Starting phenix.real_space_refine
on Wed Sep 17 06:24:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rk9_19265/09_2025/8rk9_19265.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rk9_19265/09_2025/8rk9_19265.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rk9_19265/09_2025/8rk9_19265.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rk9_19265/09_2025/8rk9_19265.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rk9_19265/09_2025/8rk9_19265.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rk9_19265/09_2025/8rk9_19265.cif"
  }
  resolution = 3.95
  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    3912      2.51       5
     N    1074      2.21       5
     O    1152      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6138
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1023
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 10, 'TRANS': 125}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.89, per 1000 atoms: 0.14
  Number of scatterers: 6138
  At special positions: 0
  Unit cell: (95.864, 95.864, 57.5184, 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    1152      8.00
     N    1074      7.00
     C    3912      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: 0.40
  Conformation dependent library (CDL) restraints added in 256.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 12 sheets defined
      19.9% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 19
      removed outlier: 5.028A  pdb=" N   ARG A  17 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
      removed outlier: 3.754A  pdb=" N   ALA A  68 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE A  69 " --> pdb=" O   GLN A  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 65 through 69'
    Processing helix  chain 'A' and resid 97 through 109
      removed outlier: 3.881A  pdb=" N   LEU A 101 " --> pdb=" O   GLU A  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 19
      removed outlier: 5.027A  pdb=" N   ARG B  17 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 3.754A  pdb=" N   ALA B  68 " --> pdb=" O   GLY B  65 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ILE B  69 " --> pdb=" O   GLN B  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 65 through 69'
    Processing helix  chain 'B' and resid 97 through 109
      removed outlier: 3.881A  pdb=" N   LEU B 101 " --> pdb=" O   GLU B  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 19
      removed outlier: 5.028A  pdb=" N   ARG C  17 " --> pdb=" O   LEU C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 65 through 69
      removed outlier: 3.754A  pdb=" N   ALA C  68 " --> pdb=" O   GLY C  65 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE C  69 " --> pdb=" O   GLN C  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 65 through 69'
    Processing helix  chain 'C' and resid 97 through 109
      removed outlier: 3.881A  pdb=" N   LEU C 101 " --> pdb=" O   GLU C  97 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 19
      removed outlier: 5.028A  pdb=" N   ARG D  17 " --> pdb=" O   LEU D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 69
      removed outlier: 3.754A  pdb=" N   ALA D  68 " --> pdb=" O   GLY D  65 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE D  69 " --> pdb=" O   GLN D  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 65 through 69'
    Processing helix  chain 'D' and resid 97 through 109
      removed outlier: 3.881A  pdb=" N   LEU D 101 " --> pdb=" O   GLU D  97 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 11 through 19
      removed outlier: 5.028A  pdb=" N   ARG E  17 " --> pdb=" O   LEU E  13 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 65 through 69
      removed outlier: 3.754A  pdb=" N   ALA E  68 " --> pdb=" O   GLY E  65 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE E  69 " --> pdb=" O   GLN E  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 65 through 69'
    Processing helix  chain 'E' and resid 97 through 109
      removed outlier: 3.881A  pdb=" N   LEU E 101 " --> pdb=" O   GLU E  97 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 11 through 19
      removed outlier: 5.028A  pdb=" N   ARG F  17 " --> pdb=" O   LEU F  13 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 65 through 69
      removed outlier: 3.754A  pdb=" N   ALA F  68 " --> pdb=" O   GLY F  65 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ILE F  69 " --> pdb=" O   GLN F  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 65 through 69'
    Processing helix  chain 'F' and resid 97 through 109
      removed outlier: 3.881A  pdb=" N   LEU F 101 " --> pdb=" O   GLU F  97 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 49 through 50
    Processing sheet with id=2, first strand: chain 'A' and resid 49 through 50
    Processing sheet with id=3, first strand: chain 'B' and resid 49 through 50
    Processing sheet with id=4, first strand: chain 'B' and resid 49 through 50
    Processing sheet with id=5, first strand: chain 'C' and resid 49 through 50
    Processing sheet with id=6, first strand: chain 'C' and resid 49 through 50
    Processing sheet with id=7, first strand: chain 'D' and resid 49 through 50
    Processing sheet with id=8, first strand: chain 'D' and resid 49 through 50
    Processing sheet with id=9, first strand: chain 'E' and resid 49 through 50
    Processing sheet with id=10, first strand: chain 'E' and resid 49 through 50
    Processing sheet with id=11, first strand: chain 'F' and resid 49 through 50
    Processing sheet with id=12, first strand: chain 'F' and resid 49 through 50

    120 hydrogen bonds defined for protein.
