Starting phenix.real_space_refine
on Fri Oct 10 11:43:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uka_42350/10_2025/8uka_42350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uka_42350/10_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_42350/10_2025/8uka_42350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uka_42350/10_2025/8uka_42350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uka_42350/10_2025/8uka_42350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uka_42350/10_2025/8uka_42350.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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:
    B, C, D, E, a, b, c, d, e
  Time building chain proxies: 0.72, per 1000 atoms: 0.17
  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: 0.28
  Conformation dependent library (CDL) restraints added in 183.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.15
  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: 0.41

  Time building geometry restraints manager: 0.40 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'a'
  selection = chain 'b'
  selection = chain 'c'
  selection = chain 'd'
  selection = chain 'e'
}

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:             18.730
  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:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.180
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.620
-------------------------------------------------------------------------------
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 : 43.96
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 TYR   0.023   0.006   TYR d  39 
 PHE   0.009   0.003   PHE B  94 
 HIS   0.001   0.000   HIS b  50 

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

*********************** 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  : 0.095 
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: 0.0594
  time to fit residues: 16.5260
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  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.5010 r_free = 0.5010 target = 0.217647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4801 r_free = 0.4801 target = 0.193289 restraints weight = 6722.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.196041 restraints weight = 4389.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.197996 restraints weight = 3235.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.199450 restraints weight = 2591.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.199978 restraints weight = 2186.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.4871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.7474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4180  Z= 0.163
  Angle     :  0.703   7.809   5660  Z= 0.402
  Chirality :  0.053   0.140    750
  Planarity :  0.003   0.020    700
  Dihedral  :  5.440  16.906    610
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers : 11.67 %
    Allowed  : 19.05 %
    Favored  : 69.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.41 (0.30), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.23), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.050   0.005   TYR A  39 
 PHE   0.008   0.002   PHE A  94 
 HIS   0.006   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4180)
  covalent geometry    : angle       0.70341 ( 5660)
  hydrogen bonds       : bond        0.05118 (   63)
  hydrogen bonds       : angle       8.47108 (  189)

*********************** 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
  196 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 147
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   88 ILE cc_start: 0.7052 (mp) cc_final: 0.6757 (tp)
REVERT: D   39 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.6034 (p90)
REVERT: D   43 LYS cc_start: 0.7325 (mptt) cc_final: 0.6835 (tmtt)
REVERT: a   46 GLU cc_start: 0.7198 (mp0) cc_final: 0.6863 (mp0)
REVERT: a   48 VAL cc_start: 0.8150 (m) cc_final: 0.7922 (p)
REVERT: c   88 ILE cc_start: 0.6499 (tt) cc_final: 0.6256 (tp)
REVERT: e   39 TYR cc_start: 0.3895 (OUTLIER) cc_final: 0.3629 (m-80)
  outliers start: 49
  outliers final: 26
  residues processed: 181
  average time/residue: 0.0421
  time to fit residues: 10.7297
Evaluate side-chains
  125 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 97
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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   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 52 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0370
   chunk 21 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 41 optimal weight:    0.1980
   chunk 45 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.6262

-------------------------------------------------------------------------------
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**
** 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 = 0.4771 r_free = 0.4771 target = 0.186569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.165420 restraints weight = 7090.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.168004 restraints weight = 4422.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.169766 restraints weight = 3089.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.170848 restraints weight = 2377.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.171624 restraints weight = 1994.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.4636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.9957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   4180  Z= 0.197
  Angle     :  0.695   6.873   5660  Z= 0.400
  Chirality :  0.053   0.140    750
  Planarity :  0.003   0.015    700
  Dihedral  :  5.790  17.211    610
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers : 14.52 %
    Allowed  : 24.29 %
    Favored  : 61.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.49 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.65 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.028   0.003   TYR A  39 
 PHE   0.014   0.002   PHE c  94 
 HIS   0.008   0.002   HIS e  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 4180)
  covalent geometry    : angle       0.69507 ( 5660)
  hydrogen bonds       : bond        0.05052 (   63)
  hydrogen bonds       : angle       8.48651 (  189)

