Starting phenix.real_space_refine
on Wed Sep 17 02:57:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oys_71033/09_2025/9oys_71033.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oys_71033/09_2025/9oys_71033.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oys_71033/09_2025/9oys_71033.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oys_71033/09_2025/9oys_71033.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oys_71033/09_2025/9oys_71033.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oys_71033/09_2025/9oys_71033.map"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C     762      2.51       5
     N     210      2.21       5
     O     228      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: 1218
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 207
          Classifications: {'peptide': 33}
          Link IDs: {'TRANS': 32}
    Chain: "B"
      Number of atoms: 199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 199
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
  Restraints were copied for chains:
    C, E, D, F
  Time building chain proxies: 0.18, per 1000 atoms: 0.15
  Number of scatterers: 1218
  At special positions: 0
  Unit cell: (58.104, 68.864, 38.736, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     228      8.00
     N     210      7.00
     C     762      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: 0.05
  Conformation dependent library (CDL) restraints added in 154.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  312

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 50.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.03
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 61
      removed outlier: 6.320A  pdb=" N   MET A  48 " --> pdb=" O   ALA C  49 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   THR C  51 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 8.978A  pdb=" N   THR A  50 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ALA C  53 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 9.123A  pdb=" N   ALA A  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 9.651A  pdb=" N   VAL C  55 " --> pdb=" O   ALA A  52 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   GLY A  54 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 8.302A  pdb=" N   VAL C  57 " --> pdb=" O   GLY A  54 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ALA A  56 " --> pdb=" O   VAL C  57 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   LEU C  59 " --> pdb=" O   ALA A  56 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   GLY A  58 " --> pdb=" O   LEU C  59 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   VAL C  61 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ALA A  60 " --> pdb=" O   VAL C  61 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   MET C  48 " --> pdb=" O   ALA E  49 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   THR E  51 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
      removed outlier: 9.020A  pdb=" N   THR C  50 " --> pdb=" O   THR E  51 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ALA E  53 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 9.015A  pdb=" N   ALA C  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 9.532A  pdb=" N   VAL E  55 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   GLY C  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 8.142A  pdb=" N   VAL E  57 " --> pdb=" O   GLY C  54 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   ALA C  56 " --> pdb=" O   VAL E  57 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   LEU E  59 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   GLY C  58 " --> pdb=" O   LEU E  59 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   VAL E  61 " --> pdb=" O   GLY C  58 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ALA C  60 " --> pdb=" O   VAL E  61 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65
    Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 73
      removed outlier: 6.945A  pdb=" N   THR C  70 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLY A  71 " --> pdb=" O   THR C  70 " (cutoff:3.500A)
      removed outlier: 8.993A  pdb=" N   LEU C  69 " --> pdb=" O   THR E  70 " (cutoff:3.500A)
      removed outlier: 9.708A  pdb=" N   ALA E  72 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   GLY C  71 " --> pdb=" O   ALA E  72 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 53
      removed outlier: 6.359A  pdb=" N   ALA D  46 " --> pdb=" O   GLN F  47 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   ALA F  49 " --> pdb=" O   ALA D  46 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   MET D  48 " --> pdb=" O   ALA F  49 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   THR F  51 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   THR D  50 " --> pdb=" O   THR F  51 " (cutoff:3.500A)
      removed outlier: 8.099A  pdb=" N   ALA F  53 " --> pdb=" O   THR D  50 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA D  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57
    Processing sheet with id=AA6, first strand: chain 'B' and resid 64 through 70
      removed outlier: 6.572A  pdb=" N   MET B  65 " --> pdb=" O   GLY D  66 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ALA D  68 " --> pdb=" O   MET B  65 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   SER B  67 " --> pdb=" O   ALA D  68 " (cutoff:3.500A)
      removed outlier: 8.141A  pdb=" N   THR D  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU B  69 " --> pdb=" O   THR D  70 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   MET D  65 " --> pdb=" O   GLY F  66 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   ALA F  68 " --> pdb=" O   MET D  65 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   SER D  67 " --> pdb=" O   ALA F  68 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   THR F  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LEU D  69 " --> pdb=" O   THR F  70 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    13 hydrogen bonds defined for protein.
