Starting phenix.real_space_refine
on Tue Feb  3 14:57:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jd8_61384/02_2026/9jd8_61384.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jd8_61384/02_2026/9jd8_61384.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jd8_61384/02_2026/9jd8_61384.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jd8_61384/02_2026/9jd8_61384.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jd8_61384/02_2026/9jd8_61384.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jd8_61384/02_2026/9jd8_61384.cif"
  }
  resolution = 3.86
  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=   0.002
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: 3
    Type Number    sf(0)   Gaussians
     C    2493      2.51       5
     N     684      2.21       5
     O     819      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3996
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "B"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "C"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "D"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "E"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "F"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "H"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
    Chain: "I"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 444
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Time building chain proxies: 1.03, per 1000 atoms: 0.26
  Number of scatterers: 3996
  At special positions: 0
  Unit cell: (108.73, 117.86, 35.69, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     819      8.00
     N     684      7.00
     C    2493      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: 0.30
  Conformation dependent library (CDL) restraints added in 170.4 milliseconds
  

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  990

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 24 sheets defined
      0.0% alpha, 21.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 38 through 40
      removed outlier: 6.446A  pdb=" N   LEU A  38 " --> pdb=" O   TYR G  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 49 through 50
      removed outlier: 6.348A  pdb=" N   VAL A  49 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 62 through 64
      removed outlier: 6.608A  pdb=" N   GLN A  62 " --> pdb=" O   VAL G  63 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   ASN G  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR A  64 " --> pdb=" O   ASN G  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 71
      removed outlier: 6.558A  pdb=" N   VAL A  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 75 through 79
      removed outlier: 6.221A  pdb=" N   ALA A  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   GLN D  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ALA A  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 82 through 83
      removed outlier: 6.216A  pdb=" N   VAL A  82 " --> pdb=" O   GLU G  83 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 88 through 89
      removed outlier: 6.496A  pdb=" N   ILE A  88 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 95 through 96
      removed outlier: 6.600A  pdb=" N   VAL A  95 " --> pdb=" O   LYS G  96 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 38 through 40
      removed outlier: 6.514A  pdb=" N   LEU B  38 " --> pdb=" O   TYR H  39 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 49 through 50
      removed outlier: 6.474A  pdb=" N   VAL B  49 " --> pdb=" O   HIS E  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 62 through 66
      removed outlier: 6.517A  pdb=" N   GLN B  62 " --> pdb=" O   VAL H  63 " (cutoff:3.500A)
      removed outlier: 8.255A  pdb=" N   ASN H  65 " --> pdb=" O   GLN B  62 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   THR B  64 " --> pdb=" O   ASN H  65 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 69 through 71
    Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 76
    Processing sheet with id=AB5, first strand: chain 'B' and resid 82 through 83
    Processing sheet with id=AB6, first strand: chain 'E' and resid 88 through 89
      removed outlier: 6.596A  pdb=" N   ILE B  88 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96
      removed outlier: 6.499A  pdb=" N   VAL B  95 " --> pdb=" O   LYS H  96 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 38 through 40
      removed outlier: 6.398A  pdb=" N   LEU C  38 " --> pdb=" O   TYR I  39 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 49 through 50
      removed outlier: 6.459A  pdb=" N   VAL C  49 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 62 through 66
    Processing sheet with id=AC2, first strand: chain 'F' and resid 69 through 71
      removed outlier: 6.522A  pdb=" N   VAL C  70 " --> pdb=" O   VAL F  71 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ALA C  69 " --> pdb=" O   VAL I  70 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'F' and resid 75 through 76
      removed outlier: 6.696A  pdb=" N   THR C  75 " --> pdb=" O   ALA I  76 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 82 through 83
    Processing sheet with id=AC5, first strand: chain 'F' and resid 88 through 89
      removed outlier: 6.551A  pdb=" N   ILE C  88 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 95 through 96
      removed outlier: 6.606A  pdb=" N   VAL C  95 " --> pdb=" O   LYS I  96 " (cutoff:3.500A)

    44 hydrogen bonds defined for protein.
    132 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: 0.60