*********************** 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
  183 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 122
  time to evaluate  : 0.168 
Fit side-chains
REVERT: C   94 PHE cc_start: 0.5654 (m-80) cc_final: 0.5227 (m-80)
REVERT: D   39 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.7069 (p90)
REVERT: a   46 GLU cc_start: 0.7287 (mp0) cc_final: 0.6983 (mp0)
REVERT: c   39 TYR cc_start: 0.6855 (p90) cc_final: 0.5905 (p90)
REVERT: d   42 SER cc_start: 0.8103 (m) cc_final: 0.7727 (m)
REVERT: e   43 LYS cc_start: 0.7603 (mptt) cc_final: 0.7385 (mttt)
  outliers start: 61
  outliers final: 46
  residues processed: 166
  average time/residue: 0.0393
  time to fit residues: 9.3604
Evaluate side-chains
  147 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 100
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
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   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   63 VAL
Chi-restraints excluded: chain D residue   39 TYR
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   71 VAL
Chi-restraints excluded: chain D residue   74 VAL
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain E residue   37 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   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 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   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   82 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 d residue   59 THR
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 10 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** E  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** d  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
e  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.174819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.157248 restraints weight = 7498.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.159272 restraints weight = 4738.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.160831 restraints weight = 3355.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.162011 restraints weight = 2610.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.162532 restraints weight = 2137.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.4570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          1.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061   4180  Z= 0.260
  Angle     :  0.814   7.802   5660  Z= 0.455
  Chirality :  0.057   0.177    750
  Planarity :  0.003   0.012    700
  Dihedral  :  6.682  23.473    610
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 18.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers : 17.86 %
    Allowed  : 24.76 %
    Favored  : 57.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.56 (0.28), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.029   0.002   TYR a  39 
 PHE   0.014   0.002   PHE E  94 
 HIS   0.011   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 4180)
  covalent geometry    : angle       0.81411 ( 5660)
  hydrogen bonds       : bond        0.04896 (   63)
  hydrogen bonds       : angle       8.39364 (  189)

*********************** 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
  185 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 110
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6427 (p90)
REVERT: C   39 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5855 (p90)
REVERT: C   95 VAL cc_start: 0.7553 (m) cc_final: 0.7130 (t)
REVERT: D   39 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7260 (p90)
REVERT: a   39 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6443 (p90)
REVERT: a   46 GLU cc_start: 0.7375 (mp0) cc_final: 0.7061 (mp0)
REVERT: c   39 TYR cc_start: 0.7312 (p90) cc_final: 0.6243 (p90)
REVERT: d   39 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.7018 (p90)
  outliers start: 75
  outliers final: 55
  residues processed: 159
  average time/residue: 0.0426
  time to fit residues: 9.6392
Evaluate side-chains
  154 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 94
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
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   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   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 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   63 VAL
Chi-restraints excluded: chain D residue   74 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   38 LEU
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 b residue   40 VAL
Chi-restraints excluded: chain b residue   55 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   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   74 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 10 optimal weight:    0.1980
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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**
c  79 GLN
** d  50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** e  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.187882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.170091 restraints weight = 7028.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.172357 restraints weight = 4317.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.174037 restraints weight = 2999.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.174972 restraints weight = 2297.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.175691 restraints weight = 1922.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          1.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4180  Z= 0.121
  Angle     :  0.606   6.791   5660  Z= 0.331
  Chirality :  0.051   0.131    750
  Planarity :  0.002   0.014    700
  Dihedral  :  4.708  14.760    610
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers : 14.52 %
    Allowed  : 28.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.44 (0.29), 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
 TYR   0.024   0.002   TYR A  39 
 PHE   0.016   0.002   PHE C  94 
 HIS   0.004   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4180)
  covalent geometry    : angle       0.60611 ( 5660)
  hydrogen bonds       : bond        0.03659 (   63)
  hydrogen bonds       : angle       7.84777 (  189)

*********************** 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
  174 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 113
  time to evaluate  : 0.099 
Fit side-chains
REVERT: C   94 PHE cc_start: 0.5732 (m-80) cc_final: 0.5466 (m-80)
REVERT: C   95 VAL cc_start: 0.7441 (m) cc_final: 0.7017 (t)
REVERT: D   39 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7484 (p90)
REVERT: D   42 SER cc_start: 0.7997 (m) cc_final: 0.7750 (m)
REVERT: a   39 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6200 (p90)
REVERT: b   88 ILE cc_start: 0.6994 (mm) cc_final: 0.6547 (tt)
REVERT: c   39 TYR cc_start: 0.7006 (p90) cc_final: 0.5951 (p90)
REVERT: d   39 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7251 (p90)
  outliers start: 61
  outliers final: 47
  residues processed: 152
  average time/residue: 0.0378
  time to fit residues: 8.2929
Evaluate side-chains
  151 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 101
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
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   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   44 THR
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   59 THR
Chi-restraints excluded: chain D residue   74 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   88 ILE
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   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   74 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0670
   chunk 43 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.3522

