Starting phenix.real_space_refine
on Wed Jul 23 19:41:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uka_42350/07_2025/8uka_42350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uka_42350/07_2025/8uka_42350.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uka_42350/07_2025/8uka_42350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uka_42350/07_2025/8uka_42350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uka_42350/07_2025/8uka_42350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uka_42350/07_2025/8uka_42350.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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    2610      2.51       5
     N     720      2.21       5
     O     830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4160
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 416
          Classifications: {'peptide': 61}
          Link IDs: {'TRANS': 60}
  Restraints were copied for chains:
    a, C, B, E, D, c, b, e, d
  Time building chain proxies: 5.03, per 1000 atoms: 1.21
  Number of scatterers: 4160
  At special positions: 0
  Unit cell: (104.41, 98.05, 39.22, 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     830      8.00
     N     720      7.00
     C    2610      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: 0.82
  Conformation dependent library (CDL) restraints added in 488.0 milliseconds
  

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1020

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 40
      removed outlier: 6.577A  pdb=" N   LEU B  38 " --> pdb=" O   TYR C  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46
      removed outlier: 6.576A  pdb=" N   LYS B  45 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   LYS A  45 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LYS D  45 " --> pdb=" O   GLU E  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 57
      removed outlier: 6.447A  pdb=" N   VAL A  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   VAL C  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   THR A  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   GLU C  57 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ALA A  56 " --> pdb=" O   GLU C  57 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63
      removed outlier: 5.888A  pdb=" N   LYS B  60 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   VAL C  63 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   GLN B  62 " --> pdb=" O   VAL C  63 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   LYS A  60 " --> pdb=" O   GLU D  61 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   LYS D  60 " --> pdb=" O   GLU E  61 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 70 through 71
      removed outlier: 6.957A  pdb=" N   VAL A  70 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 82
      removed outlier: 5.973A  pdb=" N   THR A  81 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 89
      removed outlier: 6.758A  pdb=" N   SER B  87 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ILE A  88 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   SER A  87 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   SER D  87 " --> pdb=" O   ILE E  88 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'b' and resid 38 through 40
      removed outlier: 3.588A  pdb=" N   TYR c  39 " --> pdb=" O   LEU b  38 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL b  40 " --> pdb=" O   TYR c  39 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'b' and resid 45 through 46
      removed outlier: 6.613A  pdb=" N   LYS b  45 " --> pdb=" O   GLU c  46 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   LYS a  45 " --> pdb=" O   GLU d  46 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LYS d  45 " --> pdb=" O   GLU e  46 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'b' and resid 52 through 57
      removed outlier: 6.454A  pdb=" N   VAL a  52 " --> pdb=" O   ALA c  53 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   VAL c  55 " --> pdb=" O   VAL a  52 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   THR a  54 " --> pdb=" O   VAL c  55 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   GLU c  57 " --> pdb=" O   THR a  54 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ALA a  56 " --> pdb=" O   GLU c  57 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'b' and resid 60 through 63
      removed outlier: 6.115A  pdb=" N   LYS b  60 " --> pdb=" O   GLU c  61 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   VAL c  63 " --> pdb=" O   LYS b  60 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   GLN b  62 " --> pdb=" O   VAL c  63 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   LYS a  60 " --> pdb=" O   GLU d  61 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   LYS d  60 " --> pdb=" O   GLU e  61 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'b' and resid 70 through 71
      removed outlier: 6.946A  pdb=" N   VAL a  70 " --> pdb=" O   VAL c  71 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'b' and resid 81 through 82
      removed outlier: 5.960A  pdb=" N   THR a  81 " --> pdb=" O   VAL c  82 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'b' and resid 87 through 88
      removed outlier: 6.789A  pdb=" N   SER b  87 " --> pdb=" O   ILE c  88 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   SER a  87 " --> pdb=" O   ILE d  88 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   SER d  87 " --> pdb=" O   ILE e  88 " (cutoff:3.500A)

    63 hydrogen bonds defined for protein.
    189 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: 0.94

