Starting phenix.real_space_refine
on Sat May 10 08:32:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b8i_44346/05_2025/9b8i_44346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b8i_44346/05_2025/9b8i_44346.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b8i_44346/05_2025/9b8i_44346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b8i_44346/05_2025/9b8i_44346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b8i_44346/05_2025/9b8i_44346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b8i_44346/05_2025/9b8i_44346.cif"
  }
  resolution = 3.18
  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=   0.053
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      24      5.16       5
     C    3551      2.51       5
     N     968      2.21       5
     O    1067      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5610
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 5610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 719, 5610
          Classifications: {'peptide': 719}
          Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 664}
          Chain breaks: 3
  Time building chain proxies: 4.19, per 1000 atoms: 0.75
  Number of scatterers: 5610
  At special positions: 0
  Unit cell: (92.88, 82.08, 97.2, 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      24     16.00
     O    1067      8.00
     N     968      7.00
     C    3551      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.28
  Conformation dependent library (CDL) restraints added in 792.2 milliseconds
  

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 11 sheets defined
      23.5% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'C' and resid 26 through 42
    Processing helix  chain 'C' and resid 43 through 58
      removed outlier: 3.589A  pdb=" N   VAL C  47 " --> pdb=" O   ARG C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 71
      removed outlier: 3.712A  pdb=" N   VAL C  65 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 90
      removed outlier: 3.804A  pdb=" N   LEU C  85 " --> pdb=" O   ALA C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 212
      removed outlier: 3.560A  pdb=" N   ALA C 212 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 208 through 212'
    Processing helix  chain 'C' and resid 276 through 280
    Processing helix  chain 'C' and resid 291 through 295
    Processing helix  chain 'C' and resid 371 through 390
    Processing helix  chain 'C' and resid 391 through 393
      No H-bonds generated for 'chain 'C' and resid 391 through 393'
    Processing helix  chain 'C' and resid 452 through 465
    Processing helix  chain 'C' and resid 503 through 507
    Processing helix  chain 'C' and resid 509 through 512
    Processing helix  chain 'C' and resid 662 through 670
      removed outlier: 3.906A  pdb=" N   PHE C 666 " --> pdb=" O   ASP C 662 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 691 through 709
    Processing helix  chain 'C' and resid 774 through 779
    Processing helix  chain 'C' and resid 815 through 828
    Processing helix  chain 'C' and resid 828 through 833
    Processing sheet with id=AA1, first strand: chain 'C' and resid 201 through 207
      removed outlier: 3.640A  pdb=" N   VAL C 204 " --> pdb=" O   LEU C 333 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU C 333 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU C 206 " --> pdb=" O   LEU C 331 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   LYS C 241 " --> pdb=" O   THR C 334 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   GLN C 336 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   VAL C 239 " --> pdb=" O   GLN C 336 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ASP C 324 " --> pdb=" O   THR C 249 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 201 through 207
      removed outlier: 3.640A  pdb=" N   VAL C 204 " --> pdb=" O   LEU C 333 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU C 333 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU C 206 " --> pdb=" O   LEU C 331 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   LYS C 241 " --> pdb=" O   THR C 334 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   GLN C 336 " --> pdb=" O   VAL C 239 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   VAL C 239 " --> pdb=" O   GLN C 336 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 290 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 226 through 232
      removed outlier: 3.704A  pdb=" N   VAL C 263 " --> pdb=" O   GLY C 271 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   GLY C 271 " --> pdb=" O   VAL C 263 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   LEU C 265 " --> pdb=" O   LEU C 269 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 398 through 400
      removed outlier: 3.596A  pdb=" N   ALA C 408 " --> pdb=" O   LYS C 444 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLY C 450 " --> pdb=" O   ALA C 412 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 501 through 502