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 711
        1.29 -     1.35: 612
        1.35 -     1.41: 153
        1.41 -     1.48: 657
        1.48 -     1.54: 1881
  Bond restraints: 4014
  Sorted by residual:
  bond pdb=" CA  VAL D  82 "
       pdb=" CB  VAL D  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.529  0.011 1.36e-02 5.41e+03 6.63e-01
  bond pdb=" CA  VAL G  82 "
       pdb=" CB  VAL G  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.77e-01
  bond pdb=" CA  VAL A  82 "
       pdb=" CB  VAL A  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.68e-01
  bond pdb=" CA  VAL C  82 "
       pdb=" CB  VAL C  82 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.65e-01
  bond pdb=" CB  LYS G  43 "
       pdb=" CG  LYS G  43 "
    ideal  model  delta    sigma   weight residual
    1.520  1.497  0.023 3.00e-02 1.11e+03 5.64e-01
  ... (remaining 4009 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.78: 4342
        0.78 -     1.55: 830
        1.55 -     2.33: 199
        2.33 -     3.10: 30
        3.10 -     3.88: 35
  Bond angle restraints: 5436
  Sorted by residual:
  angle pdb=" C   VAL E  49 "
        pdb=" N   HIS E  50 "
        pdb=" CA  HIS E  50 "
      ideal   model   delta    sigma   weight residual
     121.80  117.92    3.88 1.71e+00 3.42e-01 5.15e+00
  angle pdb=" C   VAL B  49 "
        pdb=" N   HIS B  50 "
        pdb=" CA  HIS B  50 "
      ideal   model   delta    sigma   weight residual
     121.80  117.92    3.88 1.71e+00 3.42e-01 5.14e+00
  angle pdb=" C   VAL H  49 "
        pdb=" N   HIS H  50 "
        pdb=" CA  HIS H  50 "
      ideal   model   delta    sigma   weight residual
     121.80  117.93    3.87 1.71e+00 3.42e-01 5.13e+00
  angle pdb=" C   VAL A  49 "
        pdb=" N   HIS A  50 "
        pdb=" CA  HIS A  50 "
      ideal   model   delta    sigma   weight residual
     121.80  117.93    3.87 1.71e+00 3.42e-01 5.11e+00
  angle pdb=" C   VAL F  49 "
        pdb=" N   HIS F  50 "
        pdb=" CA  HIS F  50 "
      ideal   model   delta    sigma   weight residual
     121.80  117.95    3.85 1.71e+00 3.42e-01 5.08e+00
  ... (remaining 5431 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.35: 2025
       12.35 -    24.70: 225
       24.70 -    37.05: 63
       37.05 -    49.40: 45
       49.40 -    61.74: 9
  Dihedral angle restraints: 2367
    sinusoidal: 810
      harmonic: 1557
  Sorted by residual:
  dihedral pdb=" CA  GLU G  61 "
           pdb=" C   GLU G  61 "
           pdb=" N   GLN G  62 "
           pdb=" CA  GLN G  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.08   17.92     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  GLU C  61 "
           pdb=" C   GLU C  61 "
           pdb=" N   GLN C  62 "
           pdb=" CA  GLN C  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.11   17.89     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  GLU F  61 "
           pdb=" C   GLU F  61 "
           pdb=" N   GLN F  62 "
           pdb=" CA  GLN F  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.12   17.88     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 2364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 374
       0.032 -    0.064: 193
       0.064 -    0.096: 64
       0.096 -    0.128: 80
       0.128 -    0.160: 9
  Chirality restraints: 720
  Sorted by residual:
  chirality pdb=" CA  VAL A  49 "
            pdb=" N   VAL A  49 "
            pdb=" C   VAL A  49 "
            pdb=" CB  VAL A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.38e-01
  chirality pdb=" CA  VAL B  49 "
            pdb=" N   VAL B  49 "
            pdb=" C   VAL B  49 "
            pdb=" CB  VAL B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CA  VAL D  49 "
            pdb=" N   VAL D  49 "
            pdb=" C   VAL D  49 "
            pdb=" CB  VAL D  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 717 not shown)

