Starting phenix.real_space_refine
on Wed Jan 22 19:55:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9chq_45598/01_2025/9chq_45598.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9chq_45598/01_2025/9chq_45598.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9chq_45598/01_2025/9chq_45598.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9chq_45598/01_2025/9chq_45598.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9chq_45598/01_2025/9chq_45598.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9chq_45598/01_2025/9chq_45598.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6292      2.51       5
     N    1568      2.21       5
     O    1600      1.98       5
     H    9596      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 19104
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 4776
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 11, 'TRANS': 281}
          Chain breaks: 3
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 10.61, per 1000 atoms: 0.56
  Number of scatterers: 19104
  At special positions: 0
  Unit cell: (122.85, 122.85, 93.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     O    1600      8.00
     N    1568      7.00
     C    6292      6.00
     H    9596      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.68
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 0 sheets defined
      82.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 404 through 432
      removed outlier: 3.512A  pdb=" N   LEU A 416 " --> pdb=" O   TRP A 412 " (cutoff:3.500A)
      Proline residue:  A 426  - end of helix
    Processing helix  chain 'A' and resid 450 through 472
      removed outlier: 3.779A  pdb=" N   ILE A 467 " --> pdb=" O   PHE A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 496
    Processing helix  chain 'A' and resid 497 through 504
    Processing helix  chain 'A' and resid 505 through 506
      No H-bonds generated for 'chain 'A' and resid 505 through 506'
    Processing helix  chain 'A' and resid 507 through 511
    Processing helix  chain 'A' and resid 517 through 525
    Processing helix  chain 'A' and resid 526 through 530
    Processing helix  chain 'A' and resid 531 through 538
      removed outlier: 3.992A  pdb=" N   VAL A 535 " --> pdb=" O   ARG A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 543
    Processing helix  chain 'A' and resid 545 through 574
    Processing helix  chain 'A' and resid 584 through 593
    Processing helix  chain 'A' and resid 606 through 624
    Processing helix  chain 'A' and resid 634 through 667
      removed outlier: 3.659A  pdb=" N   PHE A 656 " --> pdb=" O   TYR A 652 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLY A 657 " --> pdb=" O   ALA A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 688
    Processing helix  chain 'A' and resid 690 through 709
      removed outlier: 4.168A  pdb=" N   ARG A 696 " --> pdb=" O   PRO A 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 432
      removed outlier: 3.512A  pdb=" N   LEU B 416 " --> pdb=" O   TRP B 412 " (cutoff:3.500A)
      Proline residue:  B 426  - end of helix
    Processing helix  chain 'B' and resid 450 through 472
      removed outlier: 3.779A  pdb=" N   ILE B 467 " --> pdb=" O   PHE B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 496
    Processing helix  chain 'B' and resid 497 through 504
    Processing helix  chain 'B' and resid 505 through 506
      No H-bonds generated for 'chain 'B' and resid 505 through 506'
    Processing helix  chain 'B' and resid 507 through 511
    Processing helix  chain 'B' and resid 517 through 525
    Processing helix  chain 'B' and resid 526 through 530
    Processing helix  chain 'B' and resid 531 through 538
      removed outlier: 3.991A  pdb=" N   VAL B 535 " --> pdb=" O   ARG B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 543
    Processing helix  chain 'B' and resid 545 through 574
    Processing helix  chain 'B' and resid 584 through 593
    Processing helix  chain 'B' and resid 606 through 624
    Processing helix  chain 'B' and resid 634 through 667
      removed outlier: 3.659A  pdb=" N   PHE B 656 " --> pdb=" O   TYR B 652 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLY B 657 " --> pdb=" O   ALA B 653 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 688
    Processing helix  chain 'B' and resid 690 through 709
      removed outlier: 4.168A  pdb=" N   ARG B 696 " --> pdb=" O   PRO B 692 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 432
      removed outlier: 3.513A  pdb=" N   LEU C 416 " --> pdb=" O   TRP C 412 " (cutoff:3.500A)
      Proline residue:  C 426  - end of helix
    Processing helix  chain 'C' and resid 450 through 472
      removed outlier: 3.779A  pdb=" N   ILE C 467 " --> pdb=" O   PHE C 463 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 485 through 496
    Processing helix  chain 'C' and resid 497 through 504
    Processing helix  chain 'C' and resid 505 through 506
      No H-bonds generated for 'chain 'C' and resid 505 through 506'
