Starting phenix.real_space_refine
on Tue Feb  3 12:36:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lj0_63129/02_2026/9lj0_63129.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lj0_63129/02_2026/9lj0_63129.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lj0_63129/02_2026/9lj0_63129.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lj0_63129/02_2026/9lj0_63129.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lj0_63129/02_2026/9lj0_63129.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lj0_63129/02_2026/9lj0_63129.cif"
  }
  resolution = 3.3
  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=   0.001
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       9      5.16       5
     C    1326      2.51       5
     N     357      2.21       5
     O     432      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2124
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 708
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
  Restraints were copied for chains:
    A, B
  Time building chain proxies: 0.38, per 1000 atoms: 0.18
  Number of scatterers: 2124
  At special positions: 0
  Unit cell: (74.7, 95.45, 34.03, 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       9     16.00
     O     432      8.00
     N     357      7.00
     C    1326      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  89 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  89 " distance=2.02

  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: 0.13
  Conformation dependent library (CDL) restraints added in 51.9 milliseconds
  

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  510

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 39.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 18 through 22
      removed outlier: 6.395A  pdb=" N   THR C  19 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 8.211A  pdb=" N   CYS A  22 " --> pdb=" O   THR C  19 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   SER C  21 " --> pdb=" O   CYS A  22 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   THR A  19 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   CYS B  22 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   SER A  21 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 32 through 39
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
    Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 54
    Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 61
      removed outlier: 6.648A  pdb=" N   SER C  57 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   SER A  60 " --> pdb=" O   SER C  57 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   VAL C  59 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   SER A  57 " --> pdb=" O   GLY B  58 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   SER B  60 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL A  59 " --> pdb=" O   SER B  60 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 74
      removed outlier: 6.278A  pdb=" N   GLY C  69 " --> pdb=" O   THR A  70 " (cutoff:3.500A)
      removed outlier: 8.340A  pdb=" N   ALA A  72 " --> pdb=" O   GLY C  69 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   SER C  71 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
      removed outlier: 8.473A  pdb=" N   LEU A  74 " --> pdb=" O   SER C  71 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   SER C  73 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   GLY A  69 " --> pdb=" O   THR B  70 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   ALA B  72 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   SER A  71 " --> pdb=" O   ALA B  72 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   LEU B  74 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   SER A  73 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 86
    Processing sheet with id=AA8, first strand: chain 'C' and resid 91 through 93
    Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AB1, first strand: chain 'C' and resid 105 through 109
      removed outlier: 6.746A  pdb=" N   ALA C 105 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
      removed outlier: 8.374A  pdb=" N   VAL A 108 " --> pdb=" O   ALA C 105 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   LYS C 107 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ALA A 105 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 8.372A  pdb=" N   VAL B 108 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LYS A 107 " --> pdb=" O   VAL B 108 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    38 hydrogen bonds defined for protein.
    114 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: 0.21

  Time building geometry restraints manager: 0.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 684