  Planarity restraints: 675
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS G  50 "   -0.005 2.00e-02 2.50e+03   1.02e-02 1.04e+00
        pdb=" C   HIS G  50 "    0.018 2.00e-02 2.50e+03
        pdb=" O   HIS G  50 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASP G  51 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A  50 "   -0.005 2.00e-02 2.50e+03   1.00e-02 1.00e+00
        pdb=" C   HIS A  50 "    0.017 2.00e-02 2.50e+03
        pdb=" O   HIS A  50 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASP A  51 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS G  50 "   -0.010 2.00e-02 2.50e+03   8.17e-03 1.00e+00
        pdb=" CG  HIS G  50 "    0.016 2.00e-02 2.50e+03
        pdb=" ND1 HIS G  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS G  50 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 HIS G  50 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS G  50 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 672 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1175
        2.81 -     3.33: 3445
        3.33 -     3.86: 6006
        3.86 -     4.38: 6551
        4.38 -     4.90: 13427
  Nonbonded interactions: 30604
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B  46 "
            pdb=" NZ  LYS H  80 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" NZ  LYS A  80 "
            pdb=" OE1 GLU D  46 "
     model   vdw
     2.353 3.120
  nonbonded pdb=" OE1 GLU C  46 "
            pdb=" NZ  LYS I  80 "
     model   vdw
     2.365 3.120
  nonbonded pdb=" O   GLY H  84 "
            pdb=" OG  SER H  87 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" O   GLY C  84 "
            pdb=" OG  SER C  87 "
     model   vdw
     2.373 3.040
  ... (remaining 30599 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.250
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
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      :  0.005   0.023   4014  Z= 0.276
  Angle     :  0.716   3.881   5436  Z= 0.422
  Chirality :  0.054   0.160    720
  Planarity :  0.003   0.010    675
  Dihedral  : 14.069  61.743   1377
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -4.73 (0.24), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.60 (0.18), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.003   TYR D  39 
 PHE   0.003   0.001   PHE H  94 
 HIS   0.005   0.003   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 4014)
  covalent geometry    : angle       0.71562 ( 5436)
  hydrogen bonds       : bond        0.13960 (   44)
  hydrogen bonds       : angle       6.48365 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 LYS cc_start: 0.6784 (tttt) cc_final: 0.6198 (mmtm)
REVERT: C   57 GLU cc_start: 0.6662 (tt0) cc_final: 0.6427 (mt-10)
REVERT: C   62 GLN cc_start: 0.7376 (tt0) cc_final: 0.6769 (tm-30)
REVERT: C   83 GLU cc_start: 0.7804 (tt0) cc_final: 0.7540 (tt0)
REVERT: F   57 GLU cc_start: 0.6632 (tt0) cc_final: 0.6314 (tt0)
REVERT: F   62 GLN cc_start: 0.7378 (tt0) cc_final: 0.6616 (tm-30)
REVERT: F   97 LYS cc_start: 0.7738 (mttm) cc_final: 0.7527 (mttt)
REVERT: F   99 GLN cc_start: 0.5296 (mm-40) cc_final: 0.5095 (mm110)
REVERT: H   60 LYS cc_start: 0.7008 (tttt) cc_final: 0.6551 (mmtm)
REVERT: I   62 GLN cc_start: 0.8060 (tt0) cc_final: 0.7506 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1112
  time to fit residues: 7.4953
Evaluate side-chains
  48 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.0050
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0270
   chunk 19 optimal weight:   20.0000
   overall best weight:    1.5456

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.140586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.106594 restraints weight = 4790.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.110048 restraints weight = 2715.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.112528 restraints weight = 1873.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.114216 restraints weight = 1449.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.115355 restraints weight = 1205.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4014  Z= 0.099
  Angle     :  0.472   3.398   5436  Z= 0.269
  Chirality :  0.050   0.149    720
  Planarity :  0.002   0.013    675
  Dihedral  :  4.759  12.751    567
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  8.51 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -3.52 (0.29), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.22), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR E  39 
 PHE   0.005   0.001   PHE C  94 
 HIS   0.003   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00188 ( 4014)
  covalent geometry    : angle       0.47181 ( 5436)
  hydrogen bonds       : bond        0.01435 (   44)
  hydrogen bonds       : angle       3.84088 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   57 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7396 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 41
  average time/residue: 0.0909
  time to fit residues: 4.3823
Evaluate side-chains
  37 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   72 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0470
   chunk 43 optimal weight:    3.9990
   overall best weight:    3.9684