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.181701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.163850 restraints weight = 7354.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.166193 restraints weight = 4559.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.167884 restraints weight = 3158.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.168704 restraints weight = 2396.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.169771 restraints weight = 2029.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.4663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          1.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4180  Z= 0.156
  Angle     :  0.643   6.679   5660  Z= 0.354
  Chirality :  0.052   0.134    750
  Planarity :  0.002   0.010    700
  Dihedral  :  5.113  15.514    610
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers : 15.71 %
    Allowed  : 28.81 %
    Favored  : 55.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.44 (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
 TYR   0.022   0.002   TYR a  39 
 PHE   0.012   0.002   PHE A  94 
 HIS   0.007   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4180)
  covalent geometry    : angle       0.64337 ( 5660)
  hydrogen bonds       : bond        0.03743 (   63)
  hydrogen bonds       : angle       7.78615 (  189)

*********************** 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
  163 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 97
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6729 (p90)
REVERT: C   94 PHE cc_start: 0.5621 (m-80) cc_final: 0.5396 (m-80)
REVERT: D   39 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7351 (p90)
REVERT: D   42 SER cc_start: 0.8028 (m) cc_final: 0.7809 (m)
REVERT: a   46 GLU cc_start: 0.7352 (mp0) cc_final: 0.7080 (mp0)
REVERT: d   39 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7225 (p90)
  outliers start: 66
  outliers final: 53
  residues processed: 147
  average time/residue: 0.0388
  time to fit residues: 8.2139
Evaluate side-chains
  144 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 88
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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   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   77 VAL
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   75 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   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   38 LEU
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 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   75 THR
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   59 THR
Chi-restraints excluded: chain d residue   66 VAL
Chi-restraints excluded: chain d residue   74 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 42 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0970
   chunk 30 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.4782

-------------------------------------------------------------------------------
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 = 0.4764 r_free = 0.4764 target = 0.180477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.163277 restraints weight = 7521.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.165539 restraints weight = 4564.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.166958 restraints weight = 3143.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.168278 restraints weight = 2414.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.168942 restraints weight = 1967.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          1.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4180  Z= 0.165
  Angle     :  0.683   6.843   5660  Z= 0.373
  Chirality :  0.053   0.156    750
  Planarity :  0.003   0.014    700
  Dihedral  :  5.275  16.232    610
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers : 16.90 %
    Allowed  : 29.05 %
    Favored  : 54.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.39 (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
 TYR   0.034   0.003   TYR a  39 
 PHE   0.009   0.002   PHE C  94 
 HIS   0.007   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 4180)
  covalent geometry    : angle       0.68282 ( 5660)
  hydrogen bonds       : bond        0.03988 (   63)
  hydrogen bonds       : angle       7.76651 (  189)

*********************** 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
  168 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 97
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6800 (p90)
REVERT: B   88 ILE cc_start: 0.6965 (mm) cc_final: 0.6494 (tt)
REVERT: D   39 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7400 (p90)
REVERT: c   39 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.6045 (p90)
REVERT: d   39 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7053 (p90)
  outliers start: 71
  outliers final: 65
  residues processed: 147
  average time/residue: 0.0360
  time to fit residues: 7.7979
Evaluate side-chains
  152 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 83
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
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   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   75 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   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 D residue   74 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   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   82 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   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   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   48 VAL
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 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   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
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 46 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    2.7588

-------------------------------------------------------------------------------
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  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.231403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.204343 restraints weight = 8377.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.203689 restraints weight = 12427.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.203996 restraints weight = 10506.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.204116 restraints weight = 9708.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.204305 restraints weight = 8784.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.4577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          1.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   4180  Z= 0.263
  Angle     :  0.806   7.131   5660  Z= 0.444
  Chirality :  0.056   0.163    750
  Planarity :  0.003   0.016    700
  Dihedral  :  6.422  24.191    610
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.37 %
    Favored  : 87.63 %
  Rotamer:
    Outliers : 17.38 %
    Allowed  : 28.57 %
    Favored  : 54.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.54 (0.28), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.024   0.002   TYR a  39 
 PHE   0.014   0.002   PHE b  94 
 HIS   0.013   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 4180)
  covalent geometry    : angle       0.80584 ( 5660)
  hydrogen bonds       : bond        0.04774 (   63)
  hydrogen bonds       : angle       7.94533 (  189)