    324 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: 0.87

  Time building geometry restraints manager: 0.57 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: 1014
        1.29 -     1.36: 1056
        1.36 -     1.42: 588
        1.42 -     1.48: 984
        1.48 -     1.55: 2640
  Bond restraints: 6282
  Sorted by residual:
  bond pdb=" CA  VAL A  22 "
       pdb=" CB  VAL A  22 "
    ideal  model  delta    sigma   weight residual
    1.537  1.540 -0.003 5.00e-03 4.00e+04 4.72e-01
  bond pdb=" CA  VAL D  22 "
       pdb=" CB  VAL D  22 "
    ideal  model  delta    sigma   weight residual
    1.537  1.540 -0.003 5.00e-03 4.00e+04 4.72e-01
  bond pdb=" CA  VAL E  22 "
       pdb=" CB  VAL E  22 "
    ideal  model  delta    sigma   weight residual
    1.537  1.540 -0.003 5.00e-03 4.00e+04 4.56e-01
  bond pdb=" CA  VAL B  22 "
       pdb=" CB  VAL B  22 "
    ideal  model  delta    sigma   weight residual
    1.537  1.540 -0.003 5.00e-03 4.00e+04 4.56e-01
  bond pdb=" CA  ARG F  67 "
       pdb=" CB  ARG F  67 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.011 1.69e-02 3.50e+03 4.53e-01
  ... (remaining 6277 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 8356
        1.76 -     3.53: 188
        3.53 -     5.29: 24
        5.29 -     7.06: 0
        7.06 -     8.82: 12
  Bond angle restraints: 8580
  Sorted by residual:
  angle pdb=" C   GLN C  66 "
        pdb=" N   ARG C  67 "
        pdb=" CA  ARG C  67 "
      ideal   model   delta    sigma   weight residual
     121.54  126.66   -5.12 1.91e+00 2.74e-01 7.19e+00
  angle pdb=" C   GLN E  66 "
        pdb=" N   ARG E  67 "
        pdb=" CA  ARG E  67 "
      ideal   model   delta    sigma   weight residual
     121.54  126.65   -5.11 1.91e+00 2.74e-01 7.17e+00
  angle pdb=" C   GLN B  66 "
        pdb=" N   ARG B  67 "
        pdb=" CA  ARG B  67 "
      ideal   model   delta    sigma   weight residual
     121.54  126.65   -5.11 1.91e+00 2.74e-01 7.17e+00
  angle pdb=" C   GLN A  66 "
        pdb=" N   ARG A  67 "
        pdb=" CA  ARG A  67 "
      ideal   model   delta    sigma   weight residual
     121.54  126.65   -5.11 1.91e+00 2.74e-01 7.15e+00
  angle pdb=" C   GLN D  66 "
        pdb=" N   ARG D  67 "
        pdb=" CA  ARG D  67 "
      ideal   model   delta    sigma   weight residual
     121.54  126.65   -5.11 1.91e+00 2.74e-01 7.15e+00
  ... (remaining 8575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 3343
       16.74 -    33.49: 245
       33.49 -    50.23: 72
       50.23 -    66.97: 18
       66.97 -    83.72: 18
  Dihedral angle restraints: 3696
    sinusoidal: 1392
      harmonic: 2304
  Sorted by residual:
  dihedral pdb=" CA  ARG D 123 "
           pdb=" CB  ARG D 123 "
           pdb=" CG  ARG D 123 "
           pdb=" CD  ARG D 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -104.55   44.55     3      1.50e+01 4.44e-03 8.01e+00
  dihedral pdb=" CA  ARG A 123 "
           pdb=" CB  ARG A 123 "
           pdb=" CG  ARG A 123 "
           pdb=" CD  ARG A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -104.55   44.55     3      1.50e+01 4.44e-03 8.01e+00
  dihedral pdb=" CA  ARG B 123 "
           pdb=" CB  ARG B 123 "
           pdb=" CG  ARG B 123 "
           pdb=" CD  ARG B 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -104.53   44.53     3      1.50e+01 4.44e-03 8.01e+00
  ... (remaining 3693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 504
       0.025 -    0.050: 242
       0.050 -    0.075: 95
       0.075 -    0.100: 63
       0.100 -    0.125: 62
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" CA  ILE E  69 "
            pdb=" N   ILE E  69 "
            pdb=" C   ILE E  69 "
            pdb=" CB  ILE E  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  ILE F  69 "
            pdb=" N   ILE F  69 "
            pdb=" C   ILE F  69 "
            pdb=" CB  ILE F  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.76e-01
  chirality pdb=" CA  ILE A  69 "
            pdb=" N   ILE A  69 "
            pdb=" C   ILE A  69 "
            pdb=" CB  ILE A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 963 not shown)

  Planarity restraints: 1128
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN F  66 "   -0.005 2.00e-02 2.50e+03   9.17e-03 8.41e-01
        pdb=" C   GLN F  66 "    0.016 2.00e-02 2.50e+03
        pdb=" O   GLN F  66 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ARG F  67 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D  66 "    0.005 2.00e-02 2.50e+03   9.11e-03 8.31e-01
        pdb=" C   GLN D  66 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   GLN D  66 "    0.006 2.00e-02 2.50e+03
        pdb=" N   ARG D  67 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  66 "   -0.005 2.00e-02 2.50e+03   9.11e-03 8.31e-01
        pdb=" C   GLN A  66 "    0.016 2.00e-02 2.50e+03
        pdb=" O   GLN A  66 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   ARG A  67 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1125 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1868
        2.81 -     3.34: 5941
        3.34 -     3.86: 9577
        3.86 -     4.38: 10559
        4.38 -     4.90: 17722
  Nonbonded interactions: 45667
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  51 "