  Time building geometry restraints manager: 0.99 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: 720
        1.29 -     1.36: 660
        1.36 -     1.42: 170
        1.42 -     1.49: 712
        1.49 -     1.55: 1918
  Bond restraints: 4180
  Sorted by residual:
  bond pdb=" N   GLU a  46 "
       pdb=" CA  GLU a  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.19e-02 7.06e+03 6.67e+00
  bond pdb=" N   GLU D  46 "
       pdb=" CA  GLU D  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.031 1.19e-02 7.06e+03 6.60e+00
  bond pdb=" N   GLU C  46 "
       pdb=" CA  GLU C  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.19e-02 7.06e+03 6.52e+00
  bond pdb=" N   GLU c  46 "
       pdb=" CA  GLU c  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.19e-02 7.06e+03 6.49e+00
  bond pdb=" N   GLU e  46 "
       pdb=" CA  GLU e  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.19e-02 7.06e+03 6.38e+00
  ... (remaining 4175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 4795
        1.10 -     2.20: 617
        2.20 -     3.30: 179
        3.30 -     4.40: 59
        4.40 -     5.50: 10
  Bond angle restraints: 5660
  Sorted by residual:
  angle pdb=" CA  GLY B  73 "
        pdb=" C   GLY B  73 "
        pdb=" O   GLY B  73 "
      ideal   model   delta    sigma   weight residual
     122.45  119.91    2.54 7.20e-01 1.93e+00 1.25e+01
  angle pdb=" CA  GLY a  73 "
        pdb=" C   GLY a  73 "
        pdb=" O   GLY a  73 "
      ideal   model   delta    sigma   weight residual
     122.45  119.92    2.53 7.20e-01 1.93e+00 1.24e+01
  angle pdb=" CA  GLY d  73 "
        pdb=" C   GLY d  73 "
        pdb=" O   GLY d  73 "
      ideal   model   delta    sigma   weight residual
     122.45  119.93    2.52 7.20e-01 1.93e+00 1.23e+01
  angle pdb=" CA  GLY E  73 "
        pdb=" C   GLY E  73 "
        pdb=" O   GLY E  73 "
      ideal   model   delta    sigma   weight residual
     122.45  119.93    2.52 7.20e-01 1.93e+00 1.23e+01
  angle pdb=" CA  GLY c  73 "
        pdb=" C   GLY c  73 "
        pdb=" O   GLY c  73 "
      ideal   model   delta    sigma   weight residual
     122.45  119.93    2.52 7.20e-01 1.93e+00 1.22e+01
  ... (remaining 5655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.52: 2080
        8.52 -    17.04: 160
       17.04 -    25.56: 80
       25.56 -    34.08: 50
       34.08 -    42.60: 40
  Dihedral angle restraints: 2410
    sinusoidal: 780
      harmonic: 1630
  Sorted by residual:
  dihedral pdb=" CA  LYS a  60 "
           pdb=" CB  LYS a  60 "
           pdb=" CG  LYS a  60 "
           pdb=" CD  LYS a  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.40  -42.60     3      1.50e+01 4.44e-03 7.65e+00
  dihedral pdb=" CA  LYS B  60 "
           pdb=" CB  LYS B  60 "
           pdb=" CG  LYS B  60 "
           pdb=" CD  LYS B  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.41  -42.59     3      1.50e+01 4.44e-03 7.64e+00
  dihedral pdb=" CA  LYS D  60 "
           pdb=" CB  LYS D  60 "
           pdb=" CG  LYS D  60 "
           pdb=" CD  LYS D  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -137.43  -42.57     3      1.50e+01 4.44e-03 7.64e+00
  ... (remaining 2407 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 434
       0.050 -    0.100: 234
       0.100 -    0.150: 62
       0.150 -    0.199: 10
       0.199 -    0.249: 10
  Chirality restraints: 750
  Sorted by residual:
  chirality pdb=" CB  VAL E  63 "
            pdb=" CA  VAL E  63 "
            pdb=" CG1 VAL E  63 "
            pdb=" CG2 VAL E  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CB  VAL d  63 "
            pdb=" CA  VAL d  63 "
            pdb=" CG1 VAL d  63 "
            pdb=" CG2 VAL d  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CB  VAL b  63 "
            pdb=" CA  VAL b  63 "
            pdb=" CG1 VAL b  63 "
            pdb=" CG2 VAL b  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 747 not shown)