      removed outlier: 3.806A  pdb=" N   ASP C 542 " --> pdb=" O   ASP C 650 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 502
      removed outlier: 3.806A  pdb=" N   ASP C 542 " --> pdb=" O   ASP C 650 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 523 through 528
      removed outlier: 3.590A  pdb=" N   ASN C 611 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN C 570 " --> pdb=" O   ILE C 562 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   LEU C 564 " --> pdb=" O   PHE C 568 " (cutoff:3.500A)
      removed outlier: 5.415A  pdb=" N   PHE C 568 " --> pdb=" O   LEU C 564 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 533 through 534
      removed outlier: 3.554A  pdb=" N   ILE C 658 " --> pdb=" O   VAL C 858 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 625 through 626
    Processing sheet with id=AB1, first strand: chain 'C' and resid 717 through 719
      removed outlier: 6.776A  pdb=" N   THR C 682 " --> pdb=" O   THR C 717 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   THR C 719 " --> pdb=" O   THR C 682 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   THR C 684 " --> pdb=" O   THR C 719 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ILE C 683 " --> pdb=" O   MET C 733 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   ILE C 735 " --> pdb=" O   ILE C 683 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   VAL C 685 " --> pdb=" O   ILE C 735 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ILE C 732 " --> pdb=" O   ILE C 809 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   LEU C 811 " --> pdb=" O   ILE C 732 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   ILE C 734 " --> pdb=" O   LEU C 811 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ALA C 813 " --> pdb=" O   ILE C 734 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL C 841 " --> pdb=" O   ASN C 848 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 750 through 753
      removed outlier: 3.737A  pdb=" N   TRP C 758 " --> pdb=" O   LEU C 751 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   SER C 757 " --> pdb=" O   THR C 785 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   THR C 785 " --> pdb=" O   SER C 757 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   VAL C 759 " --> pdb=" O   ARG C 783 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ARG C 783 " --> pdb=" O   VAL C 759 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   THR C 761 " --> pdb=" O   GLU C 781 " (cutoff:3.500A)

    220 hydrogen bonds defined for protein.
    576 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: 1.96

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1888
        1.35 -     1.46: 1143
        1.46 -     1.58: 2655
        1.58 -     1.70: 0
        1.70 -     1.82: 46
  Bond restraints: 5732
  Sorted by residual:
  bond pdb=" N   ILE C 295 "
       pdb=" CA  ILE C 295 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.037 1.24e-02 6.50e+03 8.86e+00
  bond pdb=" N   ASN C 827 "
       pdb=" CA  ASN C 827 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.038 1.31e-02 5.83e+03 8.50e+00
  bond pdb=" N   VAL C 718 "
       pdb=" CA  VAL C 718 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.59e+00
  bond pdb=" N   ILE C 714 "
       pdb=" CA  ILE C 714 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.30e-02 5.92e+03 7.49e+00
  bond pdb=" N   LYS C 653 "
       pdb=" CA  LYS C 653 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.26e-02 6.30e+03 7.29e+00
  ... (remaining 5727 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 7394
        1.19 -     2.38: 288
        2.38 -     3.57: 96
        3.57 -     4.76: 8
        4.76 -     5.94: 7
  Bond angle restraints: 7793
  Sorted by residual:
  angle pdb=" N   ILE C 223 "
        pdb=" CA  ILE C 223 "
        pdb=" C   ILE C 223 "
      ideal   model   delta    sigma   weight residual
     112.96  109.14    3.82 1.00e+00 1.00e+00 1.46e+01
  angle pdb=" CA  VAL C  47 "
        pdb=" C   VAL C  47 "
        pdb=" O   VAL C  47 "
      ideal   model   delta    sigma   weight residual
     120.95  117.32    3.63 1.04e+00 9.25e-01 1.22e+01
  angle pdb=" CA  THR C 719 "
        pdb=" CB  THR C 719 "
        pdb=" OG1 THR C 719 "
      ideal   model   delta    sigma   weight residual
     109.60  104.65    4.95 1.50e+00 4.44e-01 1.09e+01
  angle pdb=" N   ARG C 817 "
        pdb=" CA  ARG C 817 "
        pdb=" C   ARG C 817 "
      ideal   model   delta    sigma   weight residual
     111.07  107.61    3.46 1.07e+00 8.73e-01 1.05e+01
  angle pdb=" CA  THR C 717 "
        pdb=" CB  THR C 717 "
        pdb=" OG1 THR C 717 "
      ideal   model   delta    sigma   weight residual
     109.60  104.83    4.77 1.50e+00 4.44e-01 1.01e+01
  ... (remaining 7788 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 3076
       16.90 -    33.80: 321
       33.80 -    50.70: 66
       50.70 -    67.60: 32
       67.60 -    84.50: 5
  Dihedral angle restraints: 3500
    sinusoidal: 1422
      harmonic: 2078
  Sorted by residual:
  dihedral pdb=" CA  ASP C 616 "
           pdb=" CB  ASP C 616 "
           pdb=" CG  ASP C 616 "
