Starting phenix.real_space_refine
on Tue Feb  3 12:20:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ljc_63142/02_2026/9ljc_63142.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ljc_63142/02_2026/9ljc_63142.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ljc_63142/02_2026/9ljc_63142.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ljc_63142/02_2026/9ljc_63142.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ljc_63142/02_2026/9ljc_63142.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ljc_63142/02_2026/9ljc_63142.map"
  }
  resolution = 2.7
  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=   0.003
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    1116      2.51       5
     N     291      2.21       5
     O     402      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 1818
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 606
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 3, 'TRANS': 76}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 0.67, per 1000 atoms: 0.37
  Number of scatterers: 1818
  At special positions: 0
  Unit cell: (75.53, 79.68, 37.35, 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     402      8.00
     N     291      7.00
     C    1116      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  91 " distance=2.03

  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: 0.15
  Conformation dependent library (CDL) restraints added in 78.7 milliseconds
  

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  444

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 40.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 5
      removed outlier: 6.271A  pdb=" N   LEU A   4 " --> pdb=" O   THR B   5 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 8 through 11
      removed outlier: 6.918A  pdb=" N   SER A   9 " --> pdb=" O   HIS B   8 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   HIS A   8 " --> pdb=" O   SER C   9 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   SER C  11 " --> pdb=" O   HIS A   8 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   VAL A  10 " --> pdb=" O   SER C  11 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 16
      removed outlier: 6.672A  pdb=" N   GLY A  15 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 21
      removed outlier: 6.315A  pdb=" N   THR A  19 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 38
      removed outlier: 6.497A  pdb=" N   ILE A  29 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   ASN C  32 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   SER A  31 " --> pdb=" O   ASN C  32 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   VAL C  34 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   TYR A  33 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   TRP C  36 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   GLN A  35 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   GLN C  38 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   TYR A  37 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 68
      removed outlier: 6.090A  pdb=" N   SER A  64 " --> pdb=" O   GLY C  65 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   ILE C  67 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   SER A  66 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 78
      removed outlier: 6.317A  pdb=" N   THR A  77 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 81 through 82
      removed outlier: 6.514A  pdb=" N   LEU A  81 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 89 through 95
      removed outlier: 6.243A  pdb=" N   TYR A  89 " --> pdb=" O   TYR B  90 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   GLN B  92 " --> pdb=" O   TYR A  89 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   CYS A  91 " --> pdb=" O   GLN B  92 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   TYR B  94 " --> pdb=" O   CYS A  91 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   SER A  93 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 100
      removed outlier: 6.215A  pdb=" N   THR A  98 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)

    31 hydrogen bonds defined for protein.
    93 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: 0.24