  Planarity restraints: 700
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN e  79 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.80e+00
        pdb=" C   GLN e  79 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLN e  79 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS e  80 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D  79 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.77e+00
        pdb=" C   GLN D  79 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLN D  79 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS D  80 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C  79 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   GLN C  79 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLN C  79 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS C  80 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 697 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 961
        2.80 -     3.32: 3904
        3.32 -     3.85: 6708
        3.85 -     4.37: 7262
        4.37 -     4.90: 14375
  Nonbonded interactions: 33210
  Sorted by model distance:
  nonbonded pdb=" OH  TYR a  39 "
            pdb=" OE2 GLU c  46 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OH  TYR A  39 "
            pdb=" OE2 GLU C  46 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OE2 GLU B  46 "
            pdb=" OH  TYR C  39 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   LYS d  80 "
            pdb=" N   THR e  81 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" O   LYS D  80 "
            pdb=" N   THR E  81 "
     model   vdw
     2.374 3.120
  ... (remaining 33205 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'a'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'c'
  selection = chain 'b'
  selection = chain 'e'
  selection = chain 'd'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             18.000
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.780
  Find NCS groups from input model:        0.100
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5579
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      :  0.006   0.060   4180  Z= 0.308
  Angle     :  0.920   5.502   5660  Z= 0.590
  Chirality :  0.064   0.249    750
  Planarity :  0.004   0.017    700
  Dihedral  : 11.568  42.596   1390
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 44.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.23), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS b  50 
 PHE   0.009   0.003   PHE B  94 
 TYR   0.023   0.006   TYR d  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25850 (   63)
  hydrogen bonds       : angle      11.71377 (  189)
  covalent geometry    : bond        0.00593 ( 4180)
  covalent geometry    : angle       0.92026 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A   44 THR cc_start: 0.6979 (t) cc_final: 0.5494 (t)
REVERT: B   46 GLU cc_start: 0.6567 (mt-10) cc_final: 0.6325 (mp0)
REVERT: C   88 ILE cc_start: 0.7216 (mp) cc_final: 0.6881 (tp)
REVERT: D   44 THR cc_start: 0.6770 (t) cc_final: 0.6358 (t)
REVERT: D   94 PHE cc_start: 0.5196 (m-80) cc_final: 0.4908 (m-80)
REVERT: E   40 VAL cc_start: 0.5879 (p) cc_final: 0.5488 (p)
REVERT: E   58 LYS cc_start: 0.6523 (ptpp) cc_final: 0.6172 (tttm)
REVERT: b   40 VAL cc_start: 0.8184 (p) cc_final: 0.7954 (m)
REVERT: d   42 SER cc_start: 0.7363 (p) cc_final: 0.7152 (m)
REVERT: d   46 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6552 (mt-10)
REVERT: e   40 VAL cc_start: 0.6546 (p) cc_final: 0.6202 (p)
REVERT: e   42 SER cc_start: 0.7451 (p) cc_final: 0.6743 (p)
REVERT: e   58 LYS cc_start: 0.6695 (ptpp) cc_final: 0.5865 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1492
  time to fit residues: 40.5416
Evaluate side-chains
  112 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
** B  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  65 ASN
** a  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
e  65 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.217201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.192992 restraints weight = 6654.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.195692 restraints weight = 4316.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.197454 restraints weight = 3177.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.4837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.7406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4180  Z= 0.170
  Angle     :  0.708   8.629   5660  Z= 0.403
  Chirality :  0.053   0.142    750
  Planarity :  0.003   0.020    700
  Dihedral  :  5.443  16.474    610
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers : 11.90 %
    Allowed  : 20.24 %
    Favored  : 67.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.23), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS E  50 
 PHE   0.010   0.003   PHE A  94 
 TYR   0.051   0.005   TYR A  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05175 (   63)
  hydrogen bonds       : angle       8.49600 (  189)
  covalent geometry    : bond        0.00387 ( 4180)
  covalent geometry    : angle       0.70763 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 144
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   88 ILE cc_start: 0.7119 (mp) cc_final: 0.6808 (tp)
REVERT: D   39 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.6043 (p90)
REVERT: D   43 LYS cc_start: 0.7334 (mptt) cc_final: 0.6862 (tmtt)
REVERT: a   46 GLU cc_start: 0.7211 (mp0) cc_final: 0.6841 (mp0)
REVERT: c   88 ILE cc_start: 0.6543 (tt) cc_final: 0.6292 (tp)
REVERT: e   39 TYR cc_start: 0.3859 (OUTLIER) cc_final: 0.3603 (m-80)
  outliers start: 50
  outliers final: 27
  residues processed: 180
  average time/residue: 0.1045
  time to fit residues: 25.6680
Evaluate side-chains
  127 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   42 SER
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain a residue   55 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain b residue   44 THR
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain c residue   55 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   82 VAL
Chi-restraints excluded: chain d residue   71 VAL
Chi-restraints excluded: chain e residue   39 TYR
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   74 VAL
Chi-restraints excluded: chain e residue   77 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:    0.0270
   chunk 37 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    1.2842