        1.34 -     1.45: 362
        1.45 -     1.57: 1111
        1.57 -     1.68: 0
        1.68 -     1.80: 12
  Bond restraints: 2169
  Sorted by residual:
  bond pdb=" N   SER C  64 "
       pdb=" CA  SER C  64 "
    ideal  model  delta    sigma   weight residual
    1.463  1.441  0.022 1.36e-02 5.41e+03 2.71e+00
  bond pdb=" N   SER A  64 "
       pdb=" CA  SER A  64 "
    ideal  model  delta    sigma   weight residual
    1.463  1.441  0.022 1.36e-02 5.41e+03 2.68e+00
  bond pdb=" N   SER B  64 "
       pdb=" CA  SER B  64 "
    ideal  model  delta    sigma   weight residual
    1.463  1.441  0.022 1.36e-02 5.41e+03 2.52e+00
  bond pdb=" CA  TRP A  36 "
       pdb=" CB  TRP A  36 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.021 1.46e-02 4.69e+03 2.16e+00
  bond pdb=" CA  TRP B  36 "
       pdb=" CB  TRP B  36 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.021 1.46e-02 4.69e+03 2.16e+00
  ... (remaining 2164 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 2742
        1.52 -     3.04: 163
        3.04 -     4.57: 26
        4.57 -     6.09: 6
        6.09 -     7.61: 6
  Bond angle restraints: 2943
  Sorted by residual:
  angle pdb=" N   GLY A  98 "
        pdb=" CA  GLY A  98 "
        pdb=" C   GLY A  98 "
      ideal   model   delta    sigma   weight residual
     113.18  120.79   -7.61 2.37e+00 1.78e-01 1.03e+01
  angle pdb=" N   GLY C  98 "
        pdb=" CA  GLY C  98 "
        pdb=" C   GLY C  98 "
      ideal   model   delta    sigma   weight residual
     113.18  120.77   -7.59 2.37e+00 1.78e-01 1.03e+01
  angle pdb=" N   GLY B  98 "
        pdb=" CA  GLY B  98 "
        pdb=" C   GLY B  98 "
      ideal   model   delta    sigma   weight residual
     113.18  120.75   -7.57 2.37e+00 1.78e-01 1.02e+01
  angle pdb=" N   ARG B  55 "
        pdb=" CA  ARG B  55 "
        pdb=" C   ARG B  55 "
      ideal   model   delta    sigma   weight residual
     109.81  116.22   -6.41 2.21e+00 2.05e-01 8.42e+00
  angle pdb=" N   ARG C  55 "
        pdb=" CA  ARG C  55 "
        pdb=" C   ARG C  55 "
      ideal   model   delta    sigma   weight residual
     109.81  116.16   -6.35 2.21e+00 2.05e-01 8.26e+00
  ... (remaining 2938 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.52: 1022
       10.52 -    21.04: 189
       21.04 -    31.55: 40
       31.55 -    42.07: 15
       42.07 -    52.59: 9
  Dihedral angle restraints: 1275
    sinusoidal: 468
      harmonic: 807
  Sorted by residual:
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  89 "
           pdb=" CB  CYS C  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.59  -52.59     1      1.00e+01 1.00e-02 3.77e+01
  dihedral pdb=" CB  CYS A  22 "
           pdb=" SG  CYS A  22 "
           pdb=" SG  CYS A  89 "
           pdb=" CB  CYS A  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.58  -52.58     1      1.00e+01 1.00e-02 3.77e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  89 "
           pdb=" CB  CYS B  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.58  -52.58     1      1.00e+01 1.00e-02 3.77e+01
  ... (remaining 1272 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 179
       0.034 -    0.068: 85
       0.068 -    0.102: 38
       0.102 -    0.135: 16
       0.135 -    0.169: 3
  Chirality restraints: 321
  Sorted by residual:
  chirality pdb=" CA  ARG B  55 "
            pdb=" N   ARG B  55 "
            pdb=" C   ARG B  55 "
            pdb=" CB  ARG B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" CA  ARG C  55 "
            pdb=" N   ARG C  55 "
            pdb=" C   ARG C  55 "
            pdb=" CB  ARG C  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.04e-01
  chirality pdb=" CA  ARG A  55 "
            pdb=" N   ARG A  55 "
            pdb=" C   ARG A  55 "
            pdb=" CB  ARG A  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.01e-01
  ... (remaining 318 not shown)

  Planarity restraints: 378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C  55 "   -0.027 5.00e-02 4.00e+02   4.08e-02 2.66e+00
        pdb=" N   PRO C  56 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C  56 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C  56 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  55 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.66e+00
        pdb=" N   PRO A  56 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A  56 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  56 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  55 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO B  56 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B  56 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  56 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 375 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.49: 14
        2.49 -     3.09: 1479