    Processing helix  chain 'C' and resid 507 through 511
    Processing helix  chain 'C' and resid 517 through 525
    Processing helix  chain 'C' and resid 526 through 530
    Processing helix  chain 'C' and resid 531 through 538
      removed outlier: 3.992A  pdb=" N   VAL C 535 " --> pdb=" O   ARG C 531 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 543
    Processing helix  chain 'C' and resid 545 through 574
    Processing helix  chain 'C' and resid 584 through 593
    Processing helix  chain 'C' and resid 606 through 624
    Processing helix  chain 'C' and resid 634 through 667
      removed outlier: 3.658A  pdb=" N   PHE C 656 " --> pdb=" O   TYR C 652 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLY C 657 " --> pdb=" O   ALA C 653 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 667 through 688
    Processing helix  chain 'C' and resid 690 through 709
      removed outlier: 4.168A  pdb=" N   ARG C 696 " --> pdb=" O   PRO C 692 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 432
      removed outlier: 3.512A  pdb=" N   LEU D 416 " --> pdb=" O   TRP D 412 " (cutoff:3.500A)
      Proline residue:  D 426  - end of helix
    Processing helix  chain 'D' and resid 450 through 472
      removed outlier: 3.779A  pdb=" N   ILE D 467 " --> pdb=" O   PHE D 463 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 485 through 496
    Processing helix  chain 'D' and resid 497 through 504
    Processing helix  chain 'D' and resid 505 through 506
      No H-bonds generated for 'chain 'D' and resid 505 through 506'
    Processing helix  chain 'D' and resid 507 through 511
    Processing helix  chain 'D' and resid 517 through 525
    Processing helix  chain 'D' and resid 526 through 530
    Processing helix  chain 'D' and resid 531 through 538
      removed outlier: 3.991A  pdb=" N   VAL D 535 " --> pdb=" O   ARG D 531 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 543
    Processing helix  chain 'D' and resid 545 through 574
    Processing helix  chain 'D' and resid 584 through 593
    Processing helix  chain 'D' and resid 606 through 624
    Processing helix  chain 'D' and resid 634 through 667
      removed outlier: 3.659A  pdb=" N   PHE D 656 " --> pdb=" O   TYR D 652 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLY D 657 " --> pdb=" O   ALA D 653 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 667 through 688
    Processing helix  chain 'D' and resid 690 through 709
      removed outlier: 4.168A  pdb=" N   ARG D 696 " --> pdb=" O   PRO D 692 " (cutoff:3.500A)

    692 hydrogen bonds defined for protein.
    2028 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: 6.82

  Time building geometry restraints manager: 5.60 seconds

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

  Histogram of bond lengths:
        0.96 -     1.13: 9580
        1.13 -     1.30: 1524
        1.30 -     1.48: 4047
        1.48 -     1.65: 4141
        1.65 -     1.82: 80
  Bond restraints: 19372
  Sorted by residual:
  bond pdb=" N   LEU C 559 "
       pdb=" H   LEU C 559 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.76e+01
  bond pdb=" CD2 HIS B 402 "
       pdb=" HD2 HIS B 402 "
    ideal  model  delta    sigma   weight residual
    0.930  1.082 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" N   ILE B 521 "
       pdb=" H   ILE B 521 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" N   ILE D 521 "
       pdb=" H   ILE D 521 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.71e+01
  bond pdb=" CE1 TYR D 616 "
       pdb=" HE1 TYR D 616 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.71e+01
  ... (remaining 19367 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.64: 29810
        2.64 -     5.27: 3954
        5.27 -     7.91: 1112
        7.91 -    10.54: 20
       10.54 -    13.18: 16
  Bond angle restraints: 34912
  Sorted by residual:
  angle pdb=" CB  HIS A 485 "
        pdb=" CG  HIS A 485 "
        pdb=" CD2 HIS A 485 "
      ideal   model   delta    sigma   weight residual
     131.20  125.15    6.05 1.30e+00 5.92e-01 2.16e+01
  angle pdb=" CB  HIS C 485 "
        pdb=" CG  HIS C 485 "
        pdb=" CD2 HIS C 485 "
      ideal   model   delta    sigma   weight residual
     131.20  125.15    6.05 1.30e+00 5.92e-01 2.16e+01
  angle pdb=" CB  HIS B 485 "
        pdb=" CG  HIS B 485 "
        pdb=" CD2 HIS B 485 "
      ideal   model   delta    sigma   weight residual
     131.20  125.15    6.05 1.30e+00 5.92e-01 2.16e+01
  angle pdb=" CB  HIS D 485 "
        pdb=" CG  HIS D 485 "
        pdb=" CD2 HIS D 485 "
      ideal   model   delta    sigma   weight residual
     131.20  125.15    6.05 1.30e+00 5.92e-01 2.16e+01
  angle pdb=" CA  ASN D 629 "
        pdb=" CB  ASN D 629 "
        pdb=" CG  ASN D 629 "
      ideal   model   delta    sigma   weight residual
     112.60  117.19   -4.59 1.00e+00 1.00e+00 2.11e+01
  ... (remaining 34907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.73: 8120
       12.73 -    25.45: 688
       25.45 -    38.18: 136
       38.18 -    50.91: 104
       50.91 -    63.64: 76