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

Flipped N/Q/H residues before XYZ refinement:
** B  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** b  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.192308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.171392 restraints weight = 6808.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.173810 restraints weight = 4168.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.175725 restraints weight = 2904.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.9373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   4180  Z= 0.171
  Angle     :  0.636   6.058   5660  Z= 0.367
  Chirality :  0.052   0.133    750
  Planarity :  0.003   0.013    700
  Dihedral  :  5.277  15.975    610
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers : 13.57 %
    Allowed  : 24.52 %
    Favored  : 61.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.23), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS e  50 
 PHE   0.011   0.002   PHE c  94 
 TYR   0.031   0.003   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04766 (   63)
  hydrogen bonds       : angle       8.20648 (  189)
  covalent geometry    : bond        0.00411 ( 4180)
  covalent geometry    : angle       0.63634 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 125
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A   88 ILE cc_start: 0.7342 (mp) cc_final: 0.7076 (mp)
REVERT: D   39 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6968 (p90)
REVERT: a   46 GLU cc_start: 0.7309 (mp0) cc_final: 0.7039 (mp0)
REVERT: d   42 SER cc_start: 0.8082 (m) cc_final: 0.7787 (m)
REVERT: e   43 LYS cc_start: 0.7517 (mptt) cc_final: 0.7309 (mttt)
  outliers start: 57
  outliers final: 43
  residues processed: 165
  average time/residue: 0.1043
  time to fit residues: 23.8961
Evaluate side-chains
  142 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 98
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain a residue   38 LEU
Chi-restraints excluded: chain a residue   55 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain a residue   74 VAL
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain c residue   55 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   63 VAL
Chi-restraints excluded: chain d residue   38 LEU
Chi-restraints excluded: chain d residue   44 THR
Chi-restraints excluded: chain d residue   52 VAL
Chi-restraints excluded: chain d residue   55 VAL
Chi-restraints excluded: chain e residue   40 VAL
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   74 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0470
   chunk 45 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0170
   chunk 5 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.3320

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

Flipped N/Q/H residues before XYZ refinement:
** B  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.184838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.165363 restraints weight = 7178.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.167824 restraints weight = 4417.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.169633 restraints weight = 3044.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.4648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          1.0689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4180  Z= 0.157
  Angle     :  0.658   9.138   5660  Z= 0.368
  Chirality :  0.053   0.153    750
  Planarity :  0.003   0.013    700
  Dihedral  :  5.183  15.297    610
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers : 15.48 %
    Allowed  : 26.43 %
    Favored  : 58.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.28), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.66 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS e  50 
 PHE   0.008   0.002   PHE A  94 
 TYR   0.027   0.002   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04205 (   63)
  hydrogen bonds       : angle       8.01456 (  189)
  covalent geometry    : bond        0.00373 ( 4180)
  covalent geometry    : angle       0.65806 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 114
  time to evaluate  : 0.767 
Fit side-chains
REVERT: a   39 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.5727 (p90)
REVERT: a   46 GLU cc_start: 0.7409 (mp0) cc_final: 0.7083 (mp0)
REVERT: b   88 ILE cc_start: 0.6932 (mm) cc_final: 0.6728 (tt)
REVERT: c   39 TYR cc_start: 0.6842 (p90) cc_final: 0.5917 (p90)
REVERT: d   39 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6984 (p90)
  outliers start: 65
  outliers final: 54
  residues processed: 160
  average time/residue: 0.1397
  time to fit residues: 31.9819
Evaluate side-chains
  149 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 93
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   63 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain a residue   38 LEU
Chi-restraints excluded: chain a residue   39 TYR
Chi-restraints excluded: chain a residue   40 VAL
Chi-restraints excluded: chain a residue   55 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain b residue   40 VAL
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain c residue   55 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   63 VAL
Chi-restraints excluded: chain c residue   74 VAL
Chi-restraints excluded: chain c residue   82 VAL
Chi-restraints excluded: chain d residue   38 LEU
Chi-restraints excluded: chain d residue   39 TYR
Chi-restraints excluded: chain d residue   40 VAL
Chi-restraints excluded: chain d residue   42 SER
Chi-restraints excluded: chain d residue   44 THR
Chi-restraints excluded: chain d residue   52 VAL
Chi-restraints excluded: chain d residue   55 VAL
Chi-restraints excluded: chain d residue   74 VAL
Chi-restraints excluded: chain d residue   82 VAL
Chi-restraints excluded: chain e residue   38 LEU
Chi-restraints excluded: chain e residue   40 VAL
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   74 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0040
   chunk 43 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    2.0000