        3.09 -     3.69: 3078
        3.69 -     4.30: 4125
        4.30 -     4.90: 8038
  Nonbonded interactions: 16734
  Sorted by model distance:
  nonbonded pdb=" O   GLU A  82 "
            pdb=" OD1 ASP A  83 "
     model   vdw
     1.882 3.040
  nonbonded pdb=" O   GLU C  82 "
            pdb=" OD1 ASP C  83 "
     model   vdw
     1.883 3.040
  nonbonded pdb=" O   GLU B  82 "
            pdb=" OD1 ASP B  83 "
     model   vdw
     1.883 3.040
  nonbonded pdb=" O   SER A  77 "
            pdb=" OG  SER A  77 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   SER C  77 "
            pdb=" OG  SER C  77 "
     model   vdw
     2.373 3.040
  ... (remaining 16729 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 'C'
  selection = 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 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:             2.480
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.120
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
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      :  0.008   0.045   2172  Z= 0.363
  Angle     :  0.884   7.610   2949  Z= 0.479
  Chirality :  0.050   0.169    321
  Planarity :  0.005   0.041    378
  Dihedral  : 12.023  42.315    756
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.87 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  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: -4.91 (0.29), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.73 (0.22), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  17 
 TYR   0.012   0.002   TYR A 100 
 PHE   0.011   0.003   PHE A  53 
 TRP   0.004   0.001   TRP C  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00809 ( 2169)
  covalent geometry    : angle       0.88282 ( 2943)
  SS BOND              : bond        0.00614 (    3)
  SS BOND              : angle       1.45884 (    6)
  hydrogen bonds       : bond        0.16068 (   38)
  hydrogen bonds       : angle       8.00776 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.079 
Fit side-chains
REVERT: C   46 LYS cc_start: 0.8341 (tttt) cc_final: 0.8056 (ttmt)
REVERT: C   87 TYR cc_start: 0.9179 (m-80) cc_final: 0.8941 (m-80)
REVERT: A   46 LYS cc_start: 0.8311 (tttt) cc_final: 0.7921 (ttmt)
REVERT: A  107 LYS cc_start: 0.8786 (tttm) cc_final: 0.6709 (mptt)
REVERT: B   17 ARG cc_start: 0.6335 (tpt170) cc_final: 0.6058 (ppt170)
REVERT: B   93 ASP cc_start: 0.8560 (t0) cc_final: 0.7931 (t0)
REVERT: B   94 ASP cc_start: 0.8143 (m-30) cc_final: 0.7813 (m-30)
REVERT: B  107 LYS cc_start: 0.8885 (tttm) cc_final: 0.6933 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0922
  time to fit residues: 6.5062
Evaluate side-chains
  51 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
C  33 ASN
A  33 ASN
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.116638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.107365 restraints weight = 3895.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.61
r_work: 0.3742 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2172  Z= 0.159
  Angle     :  0.752   6.691   2949  Z= 0.377
  Chirality :  0.046   0.126    321
  Planarity :  0.004   0.036    378
  Dihedral  :  6.111  18.346    309
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.38 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.61 (0.31), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.24), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  80 
 TYR   0.013   0.002   TYR A 100 
 PHE   0.010   0.002   PHE A  53 
 TRP   0.004   0.001   TRP B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 2169)
  covalent geometry    : angle       0.75157 ( 2943)
  SS BOND              : bond        0.00106 (    3)
  SS BOND              : angle       0.79780 (    6)
  hydrogen bonds       : bond        0.02482 (   38)
  hydrogen bonds       : angle       5.29835 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.051 
Fit side-chains
REVERT: C   46 LYS cc_start: 0.8049 (tttt) cc_final: 0.7520 (ttmt)
REVERT: A   46 LYS cc_start: 0.7987 (tttt) cc_final: 0.7783 (ttmt)
REVERT: A   83 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.7928 (m-30)
REVERT: A   93 ASP cc_start: 0.8967 (t0) cc_final: 0.8530 (t0)
REVERT: A   94 ASP cc_start: 0.8663 (m-30) cc_final: 0.8230 (m-30)
REVERT: A  107 LYS cc_start: 0.8585 (tttm) cc_final: 0.6042 (mptt)
REVERT: B   93 ASP cc_start: 0.9066 (t0) cc_final: 0.8793 (t0)
REVERT: B  107 LYS cc_start: 0.8957 (tttm) cc_final: 0.6650 (mptt)
  outliers start: 5
  outliers final: 3
  residues processed: 56
  average time/residue: 0.0463
  time to fit residues: 2.9762
Evaluate side-chains
  54 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 25 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.116037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.106894 restraints weight = 3951.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 2.61