            pdb=" OE1 GLN B  74 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OH  TYR C  51 "
            pdb=" OE1 GLN C  74 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OH  TYR A  51 "
            pdb=" OE1 GLN A  74 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OH  TYR D  51 "
            pdb=" OE1 GLN D  74 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OH  TYR E  51 "
            pdb=" OE1 GLN E  74 "
     model   vdw
     2.294 3.040
  ... (remaining 45662 not shown)

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

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:             9.350
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.330
  Find NCS groups from input model:        0.050
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0031
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      :  0.002   0.017   6282  Z= 0.103
  Angle     :  0.670   8.821   8580  Z= 0.324
  Chirality :  0.046   0.125    966
  Planarity :  0.003   0.016   1128
  Dihedral  : 15.379  83.718   2232
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  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: -3.79 (0.28), residues: 792
  helix: -1.04 (0.59), residues: 96
  sheet: -2.07 (0.42), residues: 156
  loop : -3.16 (0.24), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  19 
 TYR   0.007   0.001   TYR B 138 
 PHE   0.004   0.001   PHE C   9 
 TRP   0.004   0.001   TRP F  76 
 HIS   0.001   0.000   HIS C  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 6282)
  covalent geometry    : angle       0.66993 ( 8580)
  hydrogen bonds       : bond        0.24897 (  108)
  hydrogen bonds       : angle      11.90594 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1308
  time to fit residues: 16.4913
Evaluate side-chains
  34 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  62 HIS
B  62 HIS
C  62 HIS
D  62 HIS
E  62 HIS
F  62 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5390 r_free = 0.5390 target = 0.314937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5300 r_free = 0.5300 target = 0.305863 restraints weight = 23261.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.5312 r_free = 0.5312 target = 0.307332 restraints weight = 18501.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.308508 restraints weight = 14876.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.5332 r_free = 0.5332 target = 0.309550 restraints weight = 12289.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.5341 r_free = 0.5341 target = 0.310409 restraints weight = 10118.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.5339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0521
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   6282  Z= 0.183
  Angle     :  0.830   8.333   8580  Z= 0.399
  Chirality :  0.052   0.134    966
  Planarity :  0.008   0.054   1128
  Dihedral  :  4.452  14.221    894
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.88 %
    Favored  : 87.12 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.70 %
    Favored  : 87.34 %
  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: -3.81 (0.27), residues: 792
  helix: -1.10 (0.56), residues: 96
  sheet: -1.85 (0.44), residues: 144
  loop : -3.24 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  67 
 TYR   0.013   0.001   TYR D  51 
 PHE   0.020   0.002   PHE F 147 
 TRP   0.017   0.003   TRP C  76 
 HIS   0.002   0.001   HIS D  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6282)
  covalent geometry    : angle       0.83017 ( 8580)
  hydrogen bonds       : bond        0.05548 (  108)
  hydrogen bonds       : angle       9.48637 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 28
  average time/residue: 0.1081
  time to fit residues: 4.0432
Evaluate side-chains
  20 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 ILE
Chi-restraints excluded: chain F residue   27 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   chunk 30 optimal weight:    0.0980
   chunk 21 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.5332 r_free = 0.5332 target = 0.299066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.294483 restraints weight = 28087.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5305 r_free = 0.5305 target = 0.293761 restraints weight = 29900.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.5305 r_free = 0.5305 target = 0.293706 restraints weight = 27178.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.5306 r_free = 0.5306 target = 0.293614 restraints weight = 27142.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.5306 r_free = 0.5306 target = 0.293612 restraints weight = 27506.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.5324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0602
moved from start:          0.5272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6282  Z= 0.169
  Angle     :  0.770   7.860   8580  Z= 0.375
  Chirality :  0.050   0.119    966
  Planarity :  0.007   0.049   1128
  Dihedral  :  4.531  12.421    894
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 18.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.12 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.63 %
    Favored  : 78.21 %
  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: -3.66 (0.26), residues: 792
  helix: -0.36 (0.66), residues: 66
