Starting phenix.real_space_refine
on Tue Mar  3 11:15:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ctk_26993/03_2026/8ctk_26993.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ctk_26993/03_2026/8ctk_26993.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ctk_26993/03_2026/8ctk_26993.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ctk_26993/03_2026/8ctk_26993.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ctk_26993/03_2026/8ctk_26993.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ctk_26993/03_2026/8ctk_26993.cif"
  }
  resolution = 3.52
  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=   0.018
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      14      5.16       5
     C    2020      2.51       5
     N     520      2.21       5
     O     488      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3042
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1521
          Classifications: {'peptide': 188}
          Link IDs: {'PTRANS': 5, 'TRANS': 182}
  Restraints were copied for chains:
    B
  Time building chain proxies: 0.88, per 1000 atoms: 0.29
  Number of scatterers: 3042
  At special positions: 0
  Unit cell: (74.881, 54.525, 80.697, 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      14     16.00
     O     488      8.00
     N     520      7.00
     C    2020      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: 0.22
  Conformation dependent library (CDL) restraints added in 107.7 milliseconds
  

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  700

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 2 sheets defined
      48.7% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 38
      removed outlier: 3.836A  pdb=" N   ASN A  21 " --> pdb=" O   LEU A  17 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A  35 " --> pdb=" O   TRP A  31 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLN A  36 " --> pdb=" O   ILE A  32 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   PHE A  37 " --> pdb=" O   CYS A  33 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 56
    Processing helix  chain 'A' and resid 56 through 71
      removed outlier: 4.123A  pdb=" N   TYR A  71 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 107
      removed outlier: 3.853A  pdb=" N   GLY A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ARG A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 113
      removed outlier: 3.733A  pdb=" N   ASN A 113 " --> pdb=" O   TRP A 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 38
      removed outlier: 3.622A  pdb=" N   LEU B  35 " --> pdb=" O   TRP B  31 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLN B  36 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   PHE B  37 " --> pdb=" O   CYS B  33 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA B  38 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 56
    Processing helix  chain 'B' and resid 56 through 71
      removed outlier: 4.123A  pdb=" N   TYR B  71 " --> pdb=" O   LEU B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 107
      removed outlier: 3.852A  pdb=" N   GLY B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ARG B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 113
      removed outlier: 3.732A  pdb=" N   ASN B 113 " --> pdb=" O   TRP B 110 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 132
      removed outlier: 7.079A  pdb=" N   GLU A 167 " --> pdb=" O   PRO A 123 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   LEU A 176 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE A 201 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   TYR A 178 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   ALA A 195 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   SER A 184 " --> pdb=" O   PHE A 193 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   PHE A 193 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   LEU A 149 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 132
      removed outlier: 7.079A  pdb=" N   GLU B 167 " --> pdb=" O   PRO B 123 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   LEU B 176 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE B 201 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   TYR B 178 " --> pdb=" O   TYR B 199 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   ALA B 195 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   SER B 184 " --> pdb=" O   PHE B 193 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   PHE B 193 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   LEU B 149 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)

    186 hydrogen bonds defined for protein.