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

Flipped N/Q/H residues before XYZ refinement:
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.177414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.159517 restraints weight = 7765.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.161591 restraints weight = 4905.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.163311 restraints weight = 3474.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.4566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          1.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   4180  Z= 0.205
  Angle     :  0.739   9.195   5660  Z= 0.408
  Chirality :  0.054   0.151    750
  Planarity :  0.003   0.013    700
  Dihedral  :  5.925  18.718    610
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers : 16.19 %
    Allowed  : 27.14 %
    Favored  : 56.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.43 (0.28), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS E  50 
 PHE   0.006   0.002   PHE C  94 
 TYR   0.023   0.002   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04715 (   63)
  hydrogen bonds       : angle       8.04769 (  189)
  covalent geometry    : bond        0.00481 ( 4180)
  covalent geometry    : angle       0.73906 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 105
  time to evaluate  : 0.588 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6570 (p90)
REVERT: B   88 ILE cc_start: 0.7228 (mm) cc_final: 0.6760 (tt)
REVERT: C   39 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5969 (p90)
REVERT: C   95 VAL cc_start: 0.7602 (m) cc_final: 0.7049 (t)
REVERT: D   39 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7438 (p90)
REVERT: a   39 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6565 (p90)
REVERT: a   46 GLU cc_start: 0.7408 (mp0) cc_final: 0.7065 (mp0)
REVERT: b   88 ILE cc_start: 0.7016 (mm) cc_final: 0.6763 (tt)
REVERT: c   39 TYR cc_start: 0.7190 (p90) cc_final: 0.6194 (p90)
REVERT: d   39 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.7308 (p90)
  outliers start: 68
  outliers final: 54
  residues processed: 153
  average time/residue: 0.1537
  time to fit residues: 32.6350
Evaluate side-chains
  148 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 89
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   39 TYR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   63 VAL
Chi-restraints excluded: chain a residue   38 LEU
Chi-restraints excluded: chain a residue   39 TYR
Chi-restraints excluded: chain a residue   40 VAL
Chi-restraints excluded: chain a residue   55 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   95 VAL
Chi-restraints excluded: chain b residue   40 VAL
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain c residue   55 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   63 VAL
Chi-restraints excluded: chain c residue   82 VAL
Chi-restraints excluded: chain d residue   38 LEU
Chi-restraints excluded: chain d residue   39 TYR
Chi-restraints excluded: chain d residue   40 VAL
Chi-restraints excluded: chain d residue   44 THR
Chi-restraints excluded: chain d residue   52 VAL
Chi-restraints excluded: chain d residue   55 VAL
Chi-restraints excluded: chain d residue   63 VAL
Chi-restraints excluded: chain e residue   40 VAL
Chi-restraints excluded: chain e residue   44 THR
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   63 VAL
Chi-restraints excluded: chain e residue   74 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0770
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4813 r_free = 0.4813 target = 0.187891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.169057 restraints weight = 7026.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.171606 restraints weight = 4263.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.173447 restraints weight = 2899.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.4684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          1.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   4180  Z= 0.120
  Angle     :  0.617   7.574   5660  Z= 0.331
  Chirality :  0.051   0.130    750
  Planarity :  0.002   0.014    700
  Dihedral  :  4.558  14.512    610
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers : 14.76 %
    Allowed  : 30.48 %
    Favored  : 54.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.40 (0.28), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  50 
 PHE   0.007   0.002   PHE b  94 
 TYR   0.022   0.002   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (   63)
  hydrogen bonds       : angle       7.57653 (  189)
  covalent geometry    : bond        0.00300 ( 4180)
  covalent geometry    : angle       0.61675 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 103
  time to evaluate  : 1.552 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7095 (OUTLIER) cc_final: 0.6529 (p90)
REVERT: B   88 ILE cc_start: 0.7069 (mm) cc_final: 0.6698 (tt)
