.08 2.30e+00 1.89e-01 9.49e+00
  angle pdb=" CA  CYS A 525 "
        pdb=" CB  CYS A 525 "
        pdb=" SG  CYS A 525 "
      ideal   model   delta    sigma   weight residual
     114.40  120.75   -6.35 2.30e+00 1.89e-01 7.62e+00
  angle pdb=" N   CYS A 391 "
        pdb=" CA  CYS A 391 "
        pdb=" C   CYS A 391 "
      ideal   model   delta    sigma   weight residual
     108.79  112.66   -3.87 1.53e+00 4.27e-01 6.40e+00
  angle pdb=" CA  LEU A 517 "
        pdb=" CB  LEU A 517 "
        pdb=" CG  LEU A 517 "
      ideal   model   delta    sigma   weight residual
     116.30  124.32   -8.02 3.50e+00 8.16e-02 5.25e+00
  ... (remaining 9277 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.70: 3857
       21.70 -    43.40: 304
       43.40 -    65.10: 36
       65.10 -    86.80: 15
       86.80 -   108.49: 7
  Dihedral angle restraints: 4219
    sinusoidal: 1881
      harmonic: 2338
  Sorted by residual:
  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
      93.00    3.62   89.38     1      1.00e+01 1.00e-02 9.50e+01
  dihedral pdb=" CA  CYS A 525 "
           pdb=" C   CYS A 525 "
           pdb=" N   GLY A 526 "
           pdb=" CA  GLY A 526 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.28  -24.72     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  ASN F 432 "
           pdb=" C   ASN F 432 "
           pdb=" N   GLU F 433 "
           pdb=" CA  GLU F 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.36  -22.64     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 4216 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 825
       0.055 -    0.110: 164
       0.110 -    0.164: 18
       0.164 -    0.219: 2
       0.219 -    0.274: 1
  Chirality restraints: 1010
  Sorted by residual:
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CA  CYS A 391 "
            pdb=" N   CYS A 391 "
            pdb=" C   CYS A 391 "
            pdb=" CB  CYS A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 1007 not shown)

  Planarity restraints: 1191
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F 192 "   -0.129 9.50e-02 1.11e+02   5.82e-02 2.64e+00
        pdb=" NE  ARG F 192 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG F 192 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG F 192 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG F 192 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F 425 "   -0.025 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO F 426 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO F 426 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO F 426 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN F 134 "   -0.025 5.00e-02 4.00e+02   3.82e-02 2.33e+00
        pdb=" N   PRO F 135 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO F 135 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO F 135 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1188 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2068
        2.83 -     3.34: 6211
        3.34 -     3.86: 10347
        3.86 -     4.38: 11645
        4.38 -     4.90: 20266
  Nonbonded interactions: 50537
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   ARG A 452 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   THR F 125 "
            pdb=" OG1 THR F 129 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" NH1 ARG F 177 "
            pdb=" O   GLU F 495 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" NH1 ARG F 161 "
            pdb=" O   HIS F 265 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" NE1 TRP F 271 "
            pdb=" O   SER F 502 "
     model   vdw
     2.380 3.120
  ... (remaining 50532 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     18.900
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
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      :  0.003   0.036   6832  Z= 0.209
  Angle     :  0.586   8.282   9282  Z= 0.289
  Chirality :  0.044   0.274   1010
  Planarity :  0.004   0.058   1184
  Dihedral  : 15.613 108.494   2698
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.04 %
    Favored  : 94.83 %
  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: -0.34 (0.30), residues: 793
  helix:  0.72 (0.28), residues: 369
  sheet:  1.04 (0.80), residues: 47
  loop : -1.38 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F 477 
 HIS   0.006   0.001   HIS F 374 
 PHE   0.011   0.001   PHE F 603 
 TYR   0.012   0.001   TYR F  50 
 ARG   0.013   0.001   ARG F 192 