           pdb=" OD1 ASP C 616 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.86   59.86     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CA  ASP C 324 "
           pdb=" CB  ASP C 324 "
           pdb=" CG  ASP C 324 "
           pdb=" OD1 ASP C 324 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.15   53.15     1      2.00e+01 2.50e-03 9.61e+00
  dihedral pdb=" CA  LYS C 487 "
           pdb=" CB  LYS C 487 "
           pdb=" CG  LYS C 487 "
           pdb=" CD  LYS C 487 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.09  -58.91     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 3497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 619
       0.039 -    0.077: 148
       0.077 -    0.116: 87
       0.116 -    0.155: 16
       0.155 -    0.193: 3
  Chirality restraints: 873
  Sorted by residual:
  chirality pdb=" CA  VAL C 718 "
            pdb=" N   VAL C 718 "
            pdb=" C   VAL C 718 "
            pdb=" CB  VAL C 718 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.34e-01
  chirality pdb=" CA  LEU C  51 "
            pdb=" N   LEU C  51 "
            pdb=" C   LEU C  51 "
            pdb=" CB  LEU C  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.43e-01
  chirality pdb=" CA  ILE C 714 "
            pdb=" N   ILE C 714 "
            pdb=" C   ILE C 714 "
            pdb=" CB  ILE C 714 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 870 not shown)

  Planarity restraints: 1035
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 451 "   -0.261 9.50e-02 1.11e+02   1.17e-01 8.40e+00
        pdb=" NE  ARG C 451 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 451 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 451 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 451 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 224 "    0.012 2.00e-02 2.50e+03   2.47e-02 6.10e+00
        pdb=" C   ASN C 224 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   ASN C 224 "    0.016 2.00e-02 2.50e+03
        pdb=" N   PRO C 225 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  53 "    0.204 9.50e-02 1.11e+02   9.13e-02 5.16e+00
        pdb=" NE  ARG C  53 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  53 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  53 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  53 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1032 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1647
        2.82 -     3.34: 4962
        3.34 -     3.86: 8833
        3.86 -     4.38: 9901
        4.38 -     4.90: 17552
  Nonbonded interactions: 42895
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN C 342 "
            pdb=" O   MET C 434 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" O   PRO C 441 "
            pdb=" NZ  LYS C 444 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" O   THR C 361 "
            pdb=" OG1 THR C 361 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" N   GLU C 230 "
            pdb=" OE1 GLU C 230 "
     model   vdw
     2.366 3.120
  nonbonded pdb=" NE2 GLN C  28 "
            pdb=" OD2 ASP C  58 "
     model   vdw
     2.379 3.120
  ... (remaining 42890 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.830
  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:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.270
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5732  Z= 0.247
  Angle     :  0.590   5.945   7793  Z= 0.375
  Chirality :  0.046   0.193    873
  Planarity :  0.007   0.117   1035
  Dihedral  : 15.418  84.495   2156
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 18.91 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.37 (0.32), residues: 711
  helix:  0.72 (0.43), residues: 147
  sheet:  0.51 (0.37), residues: 208
  loop : -0.01 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 384 
 HIS   0.001   0.000   HIS C 437 
 PHE   0.010   0.001   PHE C 704 
 TYR   0.007   0.001   TYR C 335 
 ARG   0.005   0.000   ARG C  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20332 (  207)
  hydrogen bonds       : angle       8.46637 (  576)
  covalent geometry    : bond        0.00360 ( 5732)
  covalent geometry    : angle       0.58959 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.577 
Fit side-chains
REVERT: C  235 SER cc_start: 0.9045 (m) cc_final: 0.8833 (t)
REVERT: C  355 SER cc_start: 0.9640 (m) cc_final: 0.9409 (t)
REVERT: C  519 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8053 (mm-30)
REVERT: C  676 MET cc_start: 0.7843 (mmm) cc_final: 0.7578 (mmt)
  outliers start: 6
  outliers final: 6
  residues processed: 88
  average time/residue: 0.1642
  time to fit residues: 19.3310
Evaluate side-chains
  79 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  632 ILE
Chi-restraints excluded: chain C residue  704 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0020
   chunk 41 optimal weight:    0.0870
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.4968

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

Flipped N/Q/H residues before XYZ refinement:
C 414 ASN