REVERT: C   39 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5779 (p90)
REVERT: D   39 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7427 (p90)
REVERT: D   42 SER cc_start: 0.8071 (m) cc_final: 0.7826 (m)
REVERT: a   39 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6254 (p90)
REVERT: a   46 GLU cc_start: 0.7382 (mp0) cc_final: 0.7091 (mp0)
REVERT: c   39 TYR cc_start: 0.6987 (p90) cc_final: 0.5716 (p90)
REVERT: d   39 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.7239 (p90)
  outliers start: 62
  outliers final: 53
  residues processed: 146
  average time/residue: 0.2058
  time to fit residues: 42.5850
Evaluate side-chains
  152 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 94
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   39 TYR
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain a residue   39 TYR
Chi-restraints excluded: chain a residue   40 VAL
Chi-restraints excluded: chain a residue   55 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain b residue   40 VAL
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   63 VAL
Chi-restraints excluded: chain c residue   74 VAL
Chi-restraints excluded: chain c residue   82 VAL
Chi-restraints excluded: chain d residue   38 LEU
Chi-restraints excluded: chain d residue   39 TYR
Chi-restraints excluded: chain d residue   40 VAL
Chi-restraints excluded: chain d residue   44 THR
Chi-restraints excluded: chain d residue   48 VAL
Chi-restraints excluded: chain d residue   52 VAL
Chi-restraints excluded: chain d residue   55 VAL
Chi-restraints excluded: chain d residue   63 VAL
Chi-restraints excluded: chain e residue   40 VAL
Chi-restraints excluded: chain e residue   44 THR
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   74 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.178743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.161080 restraints weight = 7484.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.163299 restraints weight = 4737.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.164628 restraints weight = 3299.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          1.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4180  Z= 0.183
  Angle     :  0.682   6.669   5660  Z= 0.375
  Chirality :  0.053   0.137    750
  Planarity :  0.003   0.011    700
  Dihedral  :  5.409  16.148    610
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.02 %
    Favored  : 88.98 %
  Rotamer:
    Outliers : 18.10 %
    Allowed  : 27.38 %
    Favored  : 54.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS E  50 
 PHE   0.018   0.002   PHE A  94 
 TYR   0.022   0.002   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04016 (   63)
  hydrogen bonds       : angle       7.62562 (  189)
  covalent geometry    : bond        0.00431 ( 4180)
  covalent geometry    : angle       0.68203 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 98
  time to evaluate  : 1.218 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6737 (p90)
REVERT: B   88 ILE cc_start: 0.7119 (mm) cc_final: 0.6752 (tt)
REVERT: D   39 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7422 (p90)
REVERT: a   39 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6491 (p90)
REVERT: a   46 GLU cc_start: 0.7396 (mp0) cc_final: 0.7073 (mp0)
REVERT: d   39 TYR cc_start: 0.7877 (OUTLIER) cc_final: 0.7336 (p90)
  outliers start: 76
  outliers final: 61
  residues processed: 156
  average time/residue: 0.1534
  time to fit residues: 35.6000
Evaluate side-chains
  154 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 89
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   42 SER
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   39 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain a residue   39 TYR
Chi-restraints excluded: chain a residue   40 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   95 VAL
Chi-restraints excluded: chain b residue   40 VAL
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain c residue   40 VAL
Chi-restraints excluded: chain c residue   55 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   63 VAL
Chi-restraints excluded: chain c residue   75 THR
Chi-restraints excluded: chain c residue   82 VAL
Chi-restraints excluded: chain d residue   39 TYR
Chi-restraints excluded: chain d residue   40 VAL
Chi-restraints excluded: chain d residue   42 SER
Chi-restraints excluded: chain d residue   44 THR
Chi-restraints excluded: chain d residue   48 VAL
Chi-restraints excluded: chain d residue   52 VAL
Chi-restraints excluded: chain d residue   55 VAL
Chi-restraints excluded: chain d residue   63 VAL
Chi-restraints excluded: chain d residue   66 VAL
Chi-restraints excluded: chain d residue   82 VAL
Chi-restraints excluded: chain e residue   40 VAL
Chi-restraints excluded: chain e residue   44 THR
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   74 VAL
Chi-restraints excluded: chain e residue   95 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.1522