    522 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: 0.43

  Time building geometry restraints manager: 0.31 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: 924
        1.34 -     1.46: 773
        1.46 -     1.58: 1409
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3126
  Sorted by residual:
  bond pdb=" CB  ASP B 190 "
       pdb=" CG  ASP B 190 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.08e+00
  bond pdb=" CB  ASP A 190 "
       pdb=" CG  ASP A 190 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.07e+00
  bond pdb=" C   TRP A  58 "
       pdb=" N   PRO A  59 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.28e-02 6.10e+03 7.29e-01
  bond pdb=" C   TRP B  58 "
       pdb=" N   PRO B  59 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.010 1.28e-02 6.10e+03 6.67e-01
  bond pdb=" CB  ASP A 160 "
       pdb=" CG  ASP A 160 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.36e-01
  ... (remaining 3121 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 4112
        1.61 -     3.22: 114
        3.22 -     4.82: 14
        4.82 -     6.43: 12
        6.43 -     8.04: 2
  Bond angle restraints: 4254
  Sorted by residual:
  angle pdb=" N   ILE B  73 "
        pdb=" CA  ILE B  73 "
        pdb=" C   ILE B  73 "
      ideal   model   delta    sigma   weight residual
     111.62  107.80    3.82 7.90e-01 1.60e+00 2.34e+01
  angle pdb=" N   ILE A  73 "
        pdb=" CA  ILE A  73 "
        pdb=" C   ILE A  73 "
      ideal   model   delta    sigma   weight residual
     111.62  107.82    3.80 7.90e-01 1.60e+00 2.31e+01
  angle pdb=" CA  MET B  91 "
        pdb=" CB  MET B  91 "
        pdb=" CG  MET B  91 "
      ideal   model   delta    sigma   weight residual
     114.10  119.39   -5.29 2.00e+00 2.50e-01 7.00e+00
  angle pdb=" CA  MET A  91 "
        pdb=" CB  MET A  91 "
        pdb=" CG  MET A  91 "
      ideal   model   delta    sigma   weight residual
     114.10  119.35   -5.25 2.00e+00 2.50e-01 6.90e+00
  angle pdb=" CA  LEU A  56 "
        pdb=" CB  LEU A  56 "
        pdb=" CG  LEU A  56 "
      ideal   model   delta    sigma   weight residual
     116.30  124.34   -8.04 3.50e+00 8.16e-02 5.28e+00
  ... (remaining 4249 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.01: 1512
       13.01 -    26.02: 170
       26.02 -    39.03: 78
       39.03 -    52.03: 22
       52.03 -    65.04: 6
  Dihedral angle restraints: 1788
    sinusoidal: 696
      harmonic: 1092
  Sorted by residual:
  dihedral pdb=" CG  ARG A 198 "
           pdb=" CD  ARG A 198 "
           pdb=" NE  ARG A 198 "
           pdb=" CZ  ARG A 198 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.44   44.56     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG B 198 "
           pdb=" CD  ARG B 198 "
           pdb=" NE  ARG B 198 "
           pdb=" CZ  ARG B 198 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.49   44.51     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" N   MET A  84 "
           pdb=" CA  MET A  84 "
           pdb=" CB  MET A  84 "
           pdb=" CG  MET A  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.00   53.00     3      1.50e+01 4.44e-03 9.17e+00
  ... (remaining 1785 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 354
       0.045 -    0.090: 99
       0.090 -    0.134: 30
       0.134 -    0.179: 1
       0.179 -    0.224: 2
  Chirality restraints: 486
  Sorted by residual:
  chirality pdb=" CA  ILE A 118 "
            pdb=" N   ILE A 118 "
            pdb=" C   ILE A 118 "
            pdb=" CB  ILE A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE B 118 "
            pdb=" N   ILE B 118 "
            pdb=" C   ILE B 118 "
            pdb=" CB  ILE B 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  VAL A 143 "
            pdb=" N   VAL A 143 "
            pdb=" C   VAL A 143 "
            pdb=" CB  VAL A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.75e-01
  ... (remaining 483 not shown)

  Planarity restraints: 512
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  31 "    0.025 2.00e-02 2.50e+03   1.49e-02 5.55e+00
        pdb=" CG  TRP A  31 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  31 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  31 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  31 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  31 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  31 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  31 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  31 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  31 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  31 "   -0.025 2.00e-02 2.50e+03   1.48e-02 5.44e+00
        pdb=" CG  TRP B  31 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  31 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  31 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  31 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  31 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  31 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  31 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  31 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  31 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 193 "   -0.012 2.00e-02 2.50e+03   1.35e-02 3.19e+00