*********************** 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
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.6126 (tt0) cc_final: 0.5917 (tt0)
REVERT: F  427 ASP cc_start: 0.7731 (p0) cc_final: 0.7337 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1843
  time to fit residues: 15.2930
Evaluate side-chains
  47 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3251 r_free = 0.3251 target = 0.064791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.051812 restraints weight = 21343.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 3.25
r_work: 0.2825 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.053   6832  Z= 0.507
  Angle     :  0.723   9.781   9282  Z= 0.373
  Chirality :  0.049   0.261   1010
  Planarity :  0.005   0.048   1184
  Dihedral  :  8.881  57.952   1158
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.31 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  9.29 %
    Favored  : 90.29 %
  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: -0.43 (0.30), residues: 793
  helix:  0.63 (0.28), residues: 378
  sheet:  1.48 (0.81), residues: 44
  loop : -1.50 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F 477 
 HIS   0.005   0.002   HIS F 378 
 PHE   0.016   0.002   PHE F 523 
 TYR   0.018   0.002   TYR A 453 
 ARG   0.005   0.001   ARG A 403 

*********************** 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
  49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.7461 (tt0) cc_final: 0.7246 (tt0)
REVERT: F  249 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7469 (mtp)
REVERT: F  427 ASP cc_start: 0.8909 (p0) cc_final: 0.8630 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 47
  average time/residue: 0.1927
  time to fit residues: 12.7264
Evaluate side-chains
  46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  249 MET
Chi-restraints excluded: chain F residue  259 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.069598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.055406 restraints weight = 22066.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 3.38
r_work: 0.2871 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6832  Z= 0.183
  Angle     :  0.552   9.610   9282  Z= 0.281
  Chirality :  0.042   0.237   1010
  Planarity :  0.003   0.036   1184
  Dihedral  :  7.348  57.131   1158
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.79 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.71 %
    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: -0.03 (0.31), residues: 793
  helix:  1.06 (0.28), residues: 376
  sheet:  1.50 (0.83), residues: 44
  loop : -1.39 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 374 
 PHE   0.009   0.001   PHE F 523 
 TYR   0.012   0.001   TYR F 183 
 ARG   0.002   0.000   ARG F 460 

*********************** 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
  55 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.7224 (tt0) cc_final: 0.6990 (tt0)
REVERT: F  427 ASP cc_start: 0.8999 (p0) cc_final: 0.8692 (p0)
  outliers start: 6
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1875
  time to fit residues: 14.0609
Evaluate side-chains
  46 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.068415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.054134 restraints weight = 22324.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 3.39
r_work: 0.2841 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6832  Z= 0.274
  Angle     :  0.578   9.803   9282  Z= 0.294
  Chirality :  0.043   0.253   1010
  Planarity :  0.004   0.033   1184
  Dihedral  :  7.059  57.068   1158
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.17 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.86 %
    Favored  : 85.86 %
  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:  0.00 (0.31), residues: 793
  helix:  1.15 (0.28), residues: 376
  sheet:  1.50 (0.84), residues: 44
  loop : -1.45 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 374 
 PHE   0.012   0.001   PHE F 523 
 TYR   0.013   0.001   TYR F 183 
 ARG   0.003   0.000   ARG F 460 

*********************** 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
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.709 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.7404 (tt0) cc_final: 0.7142 (tt0)
REVERT: F  190 MET cc_start: 0.8851 (tmm) cc_final: 0.8572 (tmm)
REVERT: F  427 ASP cc_start: 0.8920 (p0) cc_final: 0.8651 (p0)
  outliers start: 9
  outliers final: 4
  residues processed: 54
  average time/residue: 0.1881
  time to fit residues: 14.3886
Evaluate side-chains
  48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 44
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain F residue  259 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3304 r_free = 0.3304 target = 0.069408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.055226 restraints weight = 22043.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 3.38
r_work: 0.2868 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6832  Z= 0.178
  Angle     :  0.535   9.729   9282  Z= 0.271
  Chirality :  0.041   0.246   1010
  Planarity :  0.003   0.032   1184
  Dihedral  :  6.609  55.736   1158
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.79 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.00 %
    Favored  : 84.29 %
  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:  0.15 (0.31), residues: 793
  helix:  1.33 (0.28), residues: 375
  sheet:  1.22 (0.82), residues: 46
  loop : -1.40 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 374 
 PHE   0.009   0.001   PHE F 603 
 TYR   0.013   0.001   TYR F 183 
 ARG   0.001   0.000   ARG F 460 

