Starting phenix.real_space_refine
on Fri Aug 22 16:15:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b8i_44346/08_2025/9b8i_44346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b8i_44346/08_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_44346/08_2025/9b8i_44346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b8i_44346/08_2025/9b8i_44346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b8i_44346/08_2025/9b8i_44346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b8i_44346/08_2025/9b8i_44346.cif"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.23, per 1000 atoms: 0.22
  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: 0.27
  Conformation dependent library (CDL) restraints added in 167.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.16
  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: 0.75

  Time building geometry restraints manager: 0.38 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:             5.340
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.010
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.760
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.000   ARG C  87 
 TYR   0.007   0.001   TYR C 335 
 PHE   0.010   0.001   PHE C 704 
 TRP   0.005   0.001   TRP C 384 
 HIS   0.001   0.000   HIS C 437 

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

*********************** 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  : 0.205 
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: 0.0614
  time to fit residues: 7.2518
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  : 0.126 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.114865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.089683 restraints weight = 9773.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 3.17
r_work: 0.2993 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   5732  Z= 0.191
  Angle     :  0.574   5.970   7793  Z= 0.293
  Chirality :  0.045   0.203    873
  Planarity :  0.004   0.043   1035
  Dihedral  :  5.269  54.980    783
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 18.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.31), residues: 711
  helix:  1.59 (0.44), residues: 142
  sheet:  0.46 (0.36), residues: 207
  loop : -0.05 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 451 
 TYR   0.009   0.001   TYR C 619 
 PHE   0.016   0.002   PHE C 704 
 TRP   0.006   0.001   TRP C 384 
 HIS   0.004   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 5732)
  covalent geometry    : angle       0.57421 ( 7793)
  hydrogen bonds       : bond        0.03976 (  207)
  hydrogen bonds       : angle       6.01835 (  576)

*********************** 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
  94 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.178 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.8507 (ttm-80)
REVERT: C  235 SER cc_start: 0.9238 (m) cc_final: 0.8961 (t)
REVERT: C  361 THR cc_start: 0.9187 (p) cc_final: 0.8868 (t)
REVERT: C  646 ASP cc_start: 0.8930 (t70) cc_final: 0.8299 (t0)
  outliers start: 22
  outliers final: 11
  residues processed: 90
  average time/residue: 0.0557
  time to fit residues: 6.9660
Evaluate side-chains
  83 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 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  724 THR
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 32 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.3784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.089335 restraints weight = 9626.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 3.14
r_work: 0.2996 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1406

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= 0.153
  Angle     :  0.535   6.028   7793  Z= 0.271
  Chirality :  0.044   0.191    873
  Planarity :  0.004   0.044   1035
  Dihedral  :  5.143  56.340    779
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.31), residues: 711
  helix:  1.61 (0.44), residues: 142
  sheet:  0.24 (0.34), residues: 228
  loop : -0.01 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  87 
 TYR   0.009   0.001   TYR C 619 
 PHE   0.014   0.001   PHE C 704 
 TRP   0.009   0.001   TRP C 384 
 HIS   0.003   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5732)
  covalent geometry    : angle       0.53503 ( 7793)
  hydrogen bonds       : bond        0.03487 (  207)
  hydrogen bonds       : angle       5.50848 (  576)

*********************** 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: 19
    poor density    : 79
  time to evaluate  : 0.211 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8761 (ttm-80) cc_final: 0.8453 (ttm-80)
REVERT: C   56 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7520 (mm)
REVERT: C  235 SER cc_start: 0.9283 (m) cc_final: 0.9025 (t)
REVERT: C  254 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8113 (pp)
REVERT: C  449 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8006 (t80)
REVERT: C  452 ASP cc_start: 0.7123 (p0) cc_final: 0.6861 (p0)
REVERT: C  551 MET cc_start: 0.8432 (tpp) cc_final: 0.8214 (tpp)
REVERT: C  726 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8584 (tp40)
  outliers start: 19
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0613
  time to fit residues: 7.8278
Evaluate side-chains
  86 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
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  255 LEU
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  633 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.114794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.089669 restraints weight = 9589.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 3.15
r_work: 0.3002 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1535