  Dihedral angle restraints: 9124
    sinusoidal: 4760
      harmonic: 4364
  Sorted by residual:
  dihedral pdb=" C   SER A 624 "
           pdb=" N   SER A 624 "
           pdb=" CA  SER A 624 "
           pdb=" CB  SER A 624 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.48   10.88     0      2.50e+00 1.60e-01 1.89e+01
  dihedral pdb=" C   SER B 624 "
           pdb=" N   SER B 624 "
           pdb=" CA  SER B 624 "
           pdb=" CB  SER B 624 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.48   10.88     0      2.50e+00 1.60e-01 1.89e+01
  dihedral pdb=" C   SER C 624 "
           pdb=" N   SER C 624 "
           pdb=" CA  SER C 624 "
           pdb=" CB  SER C 624 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.48   10.88     0      2.50e+00 1.60e-01 1.89e+01
  ... (remaining 9121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 970
       0.082 -    0.163: 446
       0.163 -    0.245: 64
       0.245 -    0.327: 12
       0.327 -    0.408: 4
  Chirality restraints: 1496
  Sorted by residual:
  chirality pdb=" CA  SER A 624 "
            pdb=" N   SER A 624 "
            pdb=" C   SER A 624 "
            pdb=" CB  SER A 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.16e+00
  chirality pdb=" CA  SER C 624 "
            pdb=" N   SER C 624 "
            pdb=" C   SER C 624 "
            pdb=" CB  SER C 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.16e+00
  chirality pdb=" CA  SER B 624 "
            pdb=" N   SER B 624 "
            pdb=" C   SER B 624 "
            pdb=" CB  SER B 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.16e+00
  ... (remaining 1493 not shown)

  Planarity restraints: 2732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 585 "   -0.113 2.00e-02 2.50e+03   5.22e-02 1.09e+02
        pdb=" CG  TRP D 585 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 585 "    0.042 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 585 "    0.072 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 585 "    0.063 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 585 "    0.070 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 585 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 585 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 585 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 585 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP D 585 "   -0.039 2.00e-02 2.50e+03
        pdb=" HE1 TRP D 585 "   -0.079 2.00e-02 2.50e+03
        pdb=" HE3 TRP D 585 "    0.018 2.00e-02 2.50e+03
        pdb=" HZ2 TRP D 585 "   -0.031 2.00e-02 2.50e+03
        pdb=" HZ3 TRP D 585 "   -0.039 2.00e-02 2.50e+03
        pdb=" HH2 TRP D 585 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 585 "   -0.113 2.00e-02 2.50e+03   5.22e-02 1.09e+02
        pdb=" CG  TRP B 585 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 585 "    0.042 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 585 "    0.072 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 585 "    0.063 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 585 "    0.070 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 585 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 585 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 585 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 585 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP B 585 "   -0.039 2.00e-02 2.50e+03
        pdb=" HE1 TRP B 585 "   -0.079 2.00e-02 2.50e+03
        pdb=" HE3 TRP B 585 "    0.018 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B 585 "   -0.031 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B 585 "   -0.039 2.00e-02 2.50e+03
        pdb=" HH2 TRP B 585 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 585 "   -0.113 2.00e-02 2.50e+03   5.22e-02 1.09e+02
        pdb=" CG  TRP C 585 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 585 "    0.042 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 585 "    0.072 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 585 "    0.063 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 585 "    0.070 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 585 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 585 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 585 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 585 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 TRP C 585 "   -0.039 2.00e-02 2.50e+03
        pdb=" HE1 TRP C 585 "   -0.079 2.00e-02 2.50e+03
        pdb=" HE3 TRP C 585 "    0.018 2.00e-02 2.50e+03
        pdb=" HZ2 TRP C 585 "   -0.031 2.00e-02 2.50e+03
        pdb=" HZ3 TRP C 585 "   -0.039 2.00e-02 2.50e+03
        pdb=" HH2 TRP C 585 "   -0.042 2.00e-02 2.50e+03
  ... (remaining 2729 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 948
        2.19 -     2.80: 33933
        2.80 -     3.40: 53431
        3.40 -     4.00: 70432
        4.00 -     4.60: 100229
  Nonbonded interactions: 258973
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 575 "
            pdb=" HG  SER B 636 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" OE2 GLU A 575 "