    39 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: 0.07

  Time building geometry restraints manager: 0.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 402
        1.34 -     1.46: 257
        1.46 -     1.57: 529
        1.57 -     1.69: 0
        1.69 -     1.80: 36
  Bond restraints: 1224
  Sorted by residual:
  bond pdb=" CA  ALA B  46 "
       pdb=" C   ALA B  46 "
    ideal  model  delta    sigma   weight residual
    1.519  1.528 -0.009 1.14e-02 7.69e+03 6.22e-01
  bond pdb=" CA  ALA F  46 "
       pdb=" C   ALA F  46 "
    ideal  model  delta    sigma   weight residual
    1.519  1.528 -0.009 1.14e-02 7.69e+03 6.09e-01
  bond pdb=" CA  MET E  45 "
       pdb=" CB  MET E  45 "
    ideal  model  delta    sigma   weight residual
    1.526  1.540 -0.013 1.76e-02 3.23e+03 5.84e-01
  bond pdb=" CA  MET C  45 "
       pdb=" CB  MET C  45 "
    ideal  model  delta    sigma   weight residual
    1.526  1.540 -0.013 1.76e-02 3.23e+03 5.81e-01
  bond pdb=" CA  ALA D  46 "
       pdb=" C   ALA D  46 "
    ideal  model  delta    sigma   weight residual
    1.519  1.528 -0.009 1.14e-02 7.69e+03 5.77e-01
  ... (remaining 1219 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.49: 1339
        0.49 -     0.98: 256
        0.98 -     1.47: 43
        1.47 -     1.96: 6
        1.96 -     2.45: 6
  Bond angle restraints: 1650
  Sorted by residual:
  angle pdb=" CA  MET C  45 "
        pdb=" CB  MET C  45 "
        pdb=" CG  MET C  45 "
      ideal   model   delta    sigma   weight residual
     114.10  116.46   -2.36 2.00e+00 2.50e-01 1.40e+00
  angle pdb=" CA  MET A  45 "
        pdb=" CB  MET A  45 "
        pdb=" CG  MET A  45 "
      ideal   model   delta    sigma   weight residual
     114.10  116.45   -2.35 2.00e+00 2.50e-01 1.39e+00
  angle pdb=" CA  MET E  45 "
        pdb=" CB  MET E  45 "
        pdb=" CG  MET E  45 "
      ideal   model   delta    sigma   weight residual
     114.10  116.42   -2.32 2.00e+00 2.50e-01 1.35e+00
  angle pdb=" N   MET C  65 "
        pdb=" CA  MET C  65 "
        pdb=" C   MET C  65 "
      ideal   model   delta    sigma   weight residual
     108.34  109.64   -1.30 1.64e+00 3.72e-01 6.33e-01
  angle pdb=" N   PHE D  73 "
        pdb=" CA  PHE D  73 "
        pdb=" CB  PHE D  73 "
      ideal   model   delta    sigma   weight residual
     112.13  110.94    1.19 1.51e+00 4.39e-01 6.22e-01
  ... (remaining 1645 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.54: 582
       11.54 -    23.07: 66
       23.07 -    34.61: 21
       34.61 -    46.14: 9
       46.14 -    57.68: 6
  Dihedral angle restraints: 684
    sinusoidal: 186
      harmonic: 498
  Sorted by residual:
  dihedral pdb=" CB  MET A  45 "
           pdb=" CG  MET A  45 "
           pdb=" SD  MET A  45 "
           pdb=" CE  MET A  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -122.32  -57.68     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CB  MET C  45 "
           pdb=" CG  MET C  45 "
           pdb=" SD  MET C  45 "
           pdb=" CE  MET C  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.33  -57.67     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CB  MET E  45 "
           pdb=" CG  MET E  45 "
           pdb=" SD  MET E  45 "
           pdb=" CE  MET E  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.39  -57.61     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 681 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 115
       0.024 -    0.049: 58
       0.049 -    0.073: 19
       0.073 -    0.097: 3
       0.097 -    0.121: 21
  Chirality restraints: 216
  Sorted by residual:
  chirality pdb=" CA  VAL C  55 "
            pdb=" N   VAL C  55 "
            pdb=" C   VAL C  55 "
            pdb=" CB  VAL C  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.66e-01
  chirality pdb=" CA  VAL A  55 "
            pdb=" N   VAL A  55 "
            pdb=" C   VAL A  55 "
            pdb=" CB  VAL A  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.60e-01
  chirality pdb=" CA  VAL E  55 "
            pdb=" N   VAL E  55 "
            pdb=" C   VAL E  55 "
            pdb=" CB  VAL E  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.54e-01
  ... (remaining 213 not shown)

  Planarity restraints: 204
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C  45 "    0.005 2.00e-02 2.50e+03   1.02e-02 1.04e+00
        pdb=" C   MET C  45 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   MET C  45 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ALA C  46 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A  45 "    0.005 2.00e-02 2.50e+03   1.00e-02 1.00e+00