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= 0.130
  Angle     :  0.527   7.324   7793  Z= 0.265
  Chirality :  0.044   0.179    873
  Planarity :  0.004   0.044   1035
  Dihedral  :  5.135  57.087    779
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.43 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.31), residues: 711
  helix:  1.94 (0.44), residues: 136
  sheet:  0.19 (0.35), residues: 216
  loop :  0.11 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  87 
 TYR   0.008   0.001   TYR C 619 
 PHE   0.013   0.001   PHE C 704 
 TRP   0.009   0.001   TRP C 384 
 HIS   0.003   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5732)
  covalent geometry    : angle       0.52681 ( 7793)
  hydrogen bonds       : bond        0.03129 (  207)
  hydrogen bonds       : angle       5.29516 (  576)

*********************** 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
  101 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.132 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.8528 (ttm-80)
REVERT: C  254 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8041 (pp)
REVERT: C  311 ASP cc_start: 0.8852 (t0) cc_final: 0.8471 (t0)
REVERT: C  361 THR cc_start: 0.9175 (p) cc_final: 0.8822 (t)
REVERT: C  410 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.8995 (m)
REVERT: C  449 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7989 (t80)
REVERT: C  551 MET cc_start: 0.8369 (tpp) cc_final: 0.8109 (tpp)
REVERT: C  777 ASP cc_start: 0.8901 (m-30) cc_final: 0.8503 (t70)
  outliers start: 25
  outliers final: 15
  residues processed: 93
  average time/residue: 0.0535
  time to fit residues: 6.9026
Evaluate side-chains
  93 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 LEU
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  463 ILE
Chi-restraints excluded: chain C residue  541 ILE
Chi-restraints excluded: chain C residue  550 THR
Chi-restraints excluded: chain C residue  554 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    1.2584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.088716 restraints weight = 9806.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 3.26
r_work: 0.2983 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1681

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= 0.143
  Angle     :  0.532   6.255   7793  Z= 0.267
  Chirality :  0.044   0.174    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.191  57.407    779
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.07 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.31), residues: 711
  helix:  1.94 (0.44), residues: 136
  sheet:  0.16 (0.34), residues: 222
  loop :  0.12 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 582 
 TYR   0.009   0.001   TYR C 619 
 PHE   0.014   0.001   PHE C 704 
 TRP   0.009   0.001   TRP C 384 
 HIS   0.003   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5732)
  covalent geometry    : angle       0.53176 ( 7793)
  hydrogen bonds       : bond        0.03090 (  207)
  hydrogen bonds       : angle       5.21306 (  576)

*********************** 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
  98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.138 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8551 (ttm-80)
REVERT: C  254 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8119 (pp)
REVERT: C  311 ASP cc_start: 0.8860 (t0) cc_final: 0.8495 (t0)
REVERT: C  410 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.8996 (m)
REVERT: C  449 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.7998 (t80)
REVERT: C  452 ASP cc_start: 0.7139 (p0) cc_final: 0.6904 (p0)
REVERT: C  551 MET cc_start: 0.8384 (tpp) cc_final: 0.8101 (tpp)
REVERT: C  777 ASP cc_start: 0.8950 (m-30) cc_final: 0.8561 (t70)
REVERT: C  864 PHE cc_start: 0.7603 (p90) cc_final: 0.7203 (p90)
  outliers start: 21
  outliers final: 16
  residues processed: 92
  average time/residue: 0.0547
  time to fit residues: 7.0336
Evaluate side-chains
  95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain C residue  254 LEU
Chi-restraints excluded: chain C residue  255 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  414 ASN
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 17 optimal weight:    0.0040
   chunk 43 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.9796

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
C 414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.115605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.089296 restraints weight = 9744.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 3.25
r_work: 0.2993 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5732  Z= 0.123
  Angle     :  0.527   6.183   7793  Z= 0.264
  Chirality :  0.044   0.170    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.173  57.943    779
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 19.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.31), residues: 711
  helix:  2.01 (0.44), residues: 136
  sheet:  0.17 (0.35), residues: 212
  loop :  0.13 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 582 
 TYR   0.008   0.001   TYR C 619 
 PHE   0.013   0.001   PHE C 704 
 TRP   0.009   0.001   TRP C 384 
 HIS   0.003   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5732)
  covalent geometry    : angle       0.52748 ( 7793)
  hydrogen bonds       : bond        0.02937 (  207)
  hydrogen bonds       : angle       5.14971 (  576)