  sheet: -1.45 (0.33), residues: 174
  loop : -3.28 (0.23), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 123 
 TYR   0.020   0.002   TYR D 132 
 PHE   0.015   0.002   PHE F 147 
 TRP   0.019   0.003   TRP F  76 
 HIS   0.007   0.002   HIS C  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6282)
  covalent geometry    : angle       0.76960 ( 8580)
  hydrogen bonds       : bond        0.05104 (  108)
  hydrogen bonds       : angle       8.22411 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 12
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 14
  residues processed: 38
  average time/residue: 0.0465
  time to fit residues: 3.0079
Evaluate side-chains
  26 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 12
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain B residue  138 TYR
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  110 THR
Chi-restraints excluded: chain C residue  138 TYR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain E residue  138 TYR
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  110 THR
Chi-restraints excluded: chain F residue  138 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0370
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 = 0.5311 r_free = 0.5311 target = 0.296688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.272339 restraints weight = 22790.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.272046 restraints weight = 26259.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.272046 restraints weight = 26931.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.272046 restraints weight = 26931.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5256 r_free = 0.5256 target = 0.272046 restraints weight = 26931.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.5238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0923
moved from start:          0.6332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6282  Z= 0.149
  Angle     :  0.705   7.001   8580  Z= 0.346
  Chirality :  0.048   0.125    966
  Planarity :  0.007   0.044   1128
  Dihedral  :  4.504  12.603    894
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.12 %
    Favored  : 75.00 %
  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: -3.89 (0.27), residues: 792
  helix: -1.43 (0.55), residues: 102
  sheet: -1.41 (0.35), residues: 174
  loop : -3.50 (0.23), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F 146 
 TYR   0.010   0.002   TYR D  51 
 PHE   0.014   0.002   PHE F 147 
 TRP   0.020   0.003   TRP C  76 
 HIS   0.003   0.001   HIS E  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6282)
  covalent geometry    : angle       0.70496 ( 8580)
  hydrogen bonds       : bond        0.03414 (  108)
  hydrogen bonds       : angle       7.05785 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 24
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 6
  residues processed: 42
  average time/residue: 0.0412
  time to fit residues: 3.0386
Evaluate side-chains
  18 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 12
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain B residue  138 TYR
Chi-restraints excluded: chain C residue  138 TYR
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain E residue  138 TYR
Chi-restraints excluded: chain F residue  138 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 127 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5379 r_free = 0.5379 target = 0.290577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.280877 restraints weight = 25607.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5299 r_free = 0.5299 target = 0.282274 restraints weight = 20662.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.5309 r_free = 0.5309 target = 0.283360 restraints weight = 17166.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5318 r_free = 0.5318 target = 0.284258 restraints weight = 14778.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.5325 r_free = 0.5325 target = 0.284929 restraints weight = 12809.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.5327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1056
moved from start:          0.7775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6282  Z= 0.188
  Angle     :  0.808  10.451   8580  Z= 0.394
  Chirality :  0.050   0.131    966
  Planarity :  0.007   0.045   1128
  Dihedral  :  4.870  14.256    894
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 23.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.26 %
    Favored  : 86.74 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 20.03 %
    Favored  : 74.20 %
  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: -4.12 (0.25), residues: 792
  helix: -1.05 (0.61), residues: 72
  sheet: -1.93 (0.40), residues: 126
  loop : -3.44 (0.21), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 104 
 TYR   0.020   0.002   TYR A 132 
 PHE   0.013   0.003   PHE F 147 
 TRP   0.025   0.004   TRP F  76 
 HIS   0.009   0.003   HIS C  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 6282)
  covalent geometry    : angle       0.80840 ( 8580)
  hydrogen bonds       : bond        0.05111 (  108)
  hydrogen bonds       : angle       7.41009 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 16
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 36