r_work: 0.3735 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   2172  Z= 0.210
  Angle     :  0.753   6.234   2949  Z= 0.378
  Chirality :  0.046   0.123    321
  Planarity :  0.005   0.039    378
  Dihedral  :  5.989  18.171    309
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 14.53 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.47 (0.32), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.25), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  80 
 TYR   0.014   0.002   TYR A 100 
 PHE   0.008   0.002   PHE A  53 
 TRP   0.004   0.001   TRP B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 2169)
  covalent geometry    : angle       0.75320 ( 2943)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       0.73876 (    6)
  hydrogen bonds       : bond        0.02447 (   38)
  hydrogen bonds       : angle       4.89289 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.085 
Fit side-chains
REVERT: C   46 LYS cc_start: 0.8046 (tttt) cc_final: 0.7735 (ttmt)
REVERT: C   80 ARG cc_start: 0.5174 (tpp-160) cc_final: 0.3065 (tpp-160)
REVERT: A   46 LYS cc_start: 0.7978 (tttt) cc_final: 0.7745 (ttmt)
REVERT: A   93 ASP cc_start: 0.8943 (t0) cc_final: 0.8447 (t0)
REVERT: A   94 ASP cc_start: 0.8649 (m-30) cc_final: 0.8205 (m-30)
REVERT: A  107 LYS cc_start: 0.8510 (tttm) cc_final: 0.5995 (mptt)
REVERT: B   17 ARG cc_start: 0.6804 (tpt170) cc_final: 0.5732 (ppt170)
REVERT: B   67 LYS cc_start: 0.8510 (tttt) cc_final: 0.6806 (pttm)
REVERT: B   93 ASP cc_start: 0.9020 (t0) cc_final: 0.8321 (t0)
REVERT: B   94 ASP cc_start: 0.8542 (m-30) cc_final: 0.8143 (m-30)
REVERT: B  107 LYS cc_start: 0.8982 (tttm) cc_final: 0.6634 (mptt)
  outliers start: 10
  outliers final: 9
  residues processed: 60
  average time/residue: 0.0877
  time to fit residues: 5.8890
Evaluate side-chains
  59 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   39 GLN
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0060
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    8.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    1.9202

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
B  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.118169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.108802 restraints weight = 3854.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 2.65
r_work: 0.3758 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3660 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   2172  Z= 0.149
  Angle     :  0.707   6.204   2949  Z= 0.350
  Chirality :  0.045   0.125    321
  Planarity :  0.004   0.035    378
  Dihedral  :  5.811  18.054    309
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 16.24 %
    Favored  : 79.49 %
  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: -4.39 (0.33), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.34 (0.25), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  80 
 TYR   0.013   0.002   TYR A  35 
 PHE   0.007   0.001   PHE A  53 
 TRP   0.004   0.001   TRP B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 2169)
  covalent geometry    : angle       0.70742 ( 2943)
  SS BOND              : bond        0.00188 (    3)
  SS BOND              : angle       0.64091 (    6)
  hydrogen bonds       : bond        0.01986 (   38)
  hydrogen bonds       : angle       4.66391 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.100 
Fit side-chains
REVERT: C   46 LYS cc_start: 0.8027 (tttt) cc_final: 0.7754 (ttmt)
REVERT: C   80 ARG cc_start: 0.5549 (tpp-160) cc_final: 0.3368 (tpp-160)
REVERT: A   46 LYS cc_start: 0.8010 (tttt) cc_final: 0.7785 (ttmt)
REVERT: A   83 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7967 (m-30)
REVERT: A   93 ASP cc_start: 0.8939 (t0) cc_final: 0.8348 (t0)
REVERT: A   94 ASP cc_start: 0.8663 (m-30) cc_final: 0.8181 (m-30)
REVERT: A  107 LYS cc_start: 0.8535 (tttm) cc_final: 0.6032 (mptt)
REVERT: B   17 ARG cc_start: 0.6749 (tpt170) cc_final: 0.5710 (ppt170)
REVERT: B   80 ARG cc_start: 0.8315 (ttt90) cc_final: 0.8100 (ttt90)
REVERT: B   93 ASP cc_start: 0.9028 (t0) cc_final: 0.8333 (t0)
REVERT: B   94 ASP cc_start: 0.8644 (m-30) cc_final: 0.8247 (m-30)
REVERT: B  107 LYS cc_start: 0.8969 (tttm) cc_final: 0.6653 (mptt)
  outliers start: 10
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0867
  time to fit residues: 6.1286
Evaluate side-chains
  58 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0770
   chunk 16 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    2.3744

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.118351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.108776 restraints weight = 3905.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3845 rms_B_bonded: 2.70