            pdb=" HG  SER A 636 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" OE2 GLU C 575 "
            pdb=" HG  SER C 636 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" OE2 GLU D 575 "
            pdb=" HG  SER D 636 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" HG  SER D 620 "
            pdb=" O   VAL D 625 "
     model   vdw
     1.616 2.450
  ... (remaining 258968 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.330
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     41.320
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  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:13.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
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      :  0.013   0.044   9776  Z= 0.831
  Angle     :  1.730   7.344  13288  Z= 1.200
  Chirality :  0.089   0.408   1496
  Planarity :  0.016   0.155   1620
  Dihedral  : 11.630  63.038   3420
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.36 %
  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: -0.39 (0.24), residues: 1140
  helix: -0.20 (0.16), residues: 892
  sheet:  None (None), residues: 0
  loop :  0.17 (0.46), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.083   0.016   TRP A 585 
 HIS   0.008   0.003   HIS D 587 
 PHE   0.063   0.012   PHE D 701 
 TYR   0.089   0.023   TYR D 611 
 ARG   0.007   0.001   ARG B 541 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  664 GLN cc_start: 0.6981 (mt0) cc_final: 0.6700 (mm110)
REVERT: A  691 ASN cc_start: 0.7994 (t0) cc_final: 0.7495 (m110)
REVERT: A  700 TYR cc_start: 0.7633 (t80) cc_final: 0.7345 (t80)
REVERT: B  664 GLN cc_start: 0.6980 (mt0) cc_final: 0.6701 (mm110)
REVERT: B  691 ASN cc_start: 0.7992 (t0) cc_final: 0.7495 (m110)
REVERT: B  700 TYR cc_start: 0.7633 (t80) cc_final: 0.7345 (t80)
REVERT: C  664 GLN cc_start: 0.6979 (mt0) cc_final: 0.6699 (mm110)
REVERT: C  691 ASN cc_start: 0.7990 (t0) cc_final: 0.7497 (m110)
REVERT: C  700 TYR cc_start: 0.7638 (t80) cc_final: 0.7349 (t80)
REVERT: D  664 GLN cc_start: 0.6984 (mt0) cc_final: 0.6701 (mm110)
REVERT: D  691 ASN cc_start: 0.7991 (t0) cc_final: 0.7494 (m110)
REVERT: D  700 TYR cc_start: 0.7638 (t80) cc_final: 0.7349 (t80)
  outliers start: 0
  outliers final: 4
  residues processed: 240
  average time/residue: 2.3762
  time to fit residues: 614.5544
Evaluate side-chains
  165 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 161
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain D residue  464 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    0.6980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.173583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.110950 restraints weight = 29141.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.49
r_work: 0.2916 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9776  Z= 0.208
  Angle     :  0.569   5.353  13288  Z= 0.321
  Chirality :  0.040   0.147   1496
  Planarity :  0.005   0.037   1620
  Dihedral  :  4.910  26.121   1288
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.88 %
    Favored  : 93.73 %
  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:  1.54 (0.25), residues: 1140
  helix:  1.20 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop :  0.68 (0.46), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 568 
 HIS   0.003   0.001   HIS A 674 
 PHE   0.014   0.002   PHE D 656 
 TYR   0.017   0.002   TYR B 611 
 ARG   0.004   0.001   ARG B 528 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 188
  time to evaluate  : 1.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  688 GLN cc_start: 0.7740 (mp10) cc_final: 0.7539 (mp10)
REVERT: A  691 ASN cc_start: 0.7593 (t0) cc_final: 0.7259 (m-40)
REVERT: B  691 ASN cc_start: 0.7593 (t0) cc_final: 0.7257 (m-40)
REVERT: C  691 ASN cc_start: 0.7594 (t0) cc_final: 0.7262 (m-40)
REVERT: D  688 GLN cc_start: 0.7754 (mp10) cc_final: 0.7554 (mp10)
REVERT: D  691 ASN cc_start: 0.7593 (t0) cc_final: 0.7258 (m-40)
  outliers start: 4
  outliers final: 0
  residues processed: 188
  average time/residue: 2.0598
  time to fit residues: 422.9331
Evaluate side-chains
  166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 691 ASN
A 695 GLN
B 691 ASN
B 695 GLN
C 691 ASN
C 695 GLN
D 691 ASN
D 695 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.171443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.107096 restraints weight = 29123.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.47
r_work: 0.2877 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9776  Z= 0.275
  Angle     :  0.546   4.732  13288  Z= 0.302
  Chirality :  0.040   0.137   1496
  Planarity :  0.005   0.059   1620
  Dihedral  :  4.183  14.341   1280
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 1.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.41 %
    Favored  : 88.82 %
  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:  1.77 (0.25), residues: 1140