  outliers final: 18
  residues processed: 50
  average time/residue: 0.0477
  time to fit residues: 3.9943
Evaluate side-chains
  26 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 8
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  138 TYR
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain E residue   27 ILE
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  102 LEU
Chi-restraints excluded: chain E residue  138 TYR
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain F residue  101 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 53 optimal weight:    0.4980
   chunk 18 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    0.1980
   chunk 43 optimal weight:    0.0470
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.3478

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

Flipped N/Q/H residues before XYZ refinement:
C  74 GLN
F  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5397 r_free = 0.5397 target = 0.291755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5297 r_free = 0.5297 target = 0.281610 restraints weight = 25377.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.282923 restraints weight = 20658.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5319 r_free = 0.5319 target = 0.284029 restraints weight = 17218.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.5325 r_free = 0.5325 target = 0.284605 restraints weight = 14734.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.5332 r_free = 0.5332 target = 0.285339 restraints weight = 13065.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.5333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0956
moved from start:          0.7982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6282  Z= 0.125
  Angle     :  0.694   7.463   8580  Z= 0.333
  Chirality :  0.047   0.135    966
  Planarity :  0.006   0.042   1128
  Dihedral  :  4.447  12.448    894
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 19.55 %
    Favored  : 75.64 %
  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: -3.88 (0.25), residues: 792
  helix: -0.23 (0.64), residues: 66
  sheet: -2.06 (0.40), residues: 126
  loop : -3.26 (0.20), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 146 
 TYR   0.023   0.002   TYR C 138 
 PHE   0.008   0.002   PHE F 143 
 TRP   0.019   0.002   TRP D  76 
 HIS   0.002   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6282)
  covalent geometry    : angle       0.69443 ( 8580)
  hydrogen bonds       : bond        0.04024 (  108)
  hydrogen bonds       : angle       6.83136 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 14
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 30
  outliers final: 26
  residues processed: 44
  average time/residue: 0.0430
  time to fit residues: 3.2916
Evaluate side-chains
  36 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 10
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  138 TYR
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain E residue  138 TYR
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  102 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.0030
   chunk 26 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0570
   chunk 71 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.3708

-------------------------------------------------------------------------------
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 = 0.5387 r_free = 0.5387 target = 0.291243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5297 r_free = 0.5297 target = 0.281471 restraints weight = 25617.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.282531 restraints weight = 21247.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.5315 r_free = 0.5315 target = 0.283535 restraints weight = 18183.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.284469 restraints weight = 15848.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.5328 r_free = 0.5328 target = 0.284952 restraints weight = 13918.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.5331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0985
moved from start:          0.8278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6282  Z= 0.124
  Angle     :  0.674   7.520   8580  Z= 0.324
  Chirality :  0.047   0.127    966
  Planarity :  0.006   0.040   1128
  Dihedral  :  4.255  11.967    894
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 20.67 %
    Favored  : 75.48 %
  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: -3.68 (0.25), residues: 792
  helix: -0.49 (0.63), residues: 66
  sheet: -1.27 (0.57), residues: 66
  loop : -3.10 (0.20), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 123 
 TYR   0.018   0.002   TYR C 138 
 PHE   0.017   0.002   PHE F 147 
 TRP   0.020   0.002   TRP E  76 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6282)
  covalent geometry    : angle       0.67433 ( 8580)
  hydrogen bonds       : bond        0.03878 (  108)
  hydrogen bonds       : angle       6.17737 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 10
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 22
  residues processed: 34
  average time/residue: 0.0467
  time to fit residues: 2.8323
Evaluate side-chains
  30 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 8
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  138 TYR