r_work: 0.3759 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2172  Z= 0.181
  Angle     :  0.706   6.163   2949  Z= 0.351
  Chirality :  0.045   0.125    321
  Planarity :  0.004   0.037    378
  Dihedral  :  5.767  17.881    309
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 19.66 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.36 (0.34), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.32 (0.26), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  80 
 TYR   0.015   0.002   TYR A 100 
 PHE   0.006   0.001   PHE A  53 
 TRP   0.006   0.001   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 2169)
  covalent geometry    : angle       0.70555 ( 2943)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       0.70285 (    6)
  hydrogen bonds       : bond        0.02002 (   38)
  hydrogen bonds       : angle       4.53878 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: C   46 LYS cc_start: 0.7976 (tttt) cc_final: 0.7720 (ttmt)
REVERT: C   80 ARG cc_start: 0.5616 (tpp-160) cc_final: 0.2199 (tpp80)
REVERT: C   87 TYR cc_start: 0.9208 (m-80) cc_final: 0.8515 (m-80)
REVERT: A   46 LYS cc_start: 0.8064 (tttt) cc_final: 0.7846 (ttmt)
REVERT: A   64 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8214 (p)
REVERT: A   83 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7948 (m-30)
REVERT: A  107 LYS cc_start: 0.8543 (tttm) cc_final: 0.6039 (mptt)
REVERT: B   17 ARG cc_start: 0.6848 (tpt170) cc_final: 0.5750 (ppt170)
REVERT: B   93 ASP cc_start: 0.9033 (t0) cc_final: 0.8379 (t0)
REVERT: B   94 ASP cc_start: 0.8673 (m-30) cc_final: 0.8214 (m-30)
REVERT: B  107 LYS cc_start: 0.8977 (tttm) cc_final: 0.6658 (mptt)
  outliers start: 11
  outliers final: 9
  residues processed: 60
  average time/residue: 0.0841
  time to fit residues: 5.6944
Evaluate side-chains
  61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.120687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.111250 restraints weight = 3696.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 2.64
r_work: 0.3802 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3705 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2172  Z= 0.111
  Angle     :  0.667   6.505   2949  Z= 0.329
  Chirality :  0.045   0.128    321
  Planarity :  0.004   0.042    378
  Dihedral  :  5.552  17.258    309
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 20.51 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.35 (0.34), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.26), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  80 
 TYR   0.015   0.001   TYR A 100 
 PHE   0.004   0.001   PHE A  53 
 TRP   0.005   0.001   TRP B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 2169)
  covalent geometry    : angle       0.66714 ( 2943)
  SS BOND              : bond        0.00125 (    3)
  SS BOND              : angle       0.61020 (    6)
  hydrogen bonds       : bond        0.01703 (   38)
  hydrogen bonds       : angle       4.32784 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.087 
Fit side-chains
REVERT: C   80 ARG cc_start: 0.5631 (tpp-160) cc_final: 0.2188 (tpp80)
REVERT: C   87 TYR cc_start: 0.9209 (m-80) cc_final: 0.8528 (m-80)
REVERT: A   46 LYS cc_start: 0.8076 (tttt) cc_final: 0.7857 (ttmt)
REVERT: A   64 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8168 (p)
REVERT: A   83 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7958 (m-30)
REVERT: A   93 ASP cc_start: 0.8789 (t0) cc_final: 0.8150 (t0)
REVERT: A   94 ASP cc_start: 0.8657 (m-30) cc_final: 0.8256 (m-30)
REVERT: A  107 LYS cc_start: 0.8529 (tttm) cc_final: 0.6094 (mptt)
REVERT: B   17 ARG cc_start: 0.6844 (tpt170) cc_final: 0.5729 (ppt170)
REVERT: B   93 ASP cc_start: 0.9073 (t0) cc_final: 0.8319 (t0)
REVERT: B   94 ASP cc_start: 0.8682 (m-30) cc_final: 0.8263 (m-30)
REVERT: B  107 LYS cc_start: 0.8870 (tttm) cc_final: 0.6627 (mptt)
  outliers start: 9
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0809
  time to fit residues: 5.6380
Evaluate side-chains
  61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue   83 ASP
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    0.1980
   chunk 1 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.117947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.108448 restraints weight = 3869.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 2.66
r_work: 0.3759 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3662 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   2172  Z= 0.193
  Angle     :  0.706   6.430   2949  Z= 0.353
  Chirality :  0.045   0.123    321
  Planarity :  0.004   0.038    378
  Dihedral  :  5.653  17.914    309
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.42 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 21.79 %
    Favored  : 73.50 %