*********************** 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
  100 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 77
  time to evaluate  : 0.205 
Fit side-chains
REVERT: C   53 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.8563 (ttm-80)
REVERT: C  254 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8081 (pp)
REVERT: C  311 ASP cc_start: 0.8855 (t0) cc_final: 0.8483 (t0)
REVERT: C  410 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.9000 (m)
REVERT: C  449 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7828 (t80)
REVERT: C  452 ASP cc_start: 0.7111 (p0) cc_final: 0.6831 (p0)
REVERT: C  551 MET cc_start: 0.8362 (tpp) cc_final: 0.8071 (tpp)
REVERT: C  554 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7953 (p)
REVERT: C  777 ASP cc_start: 0.8992 (m-30) cc_final: 0.8546 (t70)
REVERT: C  864 PHE cc_start: 0.7590 (p90) cc_final: 0.7155 (p90)
  outliers start: 23
  outliers final: 16
  residues processed: 93
  average time/residue: 0.0508
  time to fit residues: 6.5218
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  : 0.142 
-------------------------------------------------------------------------------
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  254 LEU
Chi-restraints excluded: chain C residue  255 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  550 THR
Chi-restraints excluded: chain C residue  554 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.3990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.111501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.085305 restraints weight = 9978.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.26
r_work: 0.2934 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   5732  Z= 0.246
  Angle     :  0.623   6.265   7793  Z= 0.313
  Chirality :  0.047   0.174    873
  Planarity :  0.005   0.048   1035
  Dihedral  :  5.524  57.329    779
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.31), residues: 711
  helix:  1.51 (0.44), residues: 141
  sheet:  0.03 (0.34), residues: 218
  loop : -0.16 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 582 
 TYR   0.014   0.001   TYR C 619 
 PHE   0.020   0.002   PHE C 704 
 TRP   0.009   0.002   TRP C 863 
 HIS   0.006   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 5732)
  covalent geometry    : angle       0.62299 ( 7793)
  hydrogen bonds       : bond        0.03577 (  207)
  hydrogen bonds       : angle       5.34752 (  576)

*********************** 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
  102 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.216 
Fit side-chains
REVERT: C  311 ASP cc_start: 0.8878 (t0) cc_final: 0.8579 (t0)
REVERT: C  410 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.9000 (m)
REVERT: C  449 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8143 (t80)
REVERT: C  452 ASP cc_start: 0.7183 (p0) cc_final: 0.6872 (p0)
REVERT: C  551 MET cc_start: 0.8353 (tpp) cc_final: 0.8051 (tpp)
REVERT: C  777 ASP cc_start: 0.8918 (m-30) cc_final: 0.8498 (t0)
REVERT: C  850 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7951 (pp)
  outliers start: 23
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0628
  time to fit residues: 8.1824
Evaluate side-chains
  88 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  204 VAL
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  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  766 THR
Chi-restraints excluded: chain C residue  785 THR
Chi-restraints excluded: chain C residue  850 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0770
   overall best weight:    0.7140

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.089338 restraints weight = 9568.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 3.17
r_work: 0.2998 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5732  Z= 0.110
  Angle     :  0.539   7.124   7793  Z= 0.268
  Chirality :  0.044   0.171    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.139  59.409    778
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.99 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.31), residues: 711
  helix:  1.94 (0.44), residues: 136
  sheet:  0.20 (0.36), residues: 200
  loop :  0.07 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 582 
 TYR   0.006   0.001   TYR C 509 
 PHE   0.011   0.001   PHE C 704 
 TRP   0.012   0.001   TRP C 384 
 HIS   0.002   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5732)
  covalent geometry    : angle       0.53925 ( 7793)
  hydrogen bonds       : bond        0.02819 (  207)
  hydrogen bonds       : angle       5.12549 (  576)