  Time building geometry restraints manager: 0.21 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: 591
        1.34 -     1.45: 289
        1.45 -     1.57: 962
        1.57 -     1.68: 0
        1.68 -     1.80: 12
  Bond restraints: 1854
  Sorted by residual:
  bond pdb=" N   GLY A  15 "
       pdb=" CA  GLY A  15 "
    ideal  model  delta    sigma   weight residual
    1.455  1.443  0.012 1.05e-02 9.07e+03 1.23e+00
  bond pdb=" N   GLY B  15 "
       pdb=" CA  GLY B  15 "
    ideal  model  delta    sigma   weight residual
    1.455  1.444  0.011 1.05e-02 9.07e+03 1.15e+00
  bond pdb=" N   GLY C  15 "
       pdb=" CA  GLY C  15 "
    ideal  model  delta    sigma   weight residual
    1.455  1.444  0.011 1.05e-02 9.07e+03 1.07e+00
  bond pdb=" CG1 ILE A  20 "
       pdb=" CD1 ILE A  20 "
    ideal  model  delta    sigma   weight residual
    1.513  1.475  0.038 3.90e-02 6.57e+02 9.62e-01
  bond pdb=" CG1 ILE B  20 "
       pdb=" CD1 ILE B  20 "
    ideal  model  delta    sigma   weight residual
    1.513  1.475  0.038 3.90e-02 6.57e+02 9.57e-01
  ... (remaining 1849 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 2283
        1.07 -     2.14: 184
        2.14 -     3.21: 32
        3.21 -     4.28: 12
        4.28 -     5.34: 3
  Bond angle restraints: 2514
  Sorted by residual:
  angle pdb=" N   ASP A  88 "
        pdb=" CA  ASP A  88 "
        pdb=" C   ASP A  88 "
      ideal   model   delta    sigma   weight residual
     110.20  115.54   -5.34 1.58e+00 4.01e-01 1.14e+01
  angle pdb=" N   ASP B  88 "
        pdb=" CA  ASP B  88 "
        pdb=" C   ASP B  88 "
      ideal   model   delta    sigma   weight residual
     110.20  115.53   -5.33 1.58e+00 4.01e-01 1.14e+01
  angle pdb=" N   ASP C  88 "
        pdb=" CA  ASP C  88 "
        pdb=" C   ASP C  88 "
      ideal   model   delta    sigma   weight residual
     110.20  115.52   -5.32 1.58e+00 4.01e-01 1.14e+01
  angle pdb=" N   TYR C  89 "
        pdb=" CA  TYR C  89 "
        pdb=" C   TYR C  89 "
      ideal   model   delta    sigma   weight residual
     109.76  106.15    3.61 1.64e+00 3.72e-01 4.86e+00
  angle pdb=" N   TYR A  89 "
        pdb=" CA  TYR A  89 "
        pdb=" C   TYR A  89 "
      ideal   model   delta    sigma   weight residual
     109.76  106.17    3.59 1.64e+00 3.72e-01 4.79e+00
  ... (remaining 2509 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.23: 942
       11.23 -    22.45: 111
       22.45 -    33.68: 18
       33.68 -    44.90: 18
       44.90 -    56.13: 9
  Dihedral angle restraints: 1098
    sinusoidal: 405
      harmonic: 693
  Sorted by residual:
  dihedral pdb=" CA  GLN B  35 "
           pdb=" C   GLN B  35 "
           pdb=" N   TRP B  36 "
           pdb=" CA  TRP B  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.09   14.91     0      5.00e+00 4.00e-02 8.90e+00
  dihedral pdb=" CA  GLN A  35 "
           pdb=" C   GLN A  35 "
           pdb=" N   TRP A  36 "
           pdb=" CA  TRP A  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.11   14.89     0      5.00e+00 4.00e-02 8.86e+00
  dihedral pdb=" CA  GLN C  35 "
           pdb=" C   GLN C  35 "
           pdb=" N   TRP C  36 "
           pdb=" CA  TRP C  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.14   14.86     0      5.00e+00 4.00e-02 8.83e+00
  ... (remaining 1095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 157
       0.033 -    0.065: 57
       0.065 -    0.098: 39
       0.098 -    0.131: 14
       0.131 -    0.163: 9
  Chirality restraints: 276
  Sorted by residual:
  chirality pdb=" CG  LEU C   4 "
            pdb=" CB  LEU C   4 "
            pdb=" CD1 LEU C   4 "
            pdb=" CD2 LEU C   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.65e-01
  chirality pdb=" CG  LEU B   4 "
            pdb=" CB  LEU B   4 "
            pdb=" CD1 LEU B   4 "
            pdb=" CD2 LEU B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.47e-01
  chirality pdb=" CG  LEU A   4 "
            pdb=" CB  LEU A   4 "
            pdb=" CD1 LEU A   4 "
            pdb=" CD2 LEU A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.46e-01
  ... (remaining 273 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  63 "    0.004 2.00e-02 2.50e+03   5.13e-03 4.61e-01
        pdb=" CG  PHE A  63 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  63 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  63 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  63 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  63 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  63 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  63 "    0.004 2.00e-02 2.50e+03   5.07e-03 4.49e-01
        pdb=" CG  PHE B  63 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  63 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  63 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  63 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  63 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  63 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  63 "    0.003 2.00e-02 2.50e+03   4.88e-03 4.17e-01
        pdb=" CG  PHE C  63 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  63 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  63 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  63 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  63 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  63 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 425
        2.80 -     3.32: 1480
        3.32 -     3.85: 2993
        3.85 -     4.37: 3254
        4.37 -     4.90: 6309
  Nonbonded interactions: 14461
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  28 "
            pdb=" OG  SER C  79 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER A  79 "
            pdb=" OG  SER B  28 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   ASP B  88 "
            pdb=" OD1 ASP B  88 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   ASP A  88 "
            pdb=" OD1 ASP A  88 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   ASP C  88 "
            pdb=" OD1 ASP C  88 "
     model   vdw
     2.387 3.040
  ... (remaining 14456 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'
  selection = chain 'C'
}