        pdb=" CG  PHE A 193 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 193 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 193 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 193 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 193 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 193 "    0.005 2.00e-02 2.50e+03
  ... (remaining 509 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1035
        2.86 -     3.37: 2693
        3.37 -     3.88: 4899
        3.88 -     4.39: 5175
        4.39 -     4.90: 8964
  Nonbonded interactions: 22766
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 132 "
            pdb=" NE2 HIS A 154 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" O   PRO B 132 "
            pdb=" NE2 HIS B 154 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" O   VAL A 187 "
            pdb=" OG  SER A 191 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" O   VAL B 187 "
            pdb=" OG  SER B 191 "
     model   vdw
     2.395 3.040
  nonbonded pdb=" N   GLU B 137 "
            pdb=" OE1 GLU B 137 "
     model   vdw
     2.407 3.120
  ... (remaining 22761 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.530
  Find NCS groups from input model:        0.020
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
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      :  0.003   0.035   3126  Z= 0.144
  Angle     :  0.691   8.040   4254  Z= 0.364
  Chirality :  0.047   0.224    486
  Planarity :  0.005   0.043    512
  Dihedral  : 14.365  65.043   1088
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.25 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.43), residues: 372
  helix:  0.55 (0.41), residues: 164
  sheet: -0.63 (0.60), residues: 78
  loop : -2.38 (0.48), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 158 
 TYR   0.007   0.001   TYR A  47 
 PHE   0.027   0.002   PHE A 193 
 TRP   0.036   0.002   TRP A  31 
 HIS   0.001   0.000   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3126)
  covalent geometry    : angle       0.69133 ( 4254)
  hydrogen bonds       : bond        0.09506 (  186)
  hydrogen bonds       : angle       6.15543 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  166 LYS cc_start: 0.7853 (tptp) cc_final: 0.7258 (mmpt)
REVERT: B  166 LYS cc_start: 0.7666 (tptp) cc_final: 0.7067 (mmpt)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0455
  time to fit residues: 3.1991
Evaluate side-chains
  49 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.219273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.181620 restraints weight = 3714.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.185805 restraints weight = 2511.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.188775 restraints weight = 1917.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.190499 restraints weight = 1584.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.191994 restraints weight = 1395.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   3126  Z= 0.138
  Angle     :  0.551   6.746   4254  Z= 0.284
  Chirality :  0.043   0.191    486
  Planarity :  0.004   0.032    512
  Dihedral  :  3.666  11.633    420
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 21.20 %
    Favored  : 77.22 %
  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 are not related in a simple way.
  whole: -0.91 (0.43), residues: 372
  helix:  0.83 (0.41), residues: 166
  sheet: -0.92 (0.58), residues: 78
  loop : -2.30 (0.49), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 200 
 TYR   0.008   0.001   TYR A 179 
 PHE   0.016   0.002   PHE B 193 
 TRP   0.022   0.002   TRP A  31 
 HIS   0.004   0.001   HIS B 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3126)
  covalent geometry    : angle       0.55084 ( 4254)
  hydrogen bonds       : bond        0.02933 (  186)
  hydrogen bonds       : angle       4.83616 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LYS cc_start: 0.7807 (tptp) cc_final: 0.7014 (mmpt)
REVERT: B   77 THR cc_start: 0.7753 (p) cc_final: 0.7453 (t)
REVERT: B  166 LYS cc_start: 0.7713 (tptp) cc_final: 0.6895 (mmpt)
  outliers start: 5
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0455
  time to fit residues: 3.2216
Evaluate side-chains
  57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  109 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4516 r_free = 0.4516 target = 0.217647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.178173 restraints weight = 3820.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.182419 restraints weight = 2671.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.185165 restraints weight = 2093.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.186789 restraints weight = 1772.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.188184 restraints weight = 1583.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3126  Z= 0.141
  Angle     :  0.549   5.955   4254  Z= 0.282
  Chirality :  0.044   0.177    486
  Planarity :  0.004   0.031    512
  Dihedral  :  3.604  11.700    420
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.30 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.42), residues: 372