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN
F  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.137096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.106440 restraints weight = 4847.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.109214 restraints weight = 2873.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.111290 restraints weight = 2038.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.112480 restraints weight = 1588.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.113452 restraints weight = 1350.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4014  Z= 0.192
  Angle     :  0.556   5.069   5436  Z= 0.319
  Chirality :  0.050   0.160    720
  Planarity :  0.002   0.011    675
  Dihedral  :  5.366  13.819    567
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  8.98 %
    Favored  : 88.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -3.12 (0.32), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.24), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.003   TYR H  39 
 PHE   0.005   0.001   PHE C  94 
 HIS   0.008   0.003   HIS I  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4014)
  covalent geometry    : angle       0.55582 ( 5436)
  hydrogen bonds       : bond        0.01733 (   44)
  hydrogen bonds       : angle       4.09364 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: C   57 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7356 (mm-30)
REVERT: E   79 GLN cc_start: 0.8396 (mt0) cc_final: 0.8121 (mp10)
REVERT: F   57 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7037 (mm-30)
  outliers start: 10
  outliers final: 10
  residues processed: 41
  average time/residue: 0.0953
  time to fit residues: 4.6660
Evaluate side-chains
  40 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   48 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 46 optimal weight:    6.9990
   chunk 25 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   chunk 39 optimal weight:    0.0570
   chunk 11 optimal weight:    9.9990
   chunk 47 optimal weight:    0.0770
   overall best weight:    4.4262

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN
F  99 GLN
** H  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.135794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.105026 restraints weight = 4891.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.107765 restraints weight = 2913.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.109606 restraints weight = 2068.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.110942 restraints weight = 1645.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.111747 restraints weight = 1393.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4014  Z= 0.203
  Angle     :  0.562   8.212   5436  Z= 0.321
  Chirality :  0.052   0.163    720
  Planarity :  0.002   0.011    675
  Dihedral  :  5.382  14.163    567
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  :  9.22 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.90 (0.33), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.002   TYR E  39 
 PHE   0.007   0.001   PHE B  94 
 HIS   0.009   0.003   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 4014)
  covalent geometry    : angle       0.56223 ( 5436)
  hydrogen bonds       : bond        0.01512 (   44)
  hydrogen bonds       : angle       4.08715 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: C   57 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7245 (mm-30)
REVERT: F   57 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7103 (mm-30)
REVERT: H   79 GLN cc_start: 0.8240 (mt0) cc_final: 0.7946 (mp10)
REVERT: I   57 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6897 (mp0)
  outliers start: 11
  outliers final: 10
  residues processed: 48
  average time/residue: 0.1033
  time to fit residues: 5.9501
Evaluate side-chains
  48 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   57 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 53 optimal weight:    0.2980
   chunk 36 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   overall best weight:    5.6588

-------------------------------------------------------------------------------
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 = 0.4110 r_free = 0.4110 target = 0.130960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.100305 restraints weight = 5080.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.102771 restraints weight = 3047.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.104546 restraints weight = 2203.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.105831 restraints weight = 1774.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.106674 restraints weight = 1516.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4014  Z= 0.260
  Angle     :  0.634   7.084   5436  Z= 0.364
  Chirality :  0.054   0.170    720
  Planarity :  0.003   0.012    675
  Dihedral  :  5.859  15.664    567
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 10.64 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.01 (0.33), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.014   0.003   TYR E  39 
 PHE   0.006   0.001   PHE B  94 
 HIS   0.011   0.004   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 ( 4014)
  covalent geometry    : angle       0.63421 ( 5436)
  hydrogen bonds       : bond        0.01834 (   44)
  hydrogen bonds       : angle       4.48193 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: C   57 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7388 (mm-30)
REVERT: C   58 LYS cc_start: 0.7951 (mttt) cc_final: 0.7661 (mttm)
REVERT: F   57 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7392 (mm-30)
REVERT: I   57 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7041 (mp0)
  outliers start: 13
  outliers final: 12
  residues processed: 59
  average time/residue: 0.0931
  time to fit residues: 6.6587
Evaluate side-chains
  58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   57 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 15 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 26 optimal weight:    0.4980
   chunk 1 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    3.8988