-------------------------------------------------------------------------------
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 = 0.4785 r_free = 0.4785 target = 0.183654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.166771 restraints weight = 7321.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.169044 restraints weight = 4474.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.170487 restraints weight = 3054.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.4654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          1.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4180  Z= 0.143
  Angle     :  0.644   7.769   5660  Z= 0.348
  Chirality :  0.051   0.134    750
  Planarity :  0.002   0.013    700
  Dihedral  :  4.879  15.029    610
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers : 16.19 %
    Allowed  : 31.19 %
    Favored  : 52.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.30 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E  50 
 PHE   0.010   0.002   PHE B  94 
 TYR   0.022   0.002   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (   63)
  hydrogen bonds       : angle       7.41621 (  189)
  covalent geometry    : bond        0.00349 ( 4180)
  covalent geometry    : angle       0.64355 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 93
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6653 (p90)
REVERT: B   88 ILE cc_start: 0.7001 (mm) cc_final: 0.6638 (tt)
REVERT: D   39 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7401 (p90)
REVERT: a   39 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.6438 (p90)
REVERT: a   46 GLU cc_start: 0.7364 (mp0) cc_final: 0.7071 (mp0)
REVERT: c   39 TYR cc_start: 0.6679 (OUTLIER) cc_final: 0.5896 (p90)
REVERT: d   39 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7325 (p90)
  outliers start: 68
  outliers final: 60
  residues processed: 143
  average time/residue: 0.0877
  time to fit residues: 17.7246
Evaluate side-chains
  151 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 86
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   39 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   44 THR
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain a residue   39 TYR
Chi-restraints excluded: chain a residue   40 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   95 VAL
Chi-restraints excluded: chain b residue   40 VAL
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain b residue   92 THR
Chi-restraints excluded: chain c residue   39 TYR
Chi-restraints excluded: chain c residue   40 VAL
Chi-restraints excluded: chain c residue   55 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   63 VAL
Chi-restraints excluded: chain c residue   82 VAL
Chi-restraints excluded: chain d residue   38 LEU
Chi-restraints excluded: chain d residue   39 TYR
Chi-restraints excluded: chain d residue   40 VAL
Chi-restraints excluded: chain d residue   44 THR
Chi-restraints excluded: chain d residue   48 VAL
Chi-restraints excluded: chain d residue   52 VAL
Chi-restraints excluded: chain d residue   55 VAL
Chi-restraints excluded: chain d residue   63 VAL
Chi-restraints excluded: chain d residue   66 VAL
Chi-restraints excluded: chain d residue   82 VAL
Chi-restraints excluded: chain e residue   44 THR
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   74 VAL
Chi-restraints excluded: chain e residue   95 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0020
   chunk 28 optimal weight:    0.0770
   chunk 51 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.6146