  helix:  1.01 (0.40), residues: 166
  sheet: -1.11 (0.56), residues: 78
  loop : -2.34 (0.48), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 200 
 TYR   0.008   0.001   TYR A 196 
 PHE   0.014   0.002   PHE A 193 
 TRP   0.018   0.002   TRP B  31 
 HIS   0.003   0.001   HIS B 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3126)
  covalent geometry    : angle       0.54945 ( 4254)
  hydrogen bonds       : bond        0.02841 (  186)
  hydrogen bonds       : angle       4.61050 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 THR cc_start: 0.8112 (p) cc_final: 0.7828 (t)
REVERT: A  166 LYS cc_start: 0.7846 (tptp) cc_final: 0.7070 (mmpt)
REVERT: B  166 LYS cc_start: 0.7766 (tptp) cc_final: 0.7023 (mmpt)
  outliers start: 9
  outliers final: 2
  residues processed: 55
  average time/residue: 0.0411
  time to fit residues: 3.0492
Evaluate side-chains
  51 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain B residue  108 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    8.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.213502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.175312 restraints weight = 3725.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.179278 restraints weight = 2528.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.182061 restraints weight = 1955.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.183211 restraints weight = 1637.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.184910 restraints weight = 1486.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   3126  Z= 0.151
  Angle     :  0.552   5.415   4254  Z= 0.283
  Chirality :  0.044   0.163    486
  Planarity :  0.004   0.030    512
  Dihedral  :  3.611  10.446    420
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 18.35 %
    Favored  : 77.22 %
  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 are not related in a simple way.
  whole: -0.85 (0.42), residues: 372
  helix:  1.14 (0.40), residues: 166
  sheet: -1.26 (0.54), residues: 78
  loop : -2.39 (0.47), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 200 
 TYR   0.009   0.001   TYR B 179 
 PHE   0.014   0.002   PHE A 193 
 TRP   0.024   0.002   TRP B  58 
 HIS   0.003   0.001   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3126)
  covalent geometry    : angle       0.55214 ( 4254)
  hydrogen bonds       : bond        0.02943 (  186)
  hydrogen bonds       : angle       4.56644 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LYS cc_start: 0.7872 (tptp) cc_final: 0.7120 (mmpt)
REVERT: B  166 LYS cc_start: 0.7770 (tptp) cc_final: 0.7047 (mmpt)
  outliers start: 14
  outliers final: 7
  residues processed: 58
  average time/residue: 0.0457
  time to fit residues: 3.5572
Evaluate side-chains
  56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  108 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0770
   chunk 6 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 22 optimal weight:    0.1980
   chunk 27 optimal weight:    0.0570
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.4456

-------------------------------------------------------------------------------
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 = 0.4513 r_free = 0.4513 target = 0.217461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.179053 restraints weight = 3775.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.183248 restraints weight = 2563.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.186098 restraints weight = 1983.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.187842 restraints weight = 1664.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.189286 restraints weight = 1476.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.2320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3126  Z= 0.106
  Angle     :  0.507   6.594   4254  Z= 0.261
  Chirality :  0.042   0.147    486
  Planarity :  0.004   0.031    512
  Dihedral  :  3.418  10.315    420
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.57 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.43), residues: 372
  helix:  1.22 (0.41), residues: 170
  sheet: -0.99 (0.57), residues: 78
  loop : -2.25 (0.50), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 200 
 TYR   0.005   0.001   TYR A 196 
 PHE   0.010   0.001   PHE A 193 
 TRP   0.016   0.001   TRP B  58 
 HIS   0.002   0.000   HIS B 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3126)
  covalent geometry    : angle       0.50738 ( 4254)
  hydrogen bonds       : bond        0.02593 (  186)
  hydrogen bonds       : angle       4.23211 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LYS cc_start: 0.7820 (tptp) cc_final: 0.7073 (mmpt)
REVERT: B  166 LYS cc_start: 0.7765 (tptp) cc_final: 0.7039 (mmpt)
  outliers start: 10
  outliers final: 9
  residues processed: 53
  average time/residue: 0.0430
  time to fit residues: 3.1208
Evaluate side-chains
  54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  120 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.216287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.176934 restraints weight = 3759.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.181569 restraints weight = 2498.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.184861 restraints weight = 1903.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.186864 restraints weight = 1569.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.187974 restraints weight = 1379.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   3126  Z= 0.130