C 578 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.119209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.093706 restraints weight = 9569.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 3.21
r_work: 0.3060 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.0918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5732  Z= 0.102
  Angle     :  0.510   6.023   7793  Z= 0.260
  Chirality :  0.043   0.196    873
  Planarity :  0.004   0.042   1035
  Dihedral  :  5.009  56.632    783
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.91 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.68 (0.31), residues: 711
  helix:  1.68 (0.44), residues: 142
  sheet:  0.52 (0.36), residues: 206
  loop : -0.00 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 384 
 HIS   0.002   0.000   HIS C 437 
 PHE   0.011   0.001   PHE C 704 
 TYR   0.007   0.001   TYR C 619 
 ARG   0.004   0.000   ARG C 451 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03472 (  207)
  hydrogen bonds       : angle       5.92507 (  576)
  covalent geometry    : bond        0.00225 ( 5732)
  covalent geometry    : angle       0.51024 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.605 
Fit side-chains
REVERT: C  235 SER cc_start: 0.9068 (m) cc_final: 0.8771 (t)
REVERT: C  355 SER cc_start: 0.9704 (m) cc_final: 0.9370 (t)
REVERT: C  452 ASP cc_start: 0.6894 (p0) cc_final: 0.6688 (p0)
REVERT: C  519 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8059 (mm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 92
  average time/residue: 0.1486
  time to fit residues: 18.9208
Evaluate side-chains
  81 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
C  48 GLN
C 414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.112603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.087126 restraints weight = 9723.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 3.17
r_work: 0.2960 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5732  Z= 0.228
  Angle     :  0.600   6.345   7793  Z= 0.304
  Chirality :  0.046   0.188    873
  Planarity :  0.005   0.045   1035
  Dihedral  :  5.318  54.888    779
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.43 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.47 (0.31), residues: 711
  helix:  1.60 (0.44), residues: 142
  sheet:  0.23 (0.34), residues: 228
  loop : -0.08 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 384 
 HIS   0.005   0.001   HIS C 437 
 PHE   0.020   0.002   PHE C 704 
 TYR   0.013   0.001   TYR C 619 
 ARG   0.004   0.001   ARG C  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  207)
  hydrogen bonds       : angle       5.55303 (  576)
  covalent geometry    : bond        0.00547 ( 5732)
  covalent geometry    : angle       0.60009 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.644 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8820 (ttm-80) cc_final: 0.8542 (ttm-80)
REVERT: C   56 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7494 (mm)
REVERT: C  254 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8138 (pp)
REVERT: C  449 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8175 (t80)
REVERT: C  542 ASP cc_start: 0.8122 (m-30) cc_final: 0.7720 (m-30)
REVERT: C  726 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8608 (tp40)
  outliers start: 21
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1484
  time to fit residues: 19.1872
Evaluate side-chains
  87 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  716 LEU
Chi-restraints excluded: chain C residue  724 THR
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0010
   overall best weight:    0.5988

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.116458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.090591 restraints weight = 9734.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 3.24
r_work: 0.3017 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5732  Z= 0.102
  Angle     :  0.505   6.087   7793  Z= 0.256
  Chirality :  0.043   0.183    873
  Planarity :  0.004   0.044   1035
  Dihedral  :  5.091  57.217    779
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 19.07 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.59 (0.31), residues: 711
  helix:  1.75 (0.44), residues: 142
  sheet:  0.17 (0.35), residues: 212
  loop :  0.09 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 384 
 HIS   0.002   0.000   HIS C 437 
 PHE   0.010   0.001   PHE C 704 
 TYR   0.009   0.001   TYR C 619 
 ARG   0.003   0.000   ARG C  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02889 (  207)
  hydrogen bonds       : angle       5.19326 (  576)
  covalent geometry    : bond        0.00235 ( 5732)
  covalent geometry    : angle       0.50463 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.606 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8798 (ttm-80) cc_final: 0.8411 (ttm-80)
REVERT: C  311 ASP cc_start: 0.8855 (t0) cc_final: 0.8465 (t0)
REVERT: C  361 THR cc_start: 0.9169 (p) cc_final: 0.8838 (t)
REVERT: C  449 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7828 (t80)