  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: -4.35 (0.34), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.26), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  80 
 TYR   0.018   0.002   TYR A 100 
 PHE   0.007   0.001   PHE A  53 
 TRP   0.004   0.001   TRP A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 2169)
  covalent geometry    : angle       0.70555 ( 2943)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       0.74840 (    6)
  hydrogen bonds       : bond        0.01910 (   38)
  hydrogen bonds       : angle       4.31638 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 ARG cc_start: 0.5681 (tpp-160) cc_final: 0.2294 (tpp80)
REVERT: C   83 ASP cc_start: 0.8310 (m-30) cc_final: 0.7695 (m-30)
REVERT: C   87 TYR cc_start: 0.9190 (m-80) cc_final: 0.8475 (m-80)
REVERT: A   46 LYS cc_start: 0.7995 (tttt) cc_final: 0.7783 (ttmt)
REVERT: A   64 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8145 (p)
REVERT: A  107 LYS cc_start: 0.8499 (tttm) cc_final: 0.6026 (mptt)
REVERT: B   17 ARG cc_start: 0.6827 (tpt170) cc_final: 0.5703 (ppt170)
REVERT: B   93 ASP cc_start: 0.9034 (t0) cc_final: 0.8329 (t0)
REVERT: B   94 ASP cc_start: 0.8716 (m-30) cc_final: 0.8241 (m-30)
REVERT: B  107 LYS cc_start: 0.8985 (tttm) cc_final: 0.6650 (mptt)
  outliers start: 11
  outliers final: 9
  residues processed: 62
  average time/residue: 0.0813
  time to fit residues: 5.7296
Evaluate side-chains
  62 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 16 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.118118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.108732 restraints weight = 3804.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 2.60
r_work: 0.3775 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3680 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2172  Z= 0.156
  Angle     :  0.698   6.670   2949  Z= 0.346
  Chirality :  0.045   0.126    321
  Planarity :  0.004   0.040    378
  Dihedral  :  5.605  17.736    309
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 22.65 %
    Favored  : 73.08 %
  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: -4.37 (0.34), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.33 (0.26), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  80 
 TYR   0.025   0.002   TYR A 100 
 PHE   0.005   0.001   PHE A  53 
 TRP   0.005   0.001   TRP B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 2169)
  covalent geometry    : angle       0.69780 ( 2943)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       0.66958 (    6)
  hydrogen bonds       : bond        0.01827 (   38)
  hydrogen bonds       : angle       4.26558 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 ARG cc_start: 0.5596 (tpp-160) cc_final: 0.2224 (tpp80)
REVERT: C   83 ASP cc_start: 0.8308 (m-30) cc_final: 0.7704 (m-30)
REVERT: C   87 TYR cc_start: 0.9231 (m-80) cc_final: 0.8612 (m-80)
REVERT: A   46 LYS cc_start: 0.7962 (tttt) cc_final: 0.7755 (ttmt)
REVERT: A   64 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8142 (p)
REVERT: A  107 LYS cc_start: 0.8454 (tttm) cc_final: 0.5992 (mptt)
REVERT: B   17 ARG cc_start: 0.6728 (tpt170) cc_final: 0.5622 (ppt170)
REVERT: B   93 ASP cc_start: 0.9031 (t0) cc_final: 0.8308 (t0)
REVERT: B   94 ASP cc_start: 0.8693 (m-30) cc_final: 0.8219 (m-30)
REVERT: B  107 LYS cc_start: 0.8950 (tttm) cc_final: 0.6637 (mptt)
  outliers start: 10
  outliers final: 8
  residues processed: 60
  average time/residue: 0.0808
  time to fit residues: 5.4863
Evaluate side-chains
  60 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 25 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0670
   chunk 14 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7522

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.124245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.114542 restraints weight = 3779.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 2.67
r_work: 0.3860 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3767 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2172  Z= 0.096
  Angle     :  0.661   6.559   2949  Z= 0.328
  Chirality :  0.046   0.132    321
  Planarity :  0.004   0.044    378
  Dihedral  :  5.335  16.985    309
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 23.50 %
    Favored  : 73.08 %
  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: -4.33 (0.34), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.26), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  80 
 TYR   0.017   0.002   TYR A 100 
 PHE   0.004   0.001   PHE C  53 
 TRP   0.007   0.001   TRP B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 2169)
  covalent geometry    : angle       0.66068 ( 2943)
  SS BOND              : bond        0.00046 (    3)
  SS BOND              : angle       0.63771 (    6)