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:             2.580
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.890
  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:7.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
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      :  0.007   0.038   1857  Z= 0.318
  Angle     :  0.697   5.344   2520  Z= 0.401
  Chirality :  0.054   0.163    276
  Planarity :  0.002   0.016    327
  Dihedral  : 12.523  56.128    645
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  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: -4.30 (0.35), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.26), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG B  62 
 TYR   0.010   0.002   TYR A  33 
 PHE   0.012   0.003   PHE A  63 
 TRP   0.003   0.001   TRP B  36 
 HIS   0.001   0.001   HIS B   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00709 ( 1854)
  covalent geometry    : angle       0.69642 ( 2514)
  SS BOND              : bond        0.00284 (    3)
  SS BOND              : angle       0.86315 (    6)
  hydrogen bonds       : bond        0.13081 (   31)
  hydrogen bonds       : angle       7.52403 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   62 ARG cc_start: 0.7580 (ttt180) cc_final: 0.7202 (ttt90)
REVERT: C   19 THR cc_start: 0.8855 (m) cc_final: 0.8618 (m)
REVERT: C   62 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7379 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.3952
  time to fit residues: 21.7863
Evaluate side-chains
  50 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A   6 GLN
A  32 ASN
B   6 GLN
B  32 ASN
B  72 ASN
B  99 GLN
C   6 GLN
C   8 HIS
C  32 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.114428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.095702 restraints weight = 2158.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.74
r_work: 0.3213 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   1857  Z= 0.099
  Angle     :  0.533   3.524   2520  Z= 0.291
  Chirality :  0.044   0.131    276
  Planarity :  0.002   0.019    327
  Dihedral  :  5.130  14.604    252
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.02 %
    Favored  : 84.98 %
  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: -3.90 (0.38), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.29), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.011   0.001   TYR B  89 
 PHE   0.009   0.001   PHE A  63 
 TRP   0.003   0.001   TRP B  36 
 HIS   0.000   0.000   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 1854)
  covalent geometry    : angle       0.53318 ( 2514)
  SS BOND              : bond        0.00076 (    3)
  SS BOND              : angle       0.28541 (    6)
  hydrogen bonds       : bond        0.02002 (   31)
  hydrogen bonds       : angle       5.13862 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.075 
Fit side-chains
REVERT: C   62 ARG cc_start: 0.8489 (ttt180) cc_final: 0.7825 (ttt90)
REVERT: C   88 ASP cc_start: 0.8586 (p0) cc_final: 0.8214 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.3680
  time to fit residues: 20.2979
Evaluate side-chains
  51 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 17 optimal weight:    0.3980
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    2.0584

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

Flipped N/Q/H residues before XYZ refinement:
B   8 HIS
B  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.112101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.093097 restraints weight = 2131.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.73
r_work: 0.3167 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8971
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1857  Z= 0.156
  Angle     :  0.548   3.550   2520  Z= 0.302
  Chirality :  0.044   0.131    276
  Planarity :  0.003   0.018    327
  Dihedral  :  5.267  15.495    252
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 15.49 %
    Favored  : 80.75 %
  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: -3.68 (0.39), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.80 (0.30), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.012   0.002   TYR B  89 
 PHE   0.010   0.002   PHE A  63 
 TRP   0.003   0.001   TRP B  36 
 HIS   0.001   0.000   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 1854)
  covalent geometry    : angle       0.54787 ( 2514)
  SS BOND              : bond        0.00095 (    3)
  SS BOND              : angle       0.39209 (    6)
  hydrogen bonds       : bond        0.01836 (   31)
  hydrogen bonds       : angle       4.74669 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.052 
Fit side-chains
REVERT: A   88 ASP cc_start: 0.8520 (p0) cc_final: 0.8067 (p0)
REVERT: C   62 ARG cc_start: 0.8490 (ttt180) cc_final: 0.7780 (ttt90)
REVERT: C   88 ASP cc_start: 0.8658 (p0) cc_final: 0.8265 (p0)
  outliers start: 8
  outliers final: 0
  residues processed: 58
  average time/residue: 0.3380
  time to fit residues: 20.0573
Evaluate side-chains
  52 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.111619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.092756 restraints weight = 2130.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.70
r_work: 0.3162 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8976
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1857  Z= 0.190
  Angle     :  0.595   5.074   2520  Z= 0.328
  Chirality :  0.045   0.131    276
  Planarity :  0.003   0.018    327
  Dihedral  :  5.511  16.084    252
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.84 %
    Favored  : 80.75 %
  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: -3.56 (0.40), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.31), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.013   0.002   TYR B  89 
 PHE   0.010   0.002   PHE A  63 
 TRP   0.004   0.001   TRP B  36 
 HIS   0.001   0.001   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 1854)
  covalent geometry    : angle       0.59514 ( 2514)
  SS BOND              : bond        0.00113 (    3)
  SS BOND              : angle       0.49143 (    6)
  hydrogen bonds       : bond        0.01799 (   31)
  hydrogen bonds       : angle       4.61304 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.080 
Fit side-chains
REVERT: C   62 ARG cc_start: 0.8489 (ttt180) cc_final: 0.7760 (ttt90)
REVERT: C   88 ASP cc_start: 0.8687 (p0) cc_final: 0.8308 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 53
  average time/residue: 0.3772
  time to fit residues: 20.4593
Evaluate side-chains
  50 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 0 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 9 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    4.5586