*********************** 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
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.7322 (tt0) cc_final: 0.7100 (tt0)
REVERT: F   82 MET cc_start: 0.9108 (mpp) cc_final: 0.8871 (mpp)
REVERT: F   95 LEU cc_start: 0.9559 (tt) cc_final: 0.9325 (tt)
REVERT: F  376 MET cc_start: 0.9453 (tpp) cc_final: 0.9168 (tpp)
REVERT: F  427 ASP cc_start: 0.8934 (p0) cc_final: 0.8639 (p0)
  outliers start: 12
  outliers final: 5
  residues processed: 61
  average time/residue: 0.1784
  time to fit residues: 15.3034
Evaluate side-chains
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  259 ILE
Chi-restraints excluded: chain F residue  401 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0970
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3296 r_free = 0.3296 target = 0.068954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.054794 restraints weight = 21785.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 3.36
r_work: 0.2860 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6832  Z= 0.220
  Angle     :  0.554   9.760   9282  Z= 0.278
  Chirality :  0.042   0.248   1010
  Planarity :  0.003   0.031   1184
  Dihedral  :  6.419  55.245   1158
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.17 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.00 %
    Favored  : 84.29 %
  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:  1.35 (0.29), residues: 375
  sheet:  1.52 (0.84), residues: 44
  loop : -1.36 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 374 
 PHE   0.011   0.001   PHE F 523 
 TYR   0.013   0.001   TYR F 183 
 ARG   0.002   0.000   ARG F 460 

*********************** 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
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.7448 (tt0) cc_final: 0.7232 (tt0)
REVERT: F   95 LEU cc_start: 0.9562 (tt) cc_final: 0.9321 (tt)
REVERT: F  376 MET cc_start: 0.9501 (tpp) cc_final: 0.9242 (mmt)
REVERT: F  427 ASP cc_start: 0.8934 (p0) cc_final: 0.8643 (p0)
REVERT: F  479 GLU cc_start: 0.8226 (pt0) cc_final: 0.7953 (pt0)
  outliers start: 12
  outliers final: 6
  residues processed: 58
  average time/residue: 0.1706
  time to fit residues: 14.0113
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  259 ILE
Chi-restraints excluded: chain F residue  401 HIS
Chi-restraints excluded: chain F residue  491 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0270
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    0.3980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
F 442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.070077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.055952 restraints weight = 21600.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 3.36
r_work: 0.2887 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6832  Z= 0.155
  Angle     :  0.542   9.722   9282  Z= 0.269
  Chirality :  0.041   0.243   1010
  Planarity :  0.003   0.030   1184
  Dihedral  :  6.215  55.315   1158
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.79 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.14 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.27 (0.31), residues: 793
  helix:  1.38 (0.29), residues: 375
  sheet:  1.58 (0.85), residues: 44
  loop : -1.31 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 374 
 PHE   0.009   0.001   PHE F 603 
 TYR   0.012   0.001   TYR F 183 
 ARG   0.001   0.000   ARG F 460 

*********************** 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
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A  442 ASP cc_start: 0.8631 (m-30) cc_final: 0.8165 (m-30)
REVERT: A  516 GLU cc_start: 0.7438 (tt0) cc_final: 0.7211 (tt0)
REVERT: F   95 LEU cc_start: 0.9554 (tt) cc_final: 0.9307 (tt)
REVERT: F  376 MET cc_start: 0.9482 (tpp) cc_final: 0.9244 (mmt)
REVERT: F  427 ASP cc_start: 0.8928 (p0) cc_final: 0.8633 (p0)
  outliers start: 9
  outliers final: 5
  residues processed: 58
  average time/residue: 0.1783
  time to fit residues: 14.7880
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  259 ILE
Chi-restraints excluded: chain F residue  401 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 17 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3304 r_free = 0.3304 target = 0.069324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.055185 restraints weight = 21944.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 3.35
r_work: 0.2869 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6832  Z= 0.210
  Angle     :  0.561   9.753   9282  Z= 0.279
  Chirality :  0.042   0.247   1010
  Planarity :  0.003   0.029   1184
  Dihedral  :  6.175  55.342   1158
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.30 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.14 %
    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:  0.27 (0.31), residues: 793
  helix:  1.39 (0.29), residues: 375
  sheet:  1.56 (0.85), residues: 44
  loop : -1.31 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 374 
 PHE   0.010   0.001   PHE F 523 
 TYR   0.013   0.001   TYR F 183 
 ARG   0.002   0.000   ARG F 460 