*********************** 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
  97 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.133 
Fit side-chains
REVERT: C  311 ASP cc_start: 0.8842 (t0) cc_final: 0.8500 (t0)
REVERT: C  410 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9003 (m)
REVERT: C  452 ASP cc_start: 0.7102 (p0) cc_final: 0.6798 (p0)
REVERT: C  551 MET cc_start: 0.8368 (tpp) cc_final: 0.8059 (tpp)
REVERT: C  777 ASP cc_start: 0.8898 (m-30) cc_final: 0.8521 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 94
  average time/residue: 0.0575
  time to fit residues: 7.4079
Evaluate side-chains
  89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
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  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  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 49 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.3386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.113836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.088369 restraints weight = 9686.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 3.19
r_work: 0.2982 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5732  Z= 0.152
  Angle     :  0.558   7.093   7793  Z= 0.277
  Chirality :  0.044   0.169    873
  Planarity :  0.004   0.047   1035
  Dihedral  :  5.197  59.851    778
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.67 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.31), residues: 711
  helix:  1.61 (0.44), residues: 142
  sheet:  0.26 (0.36), residues: 203
  loop :  0.04 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 582 
 TYR   0.009   0.001   TYR C 619 
 PHE   0.014   0.001   PHE C 704 
 TRP   0.009   0.001   TRP C 384 
 HIS   0.004   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 5732)
  covalent geometry    : angle       0.55766 ( 7793)
  hydrogen bonds       : bond        0.02986 (  207)
  hydrogen bonds       : angle       5.11913 (  576)

*********************** 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
  94 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.141 
Fit side-chains
REVERT: C  311 ASP cc_start: 0.8870 (t0) cc_final: 0.8533 (t0)
REVERT: C  410 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.8992 (m)
REVERT: C  452 ASP cc_start: 0.7067 (p0) cc_final: 0.6750 (p0)
REVERT: C  551 MET cc_start: 0.8370 (tpp) cc_final: 0.8057 (tpp)
REVERT: C  777 ASP cc_start: 0.8900 (m-30) cc_final: 0.8502 (t0)
  outliers start: 18
  outliers final: 16
  residues processed: 90
  average time/residue: 0.0526
  time to fit residues: 6.5742
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  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  349 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  527 LEU
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  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  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 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.7788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.113315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.087239 restraints weight = 9848.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 3.27
r_work: 0.2954 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5732  Z= 0.190
  Angle     :  0.591   7.124   7793  Z= 0.294
  Chirality :  0.045   0.169    873
  Planarity :  0.004   0.048   1035
  Dihedral  :  5.319  59.973    778
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 20.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.31), residues: 711
  helix:  1.53 (0.44), residues: 142
  sheet:  0.17 (0.37), residues: 195
  loop : -0.13 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 582 
 TYR   0.008   0.001   TYR C 248 
 PHE   0.017   0.001   PHE C 704 
 TRP   0.009   0.001   TRP C 863 
 HIS   0.005   0.001   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 5732)
  covalent geometry    : angle       0.59059 ( 7793)
  hydrogen bonds       : bond        0.03236 (  207)
  hydrogen bonds       : angle       5.18670 (  576)

********************** 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
  94 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.149 
Fit side-chains
REVERT: C  311 ASP cc_start: 0.8896 (t0) cc_final: 0.8586 (t0)
REVERT: C  410 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.8988 (m)
REVERT: C  452 ASP cc_start: 0.7091 (p0) cc_final: 0.6769 (p0)
REVERT: C  551 MET cc_start: 0.8371 (tpp) cc_final: 0.8061 (tpp)
REVERT: C  777 ASP cc_start: 0.8899 (m-30) cc_final: 0.8502 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0540
  time to fit residues: 6.6218
Evaluate side-chains
  92 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  349 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  527 LEU
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  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  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 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0980
   chunk 70 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0770
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
C 266 ASN
C 414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.115745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.090211 restraints weight = 9530.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 3.17
r_work: 0.3009 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5732  Z= 0.100
  Angle     :  0.524   6.556   7793  Z= 0.261
  Chirality :  0.043   0.164    873
  Planarity :  0.004   0.046   1035
  Dihedral  :  5.045  58.036    778
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 21.47 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.31), residues: 711
  helix:  1.70 (0.44), residues: 142
  sheet:  0.23 (0.36), residues: 206
  loop :  0.00 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 582 
 TYR   0.006   0.001   TYR C 509 
 PHE   0.009   0.001   PHE C 704 
 TRP   0.012   0.001   TRP C 384 
 HIS   0.002   0.000   HIS C 437 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 5732)
  covalent geometry    : angle       0.52446 ( 7793)
  hydrogen bonds       : bond        0.02622 (  207)
  hydrogen bonds       : angle       4.91129 (  576)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1153.97 seconds
wall clock time: 20 minutes 27.65 seconds (1227.65 seconds total)