  helix:  1.41 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop :  0.54 (0.46), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 568 
 HIS   0.003   0.001   HIS A 687 
 PHE   0.013   0.002   PHE B 656 
 TYR   0.016   0.002   TYR A 611 
 ARG   0.009   0.001   ARG D 679 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 1.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  499 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6492 (tm)
REVERT: A  688 GLN cc_start: 0.7817 (mp10) cc_final: 0.7561 (mp10)
REVERT: B  499 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6459 (tm)
REVERT: B  688 GLN cc_start: 0.7907 (mp10) cc_final: 0.7689 (mp10)
REVERT: C  499 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6457 (tm)
REVERT: C  688 GLN cc_start: 0.7912 (mp10) cc_final: 0.7694 (mp10)
REVERT: C  691 ASN cc_start: 0.7354 (t0) cc_final: 0.7045 (m-40)
REVERT: D  499 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6458 (tm)
REVERT: D  688 GLN cc_start: 0.7811 (mp10) cc_final: 0.7556 (mp10)
  outliers start: 18
  outliers final: 4
  residues processed: 175
  average time/residue: 2.2174
  time to fit residues: 421.1080
Evaluate side-chains
  179 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 171
  time to evaluate  : 1.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  499 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 108 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 695 GLN
B 695 GLN
C 695 GLN
D 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.173213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.109108 restraints weight = 29242.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.56
r_work: 0.2904 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   9776  Z= 0.182
  Angle     :  0.471   4.508  13288  Z= 0.259
  Chirality :  0.038   0.136   1496
  Planarity :  0.004   0.048   1620
  Dihedral  :  3.917  14.469   1280
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.37 %
    Favored  : 86.67 %
  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:  2.08 (0.25), residues: 1140
  helix:  1.64 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop :  0.58 (0.46), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 568 
 HIS   0.004   0.001   HIS C 587 
 PHE   0.011   0.001   PHE A 656 
 TYR   0.015   0.001   TYR D 611 
 ARG   0.008   0.001   ARG B 679 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 1.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  499 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6445 (tm)
REVERT: A  688 GLN cc_start: 0.7850 (mp10) cc_final: 0.7565 (mp10)
REVERT: B  499 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.6403 (tm)
REVERT: B  688 GLN cc_start: 0.7821 (mp10) cc_final: 0.7568 (mp10)
REVERT: C  499 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6431 (tm)
REVERT: C  688 GLN cc_start: 0.7842 (mp10) cc_final: 0.7599 (mp10)
REVERT: D  499 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6406 (tm)
REVERT: D  688 GLN cc_start: 0.7851 (mp10) cc_final: 0.7565 (mp10)
  outliers start: 20
  outliers final: 4
  residues processed: 175
  average time/residue: 2.3140
  time to fit residues: 439.0407
Evaluate side-chains
  170 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 162
  time to evaluate  : 1.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  499 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 695 GLN
B 695 GLN
C 695 GLN
D 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.173831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.106881 restraints weight = 28823.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.16
r_work: 0.2924 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9776  Z= 0.193
  Angle     :  0.478   4.458  13288  Z= 0.259
  Chirality :  0.038   0.137   1496
  Planarity :  0.005   0.058   1620
  Dihedral  :  3.824  14.382   1280
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.35 %
    Favored  : 86.37 %
  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:  2.23 (0.26), residues: 1140
  helix:  1.77 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop :  0.55 (0.47), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 568 
 HIS   0.003   0.001   HIS D 587 
 PHE   0.010   0.001   PHE C 656 
 TYR   0.015   0.001   TYR D 611 
 ARG   0.009   0.001   ARG D 582 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 171
  time to evaluate  : 1.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LEU cc_start: 0.6587 (mp) cc_final: 0.6366 (mp)
REVERT: A  678 LEU cc_start: 0.7792 (mt) cc_final: 0.7402 (tt)
REVERT: A  688 GLN cc_start: 0.7809 (mp10) cc_final: 0.7477 (mp10)
REVERT: B  468 LEU cc_start: 0.6586 (mp) cc_final: 0.6367 (mp)
REVERT: B  582 ARG cc_start: 0.6180 (mtp-110) cc_final: 0.5698 (mtm-85)
REVERT: B  663 ILE cc_start: 0.7109 (mm) cc_final: 0.6807 (mt)
REVERT: B  678 LEU cc_start: 0.7803 (mt) cc_final: 0.7412 (tt)
REVERT: B  688 GLN cc_start: 0.7755 (mp10) cc_final: 0.7477 (mp10)
REVERT: C  468 LEU cc_start: 0.6584 (mp) cc_final: 0.6364 (mp)
REVERT: C  663 ILE cc_start: 0.7118 (mm) cc_final: 0.6813 (mt)
REVERT: C  678 LEU cc_start: 0.7798 (mt) cc_final: 0.7408 (tt)