REVERT: C  620 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7986 (mtp)
  outliers start: 20
  outliers final: 11
  residues processed: 93
  average time/residue: 0.1578
  time to fit residues: 19.9548
Evaluate side-chains
  84 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  410 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  629 ASP
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  639 ASN
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  716 LEU
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.3465 r_free = 0.3465 target = 0.113452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.087403 restraints weight = 9689.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3088 rms_B_bonded: 3.22
r_work: 0.2961 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   5732  Z= 0.190
  Angle     :  0.575   8.207   7793  Z= 0.288
  Chirality :  0.045   0.176    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.281  56.301    779
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.39 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.58 (0.31), residues: 711
  helix:  1.91 (0.44), residues: 136
  sheet:  0.18 (0.34), residues: 226
  loop :  0.03 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 863 
 HIS   0.004   0.001   HIS C 437 
 PHE   0.017   0.001   PHE C 704 
 TYR   0.012   0.001   TYR C 619 
 ARG   0.003   0.000   ARG C 764 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  207)
  hydrogen bonds       : angle       5.24268 (  576)
  covalent geometry    : bond        0.00458 ( 5732)
  covalent geometry    : angle       0.57514 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.587 
Fit side-chains
REVERT: C  254 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8097 (pp)
REVERT: C  311 ASP cc_start: 0.8876 (t0) cc_final: 0.8515 (t0)
REVERT: C  410 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.8996 (m)
REVERT: C  449 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7992 (t80)
REVERT: C  452 ASP cc_start: 0.7155 (p0) cc_final: 0.6924 (p0)
REVERT: C  777 ASP cc_start: 0.8911 (m-30) cc_final: 0.8637 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 89
  average time/residue: 0.1474
  time to fit residues: 18.1205
Evaluate side-chains
  93 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  204 VAL
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  410 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  629 ASP
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  639 ASN
Chi-restraints excluded: chain C residue  649 ILE
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  716 LEU
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.113901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.088608 restraints weight = 9561.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 3.17
r_work: 0.2984 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5732  Z= 0.149
  Angle     :  0.544   7.343   7793  Z= 0.272
  Chirality :  0.044   0.172    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.273  57.134    779
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 19.87 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.54 (0.31), residues: 711
  helix:  1.91 (0.44), residues: 136
  sheet:  0.11 (0.35), residues: 215
  loop :  0.01 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 384 
 HIS   0.003   0.001   HIS C 437 
 PHE   0.013   0.001   PHE C 704 
 TYR   0.010   0.001   TYR C 619 
 ARG   0.003   0.000   ARG C 582 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03000 (  207)
  hydrogen bonds       : angle       5.14781 (  576)
  covalent geometry    : bond        0.00362 ( 5732)
  covalent geometry    : angle       0.54355 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.594 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8468 (ttm-80)
REVERT: C  311 ASP cc_start: 0.8854 (t0) cc_final: 0.8500 (t0)
REVERT: C  410 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.8995 (m)
REVERT: C  449 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7972 (t80)
REVERT: C  452 ASP cc_start: 0.7098 (p0) cc_final: 0.6825 (p0)
REVERT: C  777 ASP cc_start: 0.8948 (m-30) cc_final: 0.8666 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 93
  average time/residue: 0.1613
  time to fit residues: 20.5944
Evaluate side-chains
  92 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  410 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  463 ILE
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  629 ASP
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  639 ASN
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  716 LEU
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    0.2980
   chunk 55 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.114624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.088489 restraints weight = 9679.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.26
r_work: 0.2986 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5732  Z= 0.128
  Angle     :  0.541   6.742   7793  Z= 0.269
  Chirality :  0.044   0.168    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.229  58.062    779