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

Flipped N/Q/H residues before XYZ refinement:
C  99 GLN
F  99 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.133774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.103018 restraints weight = 5078.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.105642 restraints weight = 3005.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.107562 restraints weight = 2135.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.108859 restraints weight = 1688.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.109655 restraints weight = 1433.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4014  Z= 0.182
  Angle     :  0.554   7.892   5436  Z= 0.312
  Chirality :  0.052   0.163    720
  Planarity :  0.002   0.010    675
  Dihedral  :  5.252  14.903    567
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 11.82 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.86 (0.34), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR E  39 
 PHE   0.006   0.001   PHE B  94 
 HIS   0.009   0.003   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4014)
  covalent geometry    : angle       0.55392 ( 5436)
  hydrogen bonds       : bond        0.01550 (   44)
  hydrogen bonds       : angle       4.39134 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: B   46 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7476 (mt-10)
REVERT: C   57 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7357 (mm-30)
REVERT: F   57 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7392 (mm-30)
REVERT: I   57 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7156 (mp0)
  outliers start: 13
  outliers final: 11
  residues processed: 58
  average time/residue: 0.0977
  time to fit residues: 6.8128
Evaluate side-chains
  59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   57 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 1 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 32 optimal weight:   20.0000
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 39 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
F  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.129606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.099355 restraints weight = 5225.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.101915 restraints weight = 3139.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.103503 restraints weight = 2245.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.104746 restraints weight = 1807.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.105613 restraints weight = 1552.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   4014  Z= 0.274
  Angle     :  0.652   8.204   5436  Z= 0.373
  Chirality :  0.054   0.177    720
  Planarity :  0.003   0.013    675
  Dihedral  :  5.771  15.842    567
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 12.29 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.94 (0.33), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.25), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.013   0.003   TYR E  39 
 PHE   0.006   0.001   PHE B  94 
 HIS   0.012   0.004   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 ( 4014)
  covalent geometry    : angle       0.65208 ( 5436)
  hydrogen bonds       : bond        0.01844 (   44)
  hydrogen bonds       : angle       4.53591 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: C   57 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7468 (mm-30)
REVERT: C   79 GLN cc_start: 0.7965 (mt0) cc_final: 0.7754 (mt0)
REVERT: F   57 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7359 (mm-30)
REVERT: I   57 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7113 (mp0)
REVERT: I   79 GLN cc_start: 0.7955 (mt0) cc_final: 0.7732 (mt0)
  outliers start: 15
  outliers final: 13
  residues processed: 63
  average time/residue: 0.0572
  time to fit residues: 4.5087
Evaluate side-chains
  64 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   48 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   48 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   57 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 18 optimal weight:   20.0000
   chunk 26 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 52 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    8.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
D  79 GLN
F  99 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.137359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.106566 restraints weight = 4926.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.109389 restraints weight = 2882.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.111408 restraints weight = 2014.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.112620 restraints weight = 1570.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.113723 restraints weight = 1334.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4014  Z= 0.097
  Angle     :  0.478   8.002   5436  Z= 0.265
  Chirality :  0.051   0.149    720
  Planarity :  0.002   0.009    675
  Dihedral  :  4.669  13.988    567
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.71 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.65 (0.35), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR E  39 
 PHE   0.006   0.001   PHE B  94 
 HIS   0.006   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 4014)
  covalent geometry    : angle       0.47805 ( 5436)
  hydrogen bonds       : bond        0.01310 (   44)
  hydrogen bonds       : angle       4.24111 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: C   57 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7594 (mm-30)
REVERT: D   57 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7643 (mp0)
REVERT: E   79 GLN cc_start: 0.8441 (mt0) cc_final: 0.8217 (mp10)
REVERT: F   57 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7318 (mm-30)
REVERT: F   97 LYS cc_start: 0.8264 (mttt) cc_final: 0.8038 (mptt)
REVERT: I   57 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7050 (mp0)
  outliers start: 11
  outliers final: 10
  residues processed: 53
  average time/residue: 0.0768
  time to fit residues: 4.9384
Evaluate side-chains
  54 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   57 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   overall best weight:    3.7986