REVERT: C  688 GLN cc_start: 0.7762 (mp10) cc_final: 0.7486 (mp10)
REVERT: D  468 LEU cc_start: 0.6586 (mp) cc_final: 0.6366 (mp)
REVERT: D  582 ARG cc_start: 0.6179 (mtp-110) cc_final: 0.5697 (mtm-85)
REVERT: D  663 ILE cc_start: 0.7123 (mm) cc_final: 0.6815 (mt)
REVERT: D  678 LEU cc_start: 0.7801 (mt) cc_final: 0.7409 (tt)
REVERT: D  688 GLN cc_start: 0.7811 (mp10) cc_final: 0.7478 (mp10)
  outliers start: 13
  outliers final: 4
  residues processed: 175
  average time/residue: 2.4225
  time to fit residues: 457.3795
Evaluate side-chains
  175 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 171
  time to evaluate  : 1.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain D residue  462 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 695 GLN
B 695 GLN
C 695 GLN
D 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.176874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.112821 restraints weight = 28641.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.52
r_work: 0.2930 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   9776  Z= 0.153
  Angle     :  0.454   4.321  13288  Z= 0.244
  Chirality :  0.037   0.139   1496
  Planarity :  0.005   0.063   1620
  Dihedral  :  3.700  14.743   1280
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 1.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 14.02 %
    Favored  : 85.59 %
  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:  2.50 (0.26), residues: 1140
  helix:  1.92 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop :  0.83 (0.46), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 568 
 HIS   0.002   0.001   HIS C 587 
 PHE   0.010   0.001   PHE A 656 
 TYR   0.013   0.001   TYR A 611 
 ARG   0.008   0.001   ARG B 679 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 172
  time to evaluate  : 1.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LEU cc_start: 0.6543 (mp) cc_final: 0.6309 (mp)
REVERT: A  663 ILE cc_start: 0.7080 (mm) cc_final: 0.6790 (mt)
REVERT: A  678 LEU cc_start: 0.7769 (mt) cc_final: 0.7391 (tt)
REVERT: A  688 GLN cc_start: 0.7760 (mp10) cc_final: 0.7468 (mp10)
REVERT: A  695 GLN cc_start: 0.6887 (mp10) cc_final: 0.6610 (mp10)
REVERT: B  468 LEU cc_start: 0.6531 (mp) cc_final: 0.6299 (mp)
REVERT: B  582 ARG cc_start: 0.6343 (mtp-110) cc_final: 0.5806 (mtm-85)
REVERT: B  663 ILE cc_start: 0.7098 (mm) cc_final: 0.6805 (mt)
REVERT: B  678 LEU cc_start: 0.7775 (mt) cc_final: 0.7399 (tt)
REVERT: B  688 GLN cc_start: 0.7727 (mp10) cc_final: 0.7429 (mp10)
REVERT: B  695 GLN cc_start: 0.6887 (mp10) cc_final: 0.6612 (mp10)
REVERT: C  468 LEU cc_start: 0.6541 (mp) cc_final: 0.6309 (mp)
REVERT: C  663 ILE cc_start: 0.7100 (mm) cc_final: 0.6805 (mt)
REVERT: C  678 LEU cc_start: 0.7773 (mt) cc_final: 0.7397 (tt)
REVERT: C  688 GLN cc_start: 0.7736 (mp10) cc_final: 0.7438 (mp10)
REVERT: C  695 GLN cc_start: 0.6892 (mp10) cc_final: 0.6619 (mp10)
REVERT: D  468 LEU cc_start: 0.6549 (mp) cc_final: 0.6314 (mp)
REVERT: D  582 ARG cc_start: 0.6340 (mtp-110) cc_final: 0.5802 (mtm-85)
REVERT: D  663 ILE cc_start: 0.7092 (mm) cc_final: 0.6796 (mt)
REVERT: D  678 LEU cc_start: 0.7770 (mt) cc_final: 0.7393 (tt)
REVERT: D  688 GLN cc_start: 0.7768 (mp10) cc_final: 0.7434 (mp10)
REVERT: D  695 GLN cc_start: 0.6897 (mp10) cc_final: 0.6622 (mp10)
  outliers start: 4
  outliers final: 4
  residues processed: 172
  average time/residue: 2.4896
  time to fit residues: 461.1715
Evaluate side-chains
  172 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain D residue  462 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 115 optimal weight:    7.9990
   chunk 98 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.175870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.109348 restraints weight = 28406.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 2.54
r_work: 0.2886 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   9776  Z= 0.236
  Angle     :  0.490   4.409  13288  Z= 0.265
  Chirality :  0.038   0.140   1496
  Planarity :  0.005   0.064   1620
  Dihedral  :  3.749  14.459   1280
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 15.29 %
    Favored  : 83.73 %
  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:  2.30 (0.25), residues: 1140
  helix:  1.79 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop :  0.69 (0.47), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 568 
 HIS   0.003   0.001   HIS A 687 
 PHE   0.011   0.001   PHE D 656 
 TYR   0.015   0.002   TYR A 611 
 ARG   0.008   0.001   ARG C 582 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 174
  time to evaluate  : 1.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 LEU cc_start: 0.6629 (mp) cc_final: 0.6413 (mp)
REVERT: A  499 LEU cc_start: 0.6715 (OUTLIER) cc_final: 0.6419 (tm)
REVERT: A  579 MET cc_start: 0.5452 (OUTLIER) cc_final: 0.5127 (mpt)
REVERT: A  678 LEU cc_start: 0.7812 (mt) cc_final: 0.7433 (tt)
REVERT: A  688 GLN cc_start: 0.7772 (mp10) cc_final: 0.7483 (mp10)
REVERT: B  468 LEU cc_start: 0.6622 (mp) cc_final: 0.6411 (mp)