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.109550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.090635 restraints weight = 2184.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.73
r_work: 0.3126 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9003
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   1857  Z= 0.313
  Angle     :  0.663   5.091   2520  Z= 0.368
  Chirality :  0.047   0.132    276
  Planarity :  0.003   0.016    327
  Dihedral  :  5.923  16.887    252
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 19.72 %
    Favored  : 77.46 %
  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: -3.59 (0.40), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.31), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.017   0.003   TYR B  89 
 PHE   0.012   0.003   PHE B  63 
 TRP   0.005   0.002   TRP B  36 
 HIS   0.002   0.001   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00707 ( 1854)
  covalent geometry    : angle       0.66310 ( 2514)
  SS BOND              : bond        0.00185 (    3)
  SS BOND              : angle       0.75579 (    6)
  hydrogen bonds       : bond        0.02127 (   31)
  hydrogen bonds       : angle       4.74541 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.075 
Fit side-chains
REVERT: C   20 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8927 (mp)
REVERT: C   62 ARG cc_start: 0.8507 (ttt180) cc_final: 0.7770 (ttt90)
REVERT: C   88 ASP cc_start: 0.8697 (p0) cc_final: 0.8340 (p0)
  outliers start: 6
  outliers final: 0
  residues processed: 51
  average time/residue: 0.4009
  time to fit residues: 20.8825
Evaluate side-chains
  49 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   20 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    0.2980
   chunk 20 optimal weight:    8.9990
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0870
   chunk 5 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.4764

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.113167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.094396 restraints weight = 2111.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.70
r_work: 0.3194 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8961
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   1857  Z= 0.123
  Angle     :  0.552   4.319   2520  Z= 0.302
  Chirality :  0.044   0.131    276
  Planarity :  0.002   0.018    327
  Dihedral  :  5.363  15.968    252
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 21.60 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.46 (0.41), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.31), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.011   0.002   TYR A  89 
 PHE   0.009   0.002   PHE A  63 
 TRP   0.003   0.001   TRP B  36 
 HIS   0.001   0.000   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 1854)
  covalent geometry    : angle       0.55226 ( 2514)
  SS BOND              : bond        0.00049 (    3)
  SS BOND              : angle       0.24924 (    6)
  hydrogen bonds       : bond        0.01572 (   31)
  hydrogen bonds       : angle       4.45348 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   76 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8900 (tt)
REVERT: A   88 ASP cc_start: 0.8578 (p0) cc_final: 0.8149 (p0)
REVERT: C   62 ARG cc_start: 0.8491 (ttt180) cc_final: 0.7761 (ttt90)
REVERT: C   88 ASP cc_start: 0.8659 (p0) cc_final: 0.8282 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 52
  average time/residue: 0.4308
  time to fit residues: 22.8780
Evaluate side-chains
  49 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3562 r_free = 0.3562 target = 0.113026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.094097 restraints weight = 2132.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.72
r_work: 0.3184 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8963
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1857  Z= 0.139
  Angle     :  0.563   3.942   2520  Z= 0.308
  Chirality :  0.046   0.224    276
  Planarity :  0.002   0.017    327
  Dihedral  :  5.294  16.142    252
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 21.13 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.44 (0.41), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.31), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.011   0.002   TYR A  89 
 PHE   0.009   0.002   PHE B  63 
 TRP   0.003   0.001   TRP B  36 
 HIS   0.001   0.000   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 1854)
  covalent geometry    : angle       0.56335 ( 2514)
  SS BOND              : bond        0.00070 (    3)
  SS BOND              : angle       0.30125 (    6)
  hydrogen bonds       : bond        0.01610 (   31)
  hydrogen bonds       : angle       4.40140 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   88 ASP cc_start: 0.8570 (p0) cc_final: 0.8136 (p0)
REVERT: C   62 ARG cc_start: 0.8516 (ttt180) cc_final: 0.7781 (ttt90)
REVERT: C   88 ASP cc_start: 0.8668 (p0) cc_final: 0.8276 (p0)
  outliers start: 4
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2962
  time to fit residues: 15.1518
Evaluate side-chains
  50 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0370
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.5664