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  110 THR
Chi-restraints excluded: chain E residue  138 TYR
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain F residue  101 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 69 optimal weight:    0.0570
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0770
   chunk 59 optimal weight:    0.4980
   chunk 46 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
** C  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  74 GLN ** 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 = 0.5412 r_free = 0.5412 target = 0.291797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5309 r_free = 0.5309 target = 0.280718 restraints weight = 21867.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.282084 restraints weight = 17924.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.282841 restraints weight = 15432.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.5335 r_free = 0.5335 target = 0.284002 restraints weight = 13482.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.5343 r_free = 0.5343 target = 0.284911 restraints weight = 11551.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.5341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0988
moved from start:          0.8691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6282  Z= 0.125
  Angle     :  0.667   7.421   8580  Z= 0.320
  Chirality :  0.046   0.124    966
  Planarity :  0.006   0.043   1128
  Dihedral  :  4.166  12.298    894
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.31 %
    Favored  : 75.48 %
  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: -3.66 (0.25), residues: 792
  helix: -0.74 (0.62), residues: 66
  sheet: -1.22 (0.59), residues: 66
  loop : -3.06 (0.20), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 146 
 TYR   0.013   0.002   TYR C 138 
 PHE   0.009   0.002   PHE F 147 
 TRP   0.023   0.003   TRP C  76 
 HIS   0.003   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6282)
  covalent geometry    : angle       0.66658 ( 8580)
  hydrogen bonds       : bond        0.03733 (  108)
  hydrogen bonds       : angle       6.09259 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 14
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 20
  outliers final: 18
  residues processed: 34
  average time/residue: 0.0527
  time to fit residues: 2.9666
Evaluate side-chains
  26 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 8
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  138 TYR
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  138 TYR
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue  101 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    0.0020
   chunk 75 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0270
   chunk 62 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.4046

-------------------------------------------------------------------------------
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 = 0.5415 r_free = 0.5415 target = 0.291259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5315 r_free = 0.5315 target = 0.280235 restraints weight = 21735.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5328 r_free = 0.5328 target = 0.281561 restraints weight = 18205.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5337 r_free = 0.5337 target = 0.282776 restraints weight = 15630.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.5346 r_free = 0.5346 target = 0.283779 restraints weight = 13409.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.5353 r_free = 0.5353 target = 0.284691 restraints weight = 11554.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.5357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0994
moved from start:          0.9127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6282  Z= 0.125
  Angle     :  0.672   7.465   8580  Z= 0.322
  Chirality :  0.049   0.341    966
  Planarity :  0.006   0.042   1128
  Dihedral  :  4.047  12.980    894
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.63 %
    Favored  : 75.48 %
  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: -3.59 (0.25), residues: 792
  helix: -0.74 (0.62), residues: 66
  sheet: -1.18 (0.59), residues: 66
  loop : -3.00 (0.20), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 146 
 TYR   0.012   0.002   TYR C 138 
 PHE   0.017   0.001   PHE F 147 
 TRP   0.022   0.003   TRP D  76 
 HIS   0.003   0.001   HIS F  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6282)
  covalent geometry    : angle       0.67189 ( 8580)
  hydrogen bonds       : bond        0.03594 (  108)
  hydrogen bonds       : angle       5.90300 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 14
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 PRO cc_start: 0.4624 (Cg_endo) cc_final: 0.4096 (Cg_exo)
REVERT: B  114 PRO cc_start: 0.5632 (Cg_endo) cc_final: 0.5010 (Cg_exo)
REVERT: D  114 PRO cc_start: 0.4877 (Cg_endo) cc_final: 0.4333 (Cg_exo)
REVERT: E  114 PRO cc_start: 0.5529 (Cg_endo) cc_final: 0.4888 (Cg_exo)
  outliers start: 18
  outliers final: 18
  residues processed: 32
  average time/residue: 0.0713
  time to fit residues: 3.4254
Evaluate side-chains
  28 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 10
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  138 TYR