REVERT: B  499 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6378 (tm)
REVERT: B  582 ARG cc_start: 0.6411 (mtp-110) cc_final: 0.5843 (mtm-85)
REVERT: B  678 LEU cc_start: 0.7817 (mt) cc_final: 0.7439 (tt)
REVERT: B  688 GLN cc_start: 0.7753 (mp10) cc_final: 0.7462 (mp10)
REVERT: C  468 LEU cc_start: 0.6630 (mp) cc_final: 0.6416 (mp)
REVERT: C  499 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6411 (tm)
REVERT: C  579 MET cc_start: 0.5460 (OUTLIER) cc_final: 0.5132 (mpt)
REVERT: C  678 LEU cc_start: 0.7820 (mt) cc_final: 0.7443 (tt)
REVERT: C  688 GLN cc_start: 0.7761 (mp10) cc_final: 0.7470 (mp10)
REVERT: D  468 LEU cc_start: 0.6631 (mp) cc_final: 0.6418 (mp)
REVERT: D  499 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6371 (tm)
REVERT: D  582 ARG cc_start: 0.6414 (mtp-110) cc_final: 0.5845 (mtm-85)
REVERT: D  678 LEU cc_start: 0.7817 (mt) cc_final: 0.7438 (tt)
REVERT: D  688 GLN cc_start: 0.7772 (mp10) cc_final: 0.7482 (mp10)
  outliers start: 10
  outliers final: 4
  residues processed: 174
  average time/residue: 2.3996
  time to fit residues: 450.9614
Evaluate side-chains
  180 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  579 MET
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  499 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 10 optimal weight:    0.8980
   chunk 96 optimal weight:   10.0000
   chunk 113 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 695 GLN
B 695 GLN
C 695 GLN
D 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.176508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.108442 restraints weight = 28384.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 2.60
r_work: 0.2922 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   9776  Z= 0.157
  Angle     :  0.454   4.252  13288  Z= 0.242
  Chirality :  0.037   0.129   1496
  Planarity :  0.005   0.069   1620
  Dihedral  :  3.643  14.747   1280
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 1.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 14.90 %
    Favored  : 83.92 %
  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:  2.53 (0.25), residues: 1140
  helix:  1.94 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop :  0.82 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 568 
 HIS   0.002   0.001   HIS A 687 
 PHE   0.010   0.001   PHE A 656 
 TYR   0.013   0.001   TYR A 611 
 ARG   0.010   0.001   ARG C 582 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  499 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6426 (tm)
REVERT: A  579 MET cc_start: 0.5512 (OUTLIER) cc_final: 0.5227 (mpt)
REVERT: A  651 MET cc_start: 0.6928 (mtp) cc_final: 0.6405 (ttm)
REVERT: A  678 LEU cc_start: 0.7794 (mt) cc_final: 0.7420 (tt)
REVERT: A  688 GLN cc_start: 0.7765 (mp10) cc_final: 0.7465 (mp10)
REVERT: B  582 ARG cc_start: 0.6340 (mtp-110) cc_final: 0.5797 (mtm-85)
REVERT: B  678 LEU cc_start: 0.7796 (mt) cc_final: 0.7423 (tt)
REVERT: B  688 GLN cc_start: 0.7783 (mp10) cc_final: 0.7472 (mp10)
REVERT: C  499 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6390 (tm)
REVERT: C  579 MET cc_start: 0.5514 (OUTLIER) cc_final: 0.5227 (mpt)
REVERT: C  651 MET cc_start: 0.6923 (mtp) cc_final: 0.6396 (ttm)
REVERT: C  678 LEU cc_start: 0.7798 (mt) cc_final: 0.7425 (tt)
REVERT: C  688 GLN cc_start: 0.7785 (mp10) cc_final: 0.7475 (mp10)
REVERT: D  468 LEU cc_start: 0.6602 (mp) cc_final: 0.6401 (mp)
REVERT: D  582 ARG cc_start: 0.6332 (mtp-110) cc_final: 0.5786 (mtm-85)
REVERT: D  678 LEU cc_start: 0.7800 (mt) cc_final: 0.7428 (tt)
REVERT: D  688 GLN cc_start: 0.7768 (mp10) cc_final: 0.7469 (mp10)
  outliers start: 12
  outliers final: 8
  residues processed: 170
  average time/residue: 2.4067
  time to fit residues: 441.6891
Evaluate side-chains
  182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  499 LEU
Chi-restraints excluded: chain C residue  579 MET
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  464 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   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 695 GLN
B 695 GLN
C 695 GLN
D 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.183369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.118928 restraints weight = 27931.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.34
r_work: 0.2942 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   9776  Z= 0.147
  Angle     :  0.446   4.250  13288  Z= 0.237
  Chirality :  0.037   0.129   1496
  Planarity :  0.005   0.071   1620
  Dihedral  :  3.571  14.861   1280
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.29 %
    Favored  : 83.53 %
  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:  2.65 (0.25), residues: 1140
  helix:  2.03 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop :  0.85 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 568 
 HIS   0.002   0.001   HIS A 687 
 PHE   0.009   0.001   PHE D 656 
 TYR   0.013   0.001   TYR A 611 
 ARG   0.010   0.001   ARG C 582 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  579 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.5296 (mpt)