  Angle     :  0.533   7.201   4254  Z= 0.271
  Chirality :  0.042   0.148    486
  Planarity :  0.004   0.031    512
  Dihedral  :  3.436  10.114    420
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.89 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.43), residues: 372
  helix:  1.28 (0.41), residues: 170
  sheet: -1.07 (0.56), residues: 78
  loop : -2.26 (0.49), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 200 
 TYR   0.007   0.001   TYR A 196 
 PHE   0.012   0.002   PHE A 193 
 TRP   0.013   0.002   TRP B  58 
 HIS   0.002   0.001   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3126)
  covalent geometry    : angle       0.53310 ( 4254)
  hydrogen bonds       : bond        0.02735 (  186)
  hydrogen bonds       : angle       4.32252 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: B   77 THR cc_start: 0.7996 (p) cc_final: 0.7703 (t)
REVERT: B  166 LYS cc_start: 0.7816 (tptp) cc_final: 0.7080 (mmpt)
  outliers start: 11
  outliers final: 10
  residues processed: 49
  average time/residue: 0.0384
  time to fit residues: 2.6026
Evaluate side-chains
  53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  120 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.213803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.175549 restraints weight = 3801.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.179802 restraints weight = 2657.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.182572 restraints weight = 2067.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.184367 restraints weight = 1741.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.185843 restraints weight = 1548.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.4228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   3126  Z= 0.152
  Angle     :  0.564   6.907   4254  Z= 0.285
  Chirality :  0.043   0.150    486
  Planarity :  0.004   0.031    512
  Dihedral  :  3.564  10.247    420
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 20.25 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.43), residues: 372
  helix:  1.32 (0.41), residues: 168
  sheet: -1.16 (0.55), residues: 78
  loop : -2.32 (0.48), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 200 
 TYR   0.009   0.001   TYR A  95 
 PHE   0.019   0.002   PHE B 193 
 TRP   0.012   0.002   TRP B  58 
 HIS   0.003   0.001   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 3126)
  covalent geometry    : angle       0.56369 ( 4254)
  hydrogen bonds       : bond        0.02871 (  186)
  hydrogen bonds       : angle       4.45926 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
  outliers start: 14
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0334
  time to fit residues: 2.5940
Evaluate side-chains
  56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  120 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 10 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.214318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.176143 restraints weight = 3835.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.180123 restraints weight = 2619.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.182961 restraints weight = 2036.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.184702 restraints weight = 1715.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.185763 restraints weight = 1524.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.3020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3126  Z= 0.134
  Angle     :  0.584   8.745   4254  Z= 0.292
  Chirality :  0.043   0.153    486
  Planarity :  0.004   0.032    512
  Dihedral  :  3.533  12.914    420
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 19.62 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.43), residues: 372
  helix:  1.12 (0.40), residues: 168
  sheet: -1.06 (0.57), residues: 78
  loop : -2.30 (0.48), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 200 
 TYR   0.006   0.001   TYR A  95 
 PHE   0.016   0.001   PHE B 193 
 TRP   0.014   0.001   TRP B  58 
 HIS   0.002   0.001   HIS A 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3126)
  covalent geometry    : angle       0.58362 ( 4254)
  hydrogen bonds       : bond        0.02908 (  186)
  hydrogen bonds       : angle       4.39906 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 MET cc_start: 0.6413 (ppp) cc_final: 0.4721 (mtp)
  outliers start: 13
  outliers final: 12
  residues processed: 55
  average time/residue: 0.0323
  time to fit residues: 2.5316
Evaluate side-chains
  58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  120 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0470
   chunk 35 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0070