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

Flipped N/Q/H residues before XYZ refinement:
C  79 GLN
C  99 GLN
F  99 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.132628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.102040 restraints weight = 5121.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.104789 restraints weight = 3031.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.106501 restraints weight = 2131.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.107762 restraints weight = 1694.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.108722 restraints weight = 1443.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4014  Z= 0.180
  Angle     :  0.543   7.355   5436  Z= 0.309
  Chirality :  0.051   0.162    720
  Planarity :  0.002   0.010    675
  Dihedral  :  5.026  14.531    567
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 13.48 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.60 (0.35), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR E  39 
 PHE   0.005   0.001   PHE B  94 
 HIS   0.009   0.003   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4014)
  covalent geometry    : angle       0.54280 ( 5436)
  hydrogen bonds       : bond        0.01474 (   44)
  hydrogen bonds       : angle       4.17153 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: C   57 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7652 (mm-30)
REVERT: D   57 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7666 (mp0)
REVERT: E   79 GLN cc_start: 0.8493 (mt0) cc_final: 0.8283 (mp10)
REVERT: F   57 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7385 (mm-30)
REVERT: I   57 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7122 (mp0)
  outliers start: 13
  outliers final: 12
  residues processed: 58
  average time/residue: 0.0816
  time to fit residues: 5.7466
Evaluate side-chains
  61 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   57 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0170
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   chunk 4 optimal weight:    0.4980
   chunk 20 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    3.3024

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

Flipped N/Q/H residues before XYZ refinement:
G  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.133363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.102895 restraints weight = 5036.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.105604 restraints weight = 2994.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.107314 restraints weight = 2113.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.108647 restraints weight = 1684.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.109450 restraints weight = 1430.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4014  Z= 0.158
  Angle     :  0.522   7.664   5436  Z= 0.296
  Chirality :  0.051   0.154    720
  Planarity :  0.002   0.009    675
  Dihedral  :  4.903  14.912    567
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 13.48 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.48 (0.35), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR E  39 
 PHE   0.005   0.001   PHE B  94 
 HIS   0.008   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 4014)
  covalent geometry    : angle       0.52154 ( 5436)
  hydrogen bonds       : bond        0.01412 (   44)
  hydrogen bonds       : angle       4.17213 (  132)

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

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

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1098 Ramachandran restraints generated.
    549 Oldfield, 0 Emsley, 549 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: C   57 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7554 (mm-30)
REVERT: E   79 GLN cc_start: 0.8488 (mt0) cc_final: 0.8262 (mp10)
REVERT: F   57 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7309 (mm-30)
REVERT: I   57 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7156 (mp0)
  outliers start: 13
  outliers final: 12
  residues processed: 60
  average time/residue: 0.0865
  time to fit residues: 6.3620
Evaluate side-chains
  63 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain E residue   42 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   72 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain I residue   48 VAL
Chi-restraints excluded: chain I residue   57 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0010
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    0.0170
   chunk 53 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 52 optimal weight:    0.4980
   overall best weight:    0.9028

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

Flipped N/Q/H residues before XYZ refinement:
F  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.137628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.106000 restraints weight = 5117.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.109099 restraints weight = 3039.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.111325 restraints weight = 2113.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.112900 restraints weight = 1640.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.113905 restraints weight = 1374.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.017   4014  Z= 0.072
  Angle     :  0.443   7.872   5436  Z= 0.240
  Chirality :  0.050   0.137    720
  Planarity :  0.001   0.010    675
  Dihedral  :  4.163  14.242    567
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.95 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -2.12 (0.36), residues: 549
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.60 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR B  39 
 PHE   0.004   0.001   PHE B  94 
 HIS   0.004   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00149 ( 4014)
  covalent geometry    : angle       0.44332 ( 5436)
  hydrogen bonds       : bond        0.01088 (   44)
  hydrogen bonds       : angle       4.05985 (  132)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 809.61 seconds
wall clock time: 14 minutes 43.24 seconds (883.24 seconds total)