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.67 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.58 (0.31), residues: 711
  helix:  1.94 (0.44), residues: 136
  sheet:  0.08 (0.34), residues: 222
  loop :  0.08 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 384 
 HIS   0.003   0.001   HIS C 437 
 PHE   0.012   0.001   PHE C 704 
 TYR   0.009   0.001   TYR C 619 
 ARG   0.003   0.000   ARG C 582 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02878 (  207)
  hydrogen bonds       : angle       5.07586 (  576)
  covalent geometry    : bond        0.00307 ( 5732)
  covalent geometry    : angle       0.54116 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.936 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8808 (ttm-80) cc_final: 0.8431 (ttm-80)
REVERT: C  254 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8082 (pp)
REVERT: C  311 ASP cc_start: 0.8861 (t0) cc_final: 0.8506 (t0)
REVERT: C  410 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9006 (m)
REVERT: C  449 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.7922 (t80)
REVERT: C  452 ASP cc_start: 0.7110 (p0) cc_final: 0.6824 (p0)
REVERT: C  777 ASP cc_start: 0.8968 (m-30) cc_final: 0.8678 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 91
  average time/residue: 0.2105
  time to fit residues: 26.8876
Evaluate side-chains
  92 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  410 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  463 ILE
Chi-restraints excluded: chain C residue  543 MET
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  629 ASP
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  639 ASN
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  716 LEU
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0980
   chunk 37 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
C 266 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.115272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.089906 restraints weight = 9562.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 3.16
r_work: 0.3007 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5732  Z= 0.108
  Angle     :  0.524   6.394   7793  Z= 0.260
  Chirality :  0.043   0.164    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.153  59.152    779
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.19 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.65 (0.31), residues: 711
  helix:  2.06 (0.44), residues: 136
  sheet:  0.14 (0.35), residues: 212
  loop :  0.09 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 384 
 HIS   0.002   0.001   HIS C 437 
 PHE   0.010   0.001   PHE C 704 
 TYR   0.008   0.001   TYR C 619 
 ARG   0.003   0.000   ARG C 582 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02689 (  207)
  hydrogen bonds       : angle       4.94482 (  576)
  covalent geometry    : bond        0.00257 ( 5732)
  covalent geometry    : angle       0.52350 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.589 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8818 (ttm-80) cc_final: 0.8439 (ttm-80)
REVERT: C  311 ASP cc_start: 0.8834 (t0) cc_final: 0.8479 (t0)
REVERT: C  410 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.8972 (m)
REVERT: C  452 ASP cc_start: 0.7027 (p0) cc_final: 0.6736 (p0)
REVERT: C  519 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7945 (mm-30)
REVERT: C  620 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8029 (mtp)
REVERT: C  777 ASP cc_start: 0.8946 (m-30) cc_final: 0.8579 (t0)
REVERT: C  864 PHE cc_start: 0.7557 (p90) cc_final: 0.7122 (p90)
  outliers start: 19
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1786
  time to fit residues: 21.8574
Evaluate side-chains
  89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  410 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  463 ILE
Chi-restraints excluded: chain C residue  543 MET
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  629 ASP
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  639 ASN
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  716 LEU
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    0.4980
   chunk 32 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.115148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.089580 restraints weight = 9584.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 3.20
r_work: 0.3001 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5732  Z= 0.120
  Angle     :  0.555  11.730   7793  Z= 0.269
  Chirality :  0.043   0.162    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.161  58.973    779
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 20.35 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.65 (0.31), residues: 711
  helix:  2.02 (0.44), residues: 136
  sheet:  0.18 (0.35), residues: 212
  loop :  0.08 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 384 
 HIS   0.002   0.001   HIS C 437 
 PHE   0.011   0.001   PHE C 704 
 TYR   0.008   0.001   TYR C 619 
 ARG   0.004   0.000   ARG C 582 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02719 (  207)
  hydrogen bonds       : angle       4.89270 (  576)