        pdb=" C   MET A  45 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   MET A  45 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ALA A  46 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET E  45 "    0.005 2.00e-02 2.50e+03   9.86e-03 9.71e-01
        pdb=" C   MET E  45 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   MET E  45 "    0.006 2.00e-02 2.50e+03
        pdb=" N   ALA E  46 "    0.006 2.00e-02 2.50e+03
  ... (remaining 201 not shown)

  Histogram of nonbonded interaction distances:
        2.61 -     3.07: 750
        3.07 -     3.53: 1194
        3.53 -     3.98: 1665
        3.98 -     4.44: 1993
        4.44 -     4.90: 3576
  Nonbonded interactions: 9178
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  51 "
            pdb=" OG1 THR D  70 "
     model   vdw
     2.610 3.040
  nonbonded pdb=" O   LEU D  59 "
            pdb=" N   ALA F  60 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   ALA C  56 "
            pdb=" N   VAL E  57 "
     model   vdw
     2.636 3.120
  nonbonded pdb=" CB  LEU F  44 "
            pdb=" N   MET F  45 "
     model   vdw
     2.653 2.816
  nonbonded pdb=" O   LEU B  59 "
            pdb=" N   ALA D  60 "
     model   vdw
     2.653 3.120
  ... (remaining 9173 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  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:          0.010
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     2.180
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
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   0.013   1224  Z= 0.104
  Angle     :  0.410   2.452   1650  Z= 0.228
  Chirality :  0.044   0.121    216
  Planarity :  0.001   0.010    204
  Dihedral  : 13.409  57.676    372
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 25.00 %
    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: -2.71 (0.55), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.002   0.000   PHE B  73 
 HIS   0.002   0.001   HIS A  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 1224)
  covalent geometry    : angle       0.41018 ( 1650)
  hydrogen bonds       : bond        0.14264 (   13)
  hydrogen bonds       : angle       8.25202 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.022 
Fit side-chains
REVERT: E   59 LEU cc_start: 0.8926 (tp) cc_final: 0.8704 (tp)
REVERT: D   65 MET cc_start: 0.8307 (mtp) cc_final: 0.7867 (mtm)
REVERT: F   45 MET cc_start: 0.7991 (tpt) cc_final: 0.7604 (tpt)
REVERT: F   65 MET cc_start: 0.8277 (mtp) cc_final: 0.8077 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0239
  time to fit residues: 0.7373
Evaluate side-chains
  25 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.118020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.102539 restraints weight = 1200.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.82
r_work: 0.3235 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1224  Z= 0.157
  Angle     :  0.455   3.798   1650  Z= 0.238
  Chirality :  0.046   0.129    216
  Planarity :  0.002   0.007    204
  Dihedral  :  3.683   9.017    186
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 23.15 %
    Favored  : 73.15 %
  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: -2.68 (0.55), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE C  73 
 HIS   0.004   0.001   HIS E  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 1224)
  covalent geometry    : angle       0.45467 ( 1650)
  hydrogen bonds       : bond        0.01401 (   13)
  hydrogen bonds       : angle       5.28222 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.022 
Fit side-chains
REVERT: E   59 LEU cc_start: 0.8907 (tp) cc_final: 0.8593 (tp)
REVERT: D   65 MET cc_start: 0.8541 (mtp) cc_final: 0.8018 (mtm)
REVERT: D   69 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7870 (tt)
  outliers start: 4
  outliers final: 1
  residues processed: 28
  average time/residue: 0.0216
  time to fit residues: 0.7333
Evaluate side-chains
  26 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain D residue   69 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
E  63 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.112770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.097391 restraints weight = 1229.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.83
r_work: 0.3159 rms_B_bonded: 1.80 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.027   1224  Z= 0.285
  Angle     :  0.553   4.098   1650  Z= 0.293
  Chirality :  0.049   0.141    216
  Planarity :  0.002   0.008    204
  Dihedral  :  4.326  10.311    186
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 19.44 %
    Favored  : 73.15 %