-------------------------------------------------------------------------------
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 = 0.4841 r_free = 0.4841 target = 0.189136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.171586 restraints weight = 7166.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.174016 restraints weight = 4393.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.175565 restraints weight = 3027.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.4710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          1.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   4180  Z= 0.115
  Angle     :  0.597   7.754   5660  Z= 0.319
  Chirality :  0.050   0.133    750
  Planarity :  0.002   0.012    700
  Dihedral  :  4.216  13.628    610
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers : 14.52 %
    Allowed  : 32.38 %
    Favored  : 53.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS E  50 
 PHE   0.019   0.002   PHE A  94 
 TYR   0.023   0.002   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03209 (   63)
  hydrogen bonds       : angle       7.04733 (  189)
  covalent geometry    : bond        0.00279 ( 4180)
  covalent geometry    : angle       0.59719 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 93
  time to evaluate  : 0.479 
Fit side-chains
REVERT: B   88 ILE cc_start: 0.6910 (mm) cc_final: 0.6552 (tt)
REVERT: D   39 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7389 (p90)
REVERT: a   39 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6381 (p90)
REVERT: a   46 GLU cc_start: 0.7346 (mp0) cc_final: 0.7101 (mp0)
REVERT: d   39 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7359 (p90)
  outliers start: 61
  outliers final: 57
  residues processed: 137
  average time/residue: 0.0887
  time to fit residues: 17.3258
Evaluate side-chains
  147 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 87
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   39 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain a residue   39 TYR
Chi-restraints excluded: chain a residue   40 VAL
Chi-restraints excluded: chain a residue   48 VAL
Chi-restraints excluded: chain a residue   55 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   95 VAL
Chi-restraints excluded: chain b residue   40 VAL
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain b residue   92 THR
Chi-restraints excluded: chain c residue   40 VAL
Chi-restraints excluded: chain c residue   55 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   63 VAL
Chi-restraints excluded: chain c residue   74 VAL
Chi-restraints excluded: chain c residue   82 VAL
Chi-restraints excluded: chain d residue   38 LEU
Chi-restraints excluded: chain d residue   39 TYR
Chi-restraints excluded: chain d residue   40 VAL
Chi-restraints excluded: chain d residue   48 VAL
Chi-restraints excluded: chain d residue   52 VAL
Chi-restraints excluded: chain d residue   55 VAL
Chi-restraints excluded: chain d residue   63 VAL
Chi-restraints excluded: chain d residue   66 VAL
Chi-restraints excluded: chain d residue   82 VAL
Chi-restraints excluded: chain e residue   44 THR
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   74 VAL
Chi-restraints excluded: chain e residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.172366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.154886 restraints weight = 7619.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.157338 restraints weight = 4494.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.159096 restraints weight = 2991.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.4536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          1.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   4180  Z= 0.281
  Angle     :  0.829   7.657   5660  Z= 0.456
  Chirality :  0.057   0.152    750
  Planarity :  0.003   0.014    700
  Dihedral  :  6.380  21.402    610
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.71 %
    Favored  : 87.29 %
  Rotamer:
    Outliers : 16.19 %
    Allowed  : 30.48 %
    Favored  : 53.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.40 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.002   HIS E  50 
 PHE   0.012   0.003   PHE b  94 
 TYR   0.019   0.003   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04832 (   63)
  hydrogen bonds       : angle       7.68133 (  189)
  covalent geometry    : bond        0.00652 ( 4180)
  covalent geometry    : angle       0.82894 ( 5660)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 92
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.6696 (p90)
REVERT: D   39 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7049 (p90)
REVERT: a   39 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6901 (p90)
REVERT: a   46 GLU cc_start: 0.7439 (mp0) cc_final: 0.7049 (mp0)
REVERT: c   39 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5746 (p90)
REVERT: d   39 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7318 (p90)
  outliers start: 68
  outliers final: 62
  residues processed: 146
  average time/residue: 0.0897
  time to fit residues: 18.6325
Evaluate side-chains
  149 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 82
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   39 TYR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   64 THR
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   39 TYR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   44 THR
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue   55 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   55 VAL
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   74 VAL
Chi-restraints excluded: chain a residue   39 TYR
Chi-restraints excluded: chain a residue   40 VAL
Chi-restraints excluded: chain a residue   48 VAL
Chi-restraints excluded: chain a residue   55 VAL
Chi-restraints excluded: chain a residue   59 THR
Chi-restraints excluded: chain a residue   63 VAL
Chi-restraints excluded: chain a residue   70 VAL
Chi-restraints excluded: chain a residue   95 VAL
Chi-restraints excluded: chain b residue   40 VAL
Chi-restraints excluded: chain b residue   59 THR
Chi-restraints excluded: chain b residue   63 VAL
Chi-restraints excluded: chain b residue   77 VAL
Chi-restraints excluded: chain b residue   92 THR
Chi-restraints excluded: chain c residue   39 TYR
Chi-restraints excluded: chain c residue   40 VAL
Chi-restraints excluded: chain c residue   55 VAL
Chi-restraints excluded: chain c residue   59 THR
Chi-restraints excluded: chain c residue   63 VAL
Chi-restraints excluded: chain c residue   75 THR
Chi-restraints excluded: chain c residue   82 VAL
Chi-restraints excluded: chain c residue   92 THR
Chi-restraints excluded: chain d residue   38 LEU
Chi-restraints excluded: chain d residue   39 TYR
Chi-restraints excluded: chain d residue   40 VAL
Chi-restraints excluded: chain d residue   48 VAL
Chi-restraints excluded: chain d residue   52 VAL
Chi-restraints excluded: chain d residue   55 VAL
Chi-restraints excluded: chain d residue   63 VAL
Chi-restraints excluded: chain d residue   66 VAL
Chi-restraints excluded: chain e residue   44 THR
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   74 VAL
Chi-restraints excluded: chain e residue   95 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 19 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 45 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.2788

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

Flipped N/Q/H residues before XYZ refinement:
** D  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.178536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.161141 restraints weight = 7335.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.163679 restraints weight = 4475.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.165294 restraints weight = 3026.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.4607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          1.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4180  Z= 0.156
  Angle     :  0.690   7.834   5660  Z= 0.373
  Chirality :  0.052   0.142    750
  Planarity :  0.003   0.012    700
  Dihedral  :  5.310  17.612    610
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers : 16.19 %
    Allowed  : 31.67 %
    Favored  : 52.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.32 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS E  50 
 PHE   0.015   0.002   PHE b  94 
 TYR   0.021   0.002   TYR a  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03866 (   63)
  hydrogen bonds       : angle       7.39646 (  189)
  covalent geometry    : bond        0.00367 ( 4180)
  covalent geometry    : angle       0.68951 ( 5660)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3460.43 seconds
wall clock time: 64 minutes 11.39 seconds (3851.39 seconds total)