   chunk 2 optimal weight:    3.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.216771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.178976 restraints weight = 3831.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.183112 restraints weight = 2586.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.185787 restraints weight = 1992.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.187585 restraints weight = 1683.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.188801 restraints weight = 1494.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3126  Z= 0.107
  Angle     :  0.544   8.789   4254  Z= 0.272
  Chirality :  0.042   0.143    486
  Planarity :  0.004   0.031    512
  Dihedral  :  3.377  11.964    420
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.62 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.44), residues: 372
  helix:  1.58 (0.41), residues: 158
  sheet: -0.96 (0.58), residues: 78
  loop : -1.73 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 150 
 TYR   0.005   0.001   TYR A  95 
 PHE   0.013   0.001   PHE B 193 
 TRP   0.010   0.001   TRP B  58 
 HIS   0.001   0.000   HIS B 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3126)
  covalent geometry    : angle       0.54354 ( 4254)
  hydrogen bonds       : bond        0.02646 (  186)
  hydrogen bonds       : angle       4.16790 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LYS cc_start: 0.7845 (tptp) cc_final: 0.7122 (mmpt)
REVERT: B  166 LYS cc_start: 0.7820 (tptp) cc_final: 0.7088 (mmpt)
  outliers start: 12
  outliers final: 10
  residues processed: 58
  average time/residue: 0.0406
  time to fit residues: 3.1553
Evaluate side-chains
  58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  109 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0050
   chunk 34 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.214642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.176668 restraints weight = 3805.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.180534 restraints weight = 2633.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.183231 restraints weight = 2059.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.184592 restraints weight = 1741.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.185900 restraints weight = 1568.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3126  Z= 0.131
  Angle     :  0.579   8.463   4254  Z= 0.285
  Chirality :  0.043   0.140    486
  Planarity :  0.004   0.032    512
  Dihedral  :  3.460  11.649    420
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.57 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.43), residues: 372
  helix:  1.14 (0.40), residues: 170
  sheet: -0.99 (0.58), residues: 78
  loop : -2.28 (0.49), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 200 
 TYR   0.006   0.001   TYR A  95 
 PHE   0.014   0.001   PHE B 193 
 TRP   0.011   0.001   TRP A  31 
 HIS   0.002   0.001   HIS B 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3126)
  covalent geometry    : angle       0.57903 ( 4254)
  hydrogen bonds       : bond        0.02781 (  186)
  hydrogen bonds       : angle       4.21318 (  522)

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

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

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  744 Ramachandran restraints generated.
    372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 LYS cc_start: 0.7810 (tptp) cc_final: 0.7062 (mmpt)
  outliers start: 12
  outliers final: 12
  residues processed: 56
  average time/residue: 0.0379
  time to fit residues: 2.9508
Evaluate side-chains
  60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  108 SER
Chi-restraints excluded: chain B residue  109 MET
Chi-restraints excluded: chain B residue  120 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0030
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0050
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.4004

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.216968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.179550 restraints weight = 3771.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.183480 restraints weight = 2576.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.186254 restraints weight = 1989.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.188060 restraints weight = 1668.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.189162 restraints weight = 1481.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3126  Z= 0.109
  Angle     :  0.561   8.559   4254  Z= 0.278
  Chirality :  0.042   0.140    486
  Planarity :  0.004   0.033    512
  Dihedral  :  3.346  11.558    420
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 21.84 %
    Favored  : 74.37 %
  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 are not related in a simple way.
  whole: -0.18 (0.45), residues: 372
  helix:  1.68 (0.41), residues: 158
  sheet: -0.94 (0.58), residues: 78
  loop : -1.79 (0.53), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 150 
 TYR   0.004   0.001   TYR A  95 
 PHE   0.012   0.001   PHE B 193 
 TRP   0.012   0.001   TRP B  58 
 HIS   0.001   0.000   HIS B 154 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3126)
  covalent geometry    : angle       0.56064 ( 4254)
  hydrogen bonds       : bond        0.02579 (  186)
  hydrogen bonds       : angle       4.03473 (  522)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 781.46 seconds
wall clock time: 14 minutes 0.21 seconds (840.21 seconds total)