*********************** 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
  169 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 96
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7016 (p90)
REVERT: D   39 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7246 (p90)
REVERT: a   39 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.6595 (p90)
REVERT: a   46 GLU cc_start: 0.7382 (mp0) cc_final: 0.7053 (mp0)
REVERT: c   39 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.6243 (p90)
REVERT: c   95 VAL cc_start: 0.7623 (m) cc_final: 0.7165 (t)
REVERT: d   39 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.7034 (p90)
  outliers start: 73
  outliers final: 62
  residues processed: 147
  average time/residue: 0.0398
  time to fit residues: 8.5336
Evaluate side-chains
  150 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 83
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
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   55 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   75 THR
Chi-restraints excluded: chain C residue   95 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   38 LEU
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   82 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 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   48 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 d residue   74 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 18 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:    0.4980
   chunk 24 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.183830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.166515 restraints weight = 7444.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.168877 restraints weight = 4615.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.170396 restraints weight = 3160.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.171626 restraints weight = 2403.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.172107 restraints weight = 1954.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.4689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          1.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4180  Z= 0.133
  Angle     :  0.666   7.049   5660  Z= 0.358
  Chirality :  0.052   0.145    750
  Planarity :  0.002   0.013    700
  Dihedral  :  4.890  16.061    610
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers : 14.76 %
    Allowed  : 32.62 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.39 (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
 TYR   0.028   0.002   TYR a  39 
 PHE   0.011   0.002   PHE b  94 
 HIS   0.003   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4180)
  covalent geometry    : angle       0.66617 ( 5660)
  hydrogen bonds       : bond        0.03598 (   63)
  hydrogen bonds       : angle       7.60835 (  189)

*********************** 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
  153 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 91
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6908 (p90)
REVERT: B   88 ILE cc_start: 0.6923 (mm) cc_final: 0.6517 (tt)
REVERT: C   96 LYS cc_start: 0.4428 (tptp) cc_final: 0.3880 (ttmt)
REVERT: D   39 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7447 (p90)
REVERT: a   39 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6615 (p90)
REVERT: c   83 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7035 (mm-30)
REVERT: d   39 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.7029 (p90)
  outliers start: 62
  outliers final: 57
  residues processed: 134
  average time/residue: 0.0353
  time to fit residues: 6.8328
Evaluate side-chains
  149 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 88
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
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   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   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   75 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   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 D residue   74 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   72 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   82 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   39 TYR
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   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   48 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 d residue   74 VAL
Chi-restraints excluded: chain d residue   82 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
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 44 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 14 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.4758 r_free = 0.4758 target = 0.178801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.161446 restraints weight = 7218.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.164020 restraints weight = 4380.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.165639 restraints weight = 2936.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.167093 restraints weight = 2176.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.167896 restraints weight = 1731.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.4657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          1.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4180  Z= 0.152
  Angle     :  0.677   6.959   5660  Z= 0.365
  Chirality :  0.052   0.143    750
  Planarity :  0.003   0.018    700
  Dihedral  :  5.085  15.635    610
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers : 15.95 %
    Allowed  : 30.48 %
    Favored  : 53.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.34 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.023   0.002   TYR a  39 
 PHE   0.017   0.003   PHE A  94 
 HIS   0.006   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4180)
  covalent geometry    : angle       0.67677 ( 5660)
  hydrogen bonds       : bond        0.03782 (   63)
  hydrogen bonds       : angle       7.46843 (  189)

********************** 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
  156 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 89
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A   39 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6957 (p90)
REVERT: B   88 ILE cc_start: 0.6881 (mm) cc_final: 0.6487 (tt)
REVERT: D   39 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7457 (p90)
REVERT: a   39 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6680 (p90)
REVERT: d   39 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7070 (p90)
  outliers start: 67
  outliers final: 61
  residues processed: 138
  average time/residue: 0.0415
  time to fit residues: 8.2542
Evaluate side-chains
  149 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 84
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
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   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   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   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 D residue   74 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   72 THR
Chi-restraints excluded: chain E residue   74 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   82 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   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 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   48 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 d residue   74 VAL
Chi-restraints excluded: chain d residue   82 VAL
Chi-restraints excluded: chain e residue   48 VAL
Chi-restraints excluded: chain e residue   59 THR
Chi-restraints excluded: chain e residue   72 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 42 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 29 optimal weight:    0.0370
   chunk 23 optimal weight:    0.0970
   overall best weight:    1.0262

-------------------------------------------------------------------------------
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 = 0.4783 r_free = 0.4783 target = 0.181726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.164148 restraints weight = 7241.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.166795 restraints weight = 4353.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.168472 restraints weight = 2902.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.169855 restraints weight = 2142.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.171046 restraints weight = 1688.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.4684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          1.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4180  Z= 0.140
  Angle     :  0.670   6.823   5660  Z= 0.358
  Chirality :  0.051   0.143    750
  Planarity :  0.002   0.011    700
  Dihedral  :  4.824  14.619    610
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers : 16.19 %
    Allowed  : 31.43 %
    Favored  : 52.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.28 (0.29), residues: 590
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.22), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.022   0.002   TYR a  39 
 PHE   0.011   0.002   PHE b  94 
 HIS   0.004   0.001   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4180)
  covalent geometry    : angle       0.67023 ( 5660)
  hydrogen bonds       : bond        0.03577 (   63)
  hydrogen bonds       : angle       7.34909 (  189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1347.21 seconds
wall clock time: 23 minutes 59.00 seconds (1439.00 seconds total)