REVERT: A  688 GLN cc_start: 0.7750 (mp10) cc_final: 0.7416 (mp10)
REVERT: B  499 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6406 (tm)
REVERT: B  582 ARG cc_start: 0.6364 (mtp-110) cc_final: 0.5827 (mtm-85)
REVERT: B  688 GLN cc_start: 0.7777 (mp10) cc_final: 0.7466 (mp10)
REVERT: C  579 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.5288 (mpt)
REVERT: C  688 GLN cc_start: 0.7779 (mp10) cc_final: 0.7468 (mp10)
REVERT: D  499 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6402 (tm)
REVERT: D  582 ARG cc_start: 0.6358 (mtp-110) cc_final: 0.5823 (mtm-85)
REVERT: D  688 GLN cc_start: 0.7752 (mp10) cc_final: 0.7455 (mp10)
  outliers start: 12
  outliers final: 8
  residues processed: 174
  average time/residue: 2.3838
  time to fit residues: 448.2013
Evaluate side-chains
  182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 1.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  579 MET
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  464 ILE
Chi-restraints excluded: chain D residue  499 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 695 GLN
B 695 GLN
C 695 GLN
D 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.176306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.108634 restraints weight = 28366.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.66
r_work: 0.2938 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.4742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   9776  Z= 0.176
  Angle     :  0.462   4.283  13288  Z= 0.246
  Chirality :  0.037   0.130   1496
  Planarity :  0.005   0.070   1620
  Dihedral  :  3.585  14.719   1280
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 14.90 %
    Favored  : 83.73 %
  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:  2.57 (0.25), residues: 1140
  helix:  1.98 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop :  0.82 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 568 
 HIS   0.002   0.001   HIS C 687 
 PHE   0.010   0.001   PHE C 656 
 TYR   0.014   0.001   TYR C 611 
 ARG   0.011   0.001   ARG A 582 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 170
  time to evaluate  : 1.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  499 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6328 (tm)
REVERT: A  579 MET cc_start: 0.5310 (OUTLIER) cc_final: 0.5040 (mpt)
REVERT: A  688 GLN cc_start: 0.7714 (mp10) cc_final: 0.7378 (mp10)
REVERT: B  499 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6287 (tm)
REVERT: B  582 ARG cc_start: 0.6333 (mtp-110) cc_final: 0.5791 (mtm-85)
REVERT: B  688 GLN cc_start: 0.7714 (mp10) cc_final: 0.7405 (mp10)
REVERT: C  579 MET cc_start: 0.5312 (OUTLIER) cc_final: 0.5042 (mpt)
REVERT: C  688 GLN cc_start: 0.7724 (mp10) cc_final: 0.7415 (mp10)
REVERT: D  499 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6286 (tm)
REVERT: D  582 ARG cc_start: 0.6328 (mtp-110) cc_final: 0.5785 (mtm-85)
REVERT: D  688 GLN cc_start: 0.7715 (mp10) cc_final: 0.7379 (mp10)
  outliers start: 14
  outliers final: 12
  residues processed: 170
  average time/residue: 2.4293
  time to fit residues: 445.2371
Evaluate side-chains
  187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 MET
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  695 GLN
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain B residue  499 LEU
Chi-restraints excluded: chain B residue  695 GLN
Chi-restraints excluded: chain C residue  462 MET
Chi-restraints excluded: chain C residue  464 ILE
Chi-restraints excluded: chain C residue  579 MET
Chi-restraints excluded: chain C residue  695 GLN
Chi-restraints excluded: chain D residue  462 MET
Chi-restraints excluded: chain D residue  464 ILE
Chi-restraints excluded: chain D residue  499 LEU
Chi-restraints excluded: chain D residue  695 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    0.2980
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 695 GLN
B 695 GLN
C 695 GLN
D 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.176896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.110730 restraints weight = 28303.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.42
r_work: 0.2925 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.4692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9776  Z= 0.156
  Angle     :  0.465   4.846  13288  Z= 0.248
  Chirality :  0.036   0.135   1496
  Planarity :  0.005   0.069   1620
  Dihedral  :  3.560  14.819   1280
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 15.29 %
    Favored  : 82.94 %
  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:  2.64 (0.25), residues: 1140
  helix:  2.05 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop :  0.75 (0.46), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 568 
 HIS   0.002   0.001   HIS C 687 
 PHE   0.009   0.001   PHE D 656 
 TYR   0.014   0.001   TYR B 611 
 ARG   0.011   0.001   ARG A 582 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 14803.55 seconds
wall clock time: 261 minutes 10.53 seconds (15670.53 seconds total)