*********************** 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
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.708 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.7498 (tt0) cc_final: 0.7251 (tt0)
REVERT: F   95 LEU cc_start: 0.9564 (tt) cc_final: 0.9312 (tt)
REVERT: F  427 ASP cc_start: 0.8933 (p0) cc_final: 0.8643 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 58
  average time/residue: 0.1810
  time to fit residues: 15.0719
Evaluate side-chains
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  259 ILE
Chi-restraints excluded: chain F residue  401 HIS
Chi-restraints excluded: chain F residue  468 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 41 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.069961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.055821 restraints weight = 21856.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 3.38
r_work: 0.2888 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6832  Z= 0.164
  Angle     :  0.544   9.721   9282  Z= 0.270
  Chirality :  0.041   0.243   1010
  Planarity :  0.003   0.029   1184
  Dihedral  :  5.992  55.459   1158
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.04 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 15.71 %
    Favored  : 83.29 %
  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:  0.31 (0.31), residues: 793
  helix:  1.48 (0.29), residues: 369
  sheet:  1.32 (0.84), residues: 46
  loop : -1.30 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 477 
 HIS   0.003   0.001   HIS F 374 
 PHE   0.009   0.001   PHE F 603 
 TYR   0.012   0.001   TYR F 183 
 ARG   0.001   0.000   ARG F 460 

*********************** 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
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8851 (m-30) cc_final: 0.8471 (m-30)
REVERT: A  516 GLU cc_start: 0.7499 (tt0) cc_final: 0.7268 (tt0)
REVERT: F   95 LEU cc_start: 0.9555 (tt) cc_final: 0.9305 (tt)
REVERT: F  190 MET cc_start: 0.8782 (tmm) cc_final: 0.8567 (tmm)
REVERT: F  427 ASP cc_start: 0.8925 (p0) cc_final: 0.8643 (p0)
  outliers start: 7
  outliers final: 5
  residues processed: 58
  average time/residue: 0.1772
  time to fit residues: 14.5499
Evaluate side-chains
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  259 ILE
Chi-restraints excluded: chain F residue  401 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 39 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
F 508 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.068942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.054795 restraints weight = 22248.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 3.38
r_work: 0.2856 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6832  Z= 0.235
  Angle     :  0.576   9.792   9282  Z= 0.289
  Chirality :  0.042   0.246   1010
  Planarity :  0.003   0.029   1184
  Dihedral  :  6.034  55.468   1158
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.67 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 16.00 %
    Favored  : 83.14 %
  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:  0.30 (0.31), residues: 793
  helix:  1.46 (0.29), residues: 369
  sheet:  1.57 (0.85), residues: 44
  loop : -1.30 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 477 
 HIS   0.003   0.001   HIS F 374 
 PHE   0.011   0.001   PHE F 523 
 TYR   0.014   0.001   TYR F 183 
 ARG   0.002   0.000   ARG A 403 

********************** 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
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.7563 (tt0) cc_final: 0.7319 (tt0)
REVERT: F   95 LEU cc_start: 0.9562 (tt) cc_final: 0.9317 (tt)
REVERT: F  427 ASP cc_start: 0.8931 (p0) cc_final: 0.8639 (p0)
  outliers start: 6
  outliers final: 5
  residues processed: 52
  average time/residue: 0.1979
  time to fit residues: 14.4888
Evaluate side-chains
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain F residue  160 GLU
Chi-restraints excluded: chain F residue  259 ILE
Chi-restraints excluded: chain F residue  401 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 71 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.069982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.055874 restraints weight = 22065.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 3.40
r_work: 0.2888 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6832  Z= 0.163
  Angle     :  0.546   9.706   9282  Z= 0.272
  Chirality :  0.041   0.242   1010
  Planarity :  0.003   0.029   1184
  Dihedral  :  5.851  55.518   1158
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.17 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 15.86 %
    Favored  : 83.14 %
  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:  0.35 (0.31), residues: 793
  helix:  1.52 (0.29), residues: 369
  sheet:  1.62 (0.86), residues: 44
  loop : -1.29 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP F 477 
 HIS   0.004   0.001   HIS F 374 
 PHE   0.009   0.001   PHE F 603 
 TYR   0.012   0.001   TYR F 183 
 ARG   0.001   0.000   ARG A 403 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3291.63 seconds
wall clock time: 59 minutes 27.35 seconds (3567.35 seconds total)