  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: -3.02 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.002   PHE E  73 
 HIS   0.006   0.002   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 1224)
  covalent geometry    : angle       0.55297 ( 1650)
  hydrogen bonds       : bond        0.01883 (   13)
  hydrogen bonds       : angle       5.13590 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.024 
Fit side-chains
REVERT: D   48 MET cc_start: 0.8888 (mtp) cc_final: 0.8572 (mtp)
REVERT: D   59 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7508 (mt)
REVERT: D   65 MET cc_start: 0.8520 (mtp) cc_final: 0.8180 (mtp)
REVERT: D   69 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7963 (tt)
  outliers start: 8
  outliers final: 5
  residues processed: 29
  average time/residue: 0.0199
  time to fit residues: 0.7055
Evaluate side-chains
  30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain F residue   59 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 10 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
F  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.114923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.099585 restraints weight = 1264.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.84
r_work: 0.3192 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   1224  Z= 0.209
  Angle     :  0.486   3.919   1650  Z= 0.258
  Chirality :  0.047   0.137    216
  Planarity :  0.002   0.008    204
  Dihedral  :  4.092   9.880    186
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  9.26 %
    Allowed  : 19.44 %
    Favored  : 71.30 %
  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: -3.05 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.32 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE E  73 
 HIS   0.004   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 1224)
  covalent geometry    : angle       0.48647 ( 1650)
  hydrogen bonds       : bond        0.01362 (   13)
  hydrogen bonds       : angle       4.72831 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 23
  time to evaluate  : 0.023 
Fit side-chains
REVERT: C   65 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7745 (mmm)
REVERT: D   48 MET cc_start: 0.8880 (mtp) cc_final: 0.8557 (mtp)
REVERT: D   59 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7452 (mt)
REVERT: D   65 MET cc_start: 0.8503 (mtp) cc_final: 0.8163 (mtp)
REVERT: D   69 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7914 (tt)
  outliers start: 10
  outliers final: 4
  residues processed: 30
  average time/residue: 0.0186
  time to fit residues: 0.6837
Evaluate side-chains
  30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain C residue   65 MET
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain F residue   59 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
F  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.117079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.101975 restraints weight = 1197.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.78
r_work: 0.3228 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   1224  Z= 0.154
  Angle     :  0.447   3.763   1650  Z= 0.236
  Chirality :  0.046   0.133    216
  Planarity :  0.002   0.009    204
  Dihedral  :  3.833   9.333    186
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 22.22 %
    Favored  : 71.30 %
  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: -3.01 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE E  73 
 HIS   0.003   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 1224)
  covalent geometry    : angle       0.44732 ( 1650)
  hydrogen bonds       : bond        0.01125 (   13)
  hydrogen bonds       : angle       4.51635 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.039 
Fit side-chains
REVERT: C   65 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7692 (mmm)
REVERT: E   59 LEU cc_start: 0.8877 (tp) cc_final: 0.8547 (tp)
REVERT: D   48 MET cc_start: 0.8843 (mtp) cc_final: 0.8521 (mtp)
REVERT: D   69 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7900 (tt)
REVERT: F   45 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7003 (tpt)
  outliers start: 7
  outliers final: 3
  residues processed: 27
  average time/residue: 0.0299
  time to fit residues: 0.9943
Evaluate side-chains
  29 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain C residue   65 MET
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain F residue   45 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
F  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.113975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.098627 restraints weight = 1234.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.77