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  138 TYR
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain F residue  101 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0270
   chunk 74 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0670
   chunk 68 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0070
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.2394

-------------------------------------------------------------------------------
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 = 0.5413 r_free = 0.5413 target = 0.292095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5314 r_free = 0.5314 target = 0.281311 restraints weight = 21977.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.5318 r_free = 0.5318 target = 0.282264 restraints weight = 18303.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.5332 r_free = 0.5332 target = 0.283517 restraints weight = 15562.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.5342 r_free = 0.5342 target = 0.284528 restraints weight = 13270.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.5350 r_free = 0.5350 target = 0.285365 restraints weight = 11511.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.5349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0972
moved from start:          0.9342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6282  Z= 0.112
  Angle     :  0.656   7.490   8580  Z= 0.311
  Chirality :  0.046   0.122    966
  Planarity :  0.006   0.043   1128
  Dihedral  :  3.947  13.640    894
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.99 %
    Favored  : 76.12 %
  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: -3.52 (0.25), residues: 792
  helix: -0.77 (0.60), residues: 66
  sheet: -1.27 (0.59), residues: 66
  loop : -2.92 (0.20), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 146 
 TYR   0.010   0.001   TYR C 138 
 PHE   0.008   0.001   PHE F 147 
 TRP   0.021   0.002   TRP D  76 
 HIS   0.002   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6282)
  covalent geometry    : angle       0.65626 ( 8580)
  hydrogen bonds       : bond        0.03358 (  108)
  hydrogen bonds       : angle       5.70986 (  324)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 10
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 PRO cc_start: 0.4264 (Cg_endo) cc_final: 0.3786 (Cg_exo)
REVERT: B  114 PRO cc_start: 0.4805 (Cg_endo) cc_final: 0.4175 (Cg_exo)
REVERT: D  114 PRO cc_start: 0.5171 (Cg_endo) cc_final: 0.4662 (Cg_exo)
REVERT: E  114 PRO cc_start: 0.5732 (Cg_endo) cc_final: 0.5085 (Cg_exo)
  outliers start: 18
  outliers final: 16
  residues processed: 28
  average time/residue: 0.0454
  time to fit residues: 2.3222
Evaluate side-chains
  26 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 10
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  110 THR
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   82 VAL
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  110 THR
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain F residue   10 LEU
Chi-restraints excluded: chain F residue   82 VAL
Chi-restraints excluded: chain F residue  101 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.0870
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0270
   chunk 19 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0770
   chunk 42 optimal weight:    0.4980
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.1974

-------------------------------------------------------------------------------
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 = 0.5286 r_free = 0.5286 target = 0.291107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.283469 restraints weight = 22124.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.283453 restraints weight = 27517.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.283453 restraints weight = 27520.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.283453 restraints weight = 27520.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.5265 r_free = 0.5265 target = 0.283453 restraints weight = 27520.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.5288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0945
moved from start:          0.9512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6282  Z= 0.112
  Angle     :  0.657   7.539   8580  Z= 0.311
  Chirality :  0.046   0.123    966
  Planarity :  0.006   0.041   1128
  Dihedral  :  3.864  13.802    894
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.98 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.31 %
    Favored  : 76.44 %
  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: -3.45 (0.25), residues: 792
  helix: -0.72 (0.61), residues: 66
  sheet: -1.09 (0.61), residues: 66
  loop : -2.88 (0.20), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  95 
 TYR   0.012   0.002   TYR B 138 
 PHE   0.017   0.001   PHE E 139 
 TRP   0.021   0.002   TRP B  76 
 HIS   0.002   0.001   HIS B  62 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6282)
  covalent geometry    : angle       0.65731 ( 8580)
  hydrogen bonds       : bond        0.03232 (  108)
  hydrogen bonds       : angle       5.71432 (  324)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1226.91 seconds
wall clock time: 21 minutes 52.45 seconds (1312.45 seconds total)