  hydrogen bonds       : bond        0.01643 (   38)
  hydrogen bonds       : angle       4.09589 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.051 
Fit side-chains
   revert: symmetry clash
REVERT: C   80 ARG cc_start: 0.5470 (tpp-160) cc_final: 0.2455 (ttt90)
REVERT: C   83 ASP cc_start: 0.8140 (m-30) cc_final: 0.7458 (m-30)
REVERT: A   64 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8096 (p)
REVERT: A   93 ASP cc_start: 0.8601 (t0) cc_final: 0.7975 (t0)
REVERT: A   94 ASP cc_start: 0.8544 (m-30) cc_final: 0.8179 (m-30)
REVERT: A  107 LYS cc_start: 0.8401 (tttm) cc_final: 0.5969 (mptt)
REVERT: B   17 ARG cc_start: 0.6696 (tpt170) cc_final: 0.6036 (tmm160)
REVERT: B   93 ASP cc_start: 0.8939 (t0) cc_final: 0.8604 (t0)
REVERT: B  107 LYS cc_start: 0.8780 (tttm) cc_final: 0.6599 (mptt)
  outliers start: 8
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0672
  time to fit residues: 4.6596
Evaluate side-chains
  61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 1 optimal weight:    7.9990
   chunk 19 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.120769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.110973 restraints weight = 3894.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.73
r_work: 0.3814 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2172  Z= 0.140
  Angle     :  0.671   6.857   2949  Z= 0.335
  Chirality :  0.045   0.128    321
  Planarity :  0.004   0.041    378
  Dihedral  :  5.421  17.373    309
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 23.93 %
    Favored  : 72.65 %
  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: -4.33 (0.34), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.26), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  80 
 TYR   0.011   0.001   TYR A 100 
 PHE   0.005   0.001   PHE A  53 
 TRP   0.004   0.001   TRP B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 2169)
  covalent geometry    : angle       0.67150 ( 2943)
  SS BOND              : bond        0.00178 (    3)
  SS BOND              : angle       0.65110 (    6)
  hydrogen bonds       : bond        0.01766 (   38)
  hydrogen bonds       : angle       4.13859 (  114)

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

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

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  552 Ramachandran restraints generated.
    276 Oldfield, 0 Emsley, 276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   80 ARG cc_start: 0.5651 (tpp-160) cc_final: 0.2310 (tpp80)
REVERT: C   83 ASP cc_start: 0.8189 (m-30) cc_final: 0.7549 (m-30)
REVERT: C   87 TYR cc_start: 0.9135 (m-80) cc_final: 0.8392 (m-80)
REVERT: A   64 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8109 (p)
REVERT: A  107 LYS cc_start: 0.8459 (tttm) cc_final: 0.5919 (mptt)
REVERT: B   17 ARG cc_start: 0.6778 (tpt170) cc_final: 0.6070 (tmm160)
REVERT: B   93 ASP cc_start: 0.8967 (t0) cc_final: 0.8679 (t0)
REVERT: B  107 LYS cc_start: 0.8873 (tttm) cc_final: 0.6637 (mptt)
  outliers start: 8
  outliers final: 7
  residues processed: 60
  average time/residue: 0.0780
  time to fit residues: 5.3163
Evaluate side-chains
  61 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   64 SER
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0070
   chunk 9 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   overall best weight:    0.9600

-------------------------------------------------------------------------------
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 = 0.4068 r_free = 0.4068 target = 0.124362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.114499 restraints weight = 3758.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 2.70
r_work: 0.3858 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2172  Z= 0.103
  Angle     :  0.658   6.839   2949  Z= 0.326
  Chirality :  0.045   0.131    321
  Planarity :  0.004   0.043    378
  Dihedral  :  5.294  16.968    309
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 23.93 %
    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 are not related in a simple way.
  whole: -4.33 (0.34), residues: 276
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.26), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  80 
 TYR   0.016   0.002   TYR A 100 
 PHE   0.003   0.001   PHE B  53 
 TRP   0.007   0.001   TRP B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 2169)
  covalent geometry    : angle       0.65780 ( 2943)
  SS BOND              : bond        0.00079 (    3)
  SS BOND              : angle       0.61822 (    6)
  hydrogen bonds       : bond        0.01620 (   38)
  hydrogen bonds       : angle       4.15409 (  114)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 848.41 seconds
wall clock time: 15 minutes 14.49 seconds (914.49 seconds total)