r_work: 0.3147 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.031   1224  Z= 0.351
  Angle     :  0.600   4.118   1650  Z= 0.323
  Chirality :  0.051   0.147    216
  Planarity :  0.003   0.009    204
  Dihedral  :  4.499  10.946    186
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 19.44 %
    Favored  : 72.22 %
  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: -3.23 (0.52), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.002   PHE E  73 
 HIS   0.008   0.002   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00712 ( 1224)
  covalent geometry    : angle       0.60024 ( 1650)
  hydrogen bonds       : bond        0.01810 (   13)
  hydrogen bonds       : angle       4.96525 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 24
  time to evaluate  : 0.046 
Fit side-chains
REVERT: C   65 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7743 (tpp)
REVERT: D   48 MET cc_start: 0.8930 (mtp) cc_final: 0.8615 (mtp)
REVERT: D   59 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7571 (mt)
REVERT: D   69 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8010 (tt)
  outliers start: 9
  outliers final: 5
  residues processed: 30
  average time/residue: 0.0328
  time to fit residues: 1.2029
Evaluate side-chains
  31 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 23
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain C residue   65 MET
Chi-restraints excluded: chain E residue   69 LEU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain F residue   59 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
F  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.116166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.101404 restraints weight = 1209.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.78
r_work: 0.3222 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1224  Z= 0.125
  Angle     :  0.441   4.214   1650  Z= 0.232
  Chirality :  0.046   0.131    216
  Planarity :  0.002   0.010    204
  Dihedral  :  3.775   9.179    186
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 22.22 %
    Favored  : 70.37 %
  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: -3.08 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE E  73 
 HIS   0.003   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 1224)
  covalent geometry    : angle       0.44056 ( 1650)
  hydrogen bonds       : bond        0.01000 (   13)
  hydrogen bonds       : angle       4.44523 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.046 
Fit side-chains
REVERT: C   65 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7740 (tpp)
REVERT: E   59 LEU cc_start: 0.8837 (tp) cc_final: 0.8559 (tp)
REVERT: D   48 MET cc_start: 0.8845 (mtp) cc_final: 0.8526 (mtp)
REVERT: D   59 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7445 (mt)
REVERT: D   69 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7990 (tt)
  outliers start: 8
  outliers final: 3
  residues processed: 30
  average time/residue: 0.0396
  time to fit residues: 1.4216
Evaluate side-chains
  31 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain C residue   65 MET
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain F residue   59 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0770
   chunk 15 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5456

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.119049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.104320 restraints weight = 1244.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.76
r_work: 0.3234 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1224  Z= 0.121
  Angle     :  0.431   3.894   1650  Z= 0.226
  Chirality :  0.046   0.132    216
  Planarity :  0.002   0.009    204
  Dihedral  :  3.600   9.118    186
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 24.07 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.06 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE E  73 
 HIS   0.003   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 1224)
  covalent geometry    : angle       0.43125 ( 1650)
  hydrogen bonds       : bond        0.00992 (   13)
  hydrogen bonds       : angle       4.27956 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.041 
Fit side-chains
REVERT: C   65 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7702 (mmm)
REVERT: E   59 LEU cc_start: 0.8835 (tp) cc_final: 0.8555 (tp)
REVERT: D   48 MET cc_start: 0.8835 (mtp) cc_final: 0.8516 (mtp)
REVERT: D   59 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7472 (mt)