  covalent geometry    : bond        0.00292 ( 5732)
  covalent geometry    : angle       0.55500 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.705 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8819 (ttm-80) cc_final: 0.8429 (ttm-80)
REVERT: C  254 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8016 (pp)
REVERT: C  311 ASP cc_start: 0.8851 (t0) cc_final: 0.8500 (t0)
REVERT: C  452 ASP cc_start: 0.7035 (p0) cc_final: 0.6683 (p0)
REVERT: C  620 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7871 (mtp)
REVERT: C  777 ASP cc_start: 0.8970 (m-30) cc_final: 0.8507 (t0)
REVERT: C  864 PHE cc_start: 0.7560 (p90) cc_final: 0.7165 (p90)
  outliers start: 20
  outliers final: 16
  residues processed: 83
  average time/residue: 0.1626
  time to fit residues: 18.4900
Evaluate side-chains
  88 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  410 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  463 ILE
Chi-restraints excluded: chain C residue  543 MET
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  629 ASP
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  639 ASN
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0980
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 46 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0670
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.4920

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.116408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.090915 restraints weight = 9693.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 3.21
r_work: 0.3022 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5732  Z= 0.098
  Angle     :  0.540  11.257   7793  Z= 0.262
  Chirality :  0.043   0.140    873
  Planarity :  0.004   0.048   1035
  Dihedral  :  5.074  59.907    779
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.31 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.71 (0.31), residues: 711
  helix:  2.12 (0.45), residues: 136
  sheet:  0.25 (0.35), residues: 214
  loop :  0.06 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 384 
 HIS   0.002   0.001   HIS C 346 
 PHE   0.009   0.001   PHE C 704 
 TYR   0.006   0.001   TYR C 619 
 ARG   0.004   0.000   ARG C 582 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02563 (  207)
  hydrogen bonds       : angle       4.70572 (  576)
  covalent geometry    : bond        0.00232 ( 5732)
  covalent geometry    : angle       0.54040 ( 7793)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.633 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8809 (ttm-80) cc_final: 0.8425 (ttm-80)
REVERT: C  254 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7942 (pp)
REVERT: C  311 ASP cc_start: 0.8863 (t0) cc_final: 0.8514 (t0)
REVERT: C  361 THR cc_start: 0.9118 (p) cc_final: 0.8834 (t)
REVERT: C  410 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.8960 (m)
REVERT: C  519 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7936 (mm-30)
REVERT: C  620 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7930 (mtp)
REVERT: C  777 ASP cc_start: 0.8963 (m-30) cc_final: 0.8512 (t0)
REVERT: C  864 PHE cc_start: 0.7535 (p90) cc_final: 0.7128 (p90)
  outliers start: 17
  outliers final: 13
  residues processed: 86
  average time/residue: 0.1590
  time to fit residues: 18.6547
Evaluate side-chains
  85 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  365 VAL
Chi-restraints excluded: chain C residue  410 VAL
Chi-restraints excluded: chain C residue  449 PHE
Chi-restraints excluded: chain C residue  543 MET
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  620 MET
Chi-restraints excluded: chain C residue  629 ASP
Chi-restraints excluded: chain C residue  633 THR
Chi-restraints excluded: chain C residue  639 ASN
Chi-restraints excluded: chain C residue  704 PHE
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  785 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 224 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.090160 restraints weight = 9691.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 3.24
r_work: 0.3012 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5732  Z= 0.114
  Angle     :  0.557  11.340   7793  Z= 0.274
  Chirality :  0.043   0.157    873
  Planarity :  0.004   0.048   1035
  Dihedral  :  5.081  59.597    779
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.99 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.70 (0.31), residues: 711
  helix:  2.15 (0.45), residues: 136
  sheet:  0.26 (0.35), residues: 214
  loop :  0.03 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 384 
 HIS   0.002   0.001   HIS C 437 
 PHE   0.010   0.001   PHE C 704 
 TYR   0.008   0.001   TYR C 619 
 ARG   0.004   0.000   ARG C 582 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02606 (  207)
  hydrogen bonds       : angle       4.70372 (  576)
  covalent geometry    : bond        0.00271 ( 5732)
  covalent geometry    : angle       0.55673 ( 7793)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2872.73 seconds
wall clock time: 50 minutes 31.14 seconds (3031.14 seconds total)