REVERT: D   69 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7989 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 31
  average time/residue: 0.0350
  time to fit residues: 1.3172
Evaluate side-chains
  33 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain C residue   65 MET
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain F residue   59 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3545 r_free = 0.3545 target = 0.117324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.101909 restraints weight = 1178.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.78
r_work: 0.3228 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   1224  Z= 0.147
  Angle     :  0.446   3.916   1650  Z= 0.235
  Chirality :  0.046   0.134    216
  Planarity :  0.002   0.009    204
  Dihedral  :  3.715   9.260    186
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 25.00 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.07 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE E  73 
 HIS   0.003   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 1224)
  covalent geometry    : angle       0.44578 ( 1650)
  hydrogen bonds       : bond        0.01069 (   13)
  hydrogen bonds       : angle       4.35716 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.042 
Fit side-chains
REVERT: C   65 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7726 (mmm)
REVERT: E   59 LEU cc_start: 0.8872 (tp) cc_final: 0.8572 (tp)
REVERT: D   48 MET cc_start: 0.8843 (mtp) cc_final: 0.8528 (mtp)
REVERT: D   59 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7504 (mt)
REVERT: D   69 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7979 (tt)
  outliers start: 7
  outliers final: 4
  residues processed: 30
  average time/residue: 0.0370
  time to fit residues: 1.3492
Evaluate side-chains
  32 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain C residue   65 MET
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain F residue   59 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3497 r_free = 0.3497 target = 0.114609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.098764 restraints weight = 1176.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.80
r_work: 0.3181 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   1224  Z= 0.221
  Angle     :  0.501   3.907   1650  Z= 0.266
  Chirality :  0.047   0.139    216
  Planarity :  0.002   0.008    204
  Dihedral  :  4.022   9.898    186
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 25.00 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.16 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE E  73 
 HIS   0.005   0.001   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 1224)
  covalent geometry    : angle       0.50138 ( 1650)
  hydrogen bonds       : bond        0.01359 (   13)
  hydrogen bonds       : angle       4.57027 (   39)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.043 
Fit side-chains
REVERT: C   65 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7767 (tpp)
REVERT: D   48 MET cc_start: 0.8872 (mtp) cc_final: 0.8553 (mtp)
REVERT: D   59 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7526 (mt)
REVERT: D   69 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8094 (tt)
  outliers start: 7
  outliers final: 4
  residues processed: 28
  average time/residue: 0.0351
  time to fit residues: 1.1934
Evaluate side-chains
  30 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain C residue   65 MET
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   69 LEU
Chi-restraints excluded: chain F residue   59 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.115664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.100361 restraints weight = 1217.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.75
r_work: 0.3176 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   1224  Z= 0.270
  Angle     :  0.539   3.792   1650  Z= 0.290
  Chirality :  0.049   0.142    216
  Planarity :  0.002   0.008    204
  Dihedral  :  4.270  10.344    186
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 25.00 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.30 (0.52), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.39), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE E  73 
 HIS   0.006   0.002   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 1224)
  covalent geometry    : angle       0.53948 ( 1650)
  hydrogen bonds       : bond        0.01514 (   13)
  hydrogen bonds       : angle       4.75303 (   39)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 532.03 seconds
wall clock time: 9 minutes 58.54 seconds (598.54 seconds total)