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.113596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.094919 restraints weight = 2126.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.71
r_work: 0.3198 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1857  Z= 0.127
  Angle     :  0.542   3.856   2520  Z= 0.297
  Chirality :  0.045   0.131    276
  Planarity :  0.002   0.018    327
  Dihedral  :  5.223  16.459    252
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 22.54 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.41), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.32), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.011   0.002   TYR A  89 
 PHE   0.009   0.002   PHE A  63 
 TRP   0.003   0.001   TRP B  36 
 HIS   0.001   0.000   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 1854)
  covalent geometry    : angle       0.54287 ( 2514)
  SS BOND              : bond        0.00066 (    3)
  SS BOND              : angle       0.28175 (    6)
  hydrogen bonds       : bond        0.01584 (   31)
  hydrogen bonds       : angle       4.35787 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.045 
Fit side-chains
REVERT: A   88 ASP cc_start: 0.8574 (p0) cc_final: 0.8135 (p0)
REVERT: C   62 ARG cc_start: 0.8513 (ttt180) cc_final: 0.7784 (ttt90)
REVERT: C   88 ASP cc_start: 0.8677 (p0) cc_final: 0.8289 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2703
  time to fit residues: 14.1223
Evaluate side-chains
  50 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3577 r_free = 0.3577 target = 0.114106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.095469 restraints weight = 2134.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.71
r_work: 0.3205 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8951
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   1857  Z= 0.113
  Angle     :  0.530   3.531   2520  Z= 0.291
  Chirality :  0.044   0.131    276
  Planarity :  0.002   0.018    327
  Dihedral  :  5.061  16.475    252
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 22.07 %
    Favored  : 76.53 %
  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: -3.38 (0.41), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.56 (0.32), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.011   0.001   TYR A  89 
 PHE   0.009   0.002   PHE B  63 
 TRP   0.003   0.001   TRP B  36 
 HIS   0.001   0.000   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 1854)
  covalent geometry    : angle       0.53100 ( 2514)
  SS BOND              : bond        0.00056 (    3)
  SS BOND              : angle       0.23825 (    6)
  hydrogen bonds       : bond        0.01559 (   31)
  hydrogen bonds       : angle       4.37056 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.045 
Fit side-chains
REVERT: A   88 ASP cc_start: 0.8573 (p0) cc_final: 0.8132 (p0)
REVERT: C   62 ARG cc_start: 0.8506 (ttt180) cc_final: 0.7778 (ttt90)
REVERT: C   88 ASP cc_start: 0.8673 (p0) cc_final: 0.8279 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 53
  average time/residue: 0.3199
  time to fit residues: 17.3234
Evaluate side-chains
  51 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 23 optimal weight:    8.9990
   chunk 8 optimal weight:    0.5980
   chunk 2 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   overall best weight:    3.9188

-------------------------------------------------------------------------------
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 = 0.3520 r_free = 0.3520 target = 0.110364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.091711 restraints weight = 2165.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.72
r_work: 0.3143 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8988
moved from start:          0.1805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   1857  Z= 0.274
  Angle     :  0.640   5.070   2520  Z= 0.354
  Chirality :  0.048   0.174    276
  Planarity :  0.003   0.014    327
  Dihedral  :  5.727  17.459    252
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 23.00 %
    Favored  : 76.06 %
  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: -3.52 (0.41), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.31), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  62 
 TYR   0.016   0.002   TYR B  89 
 PHE   0.011   0.003   PHE B  63 
 TRP   0.004   0.002   TRP B  36 
 HIS   0.002   0.001   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 1854)
  covalent geometry    : angle       0.63980 ( 2514)
  SS BOND              : bond        0.00155 (    3)
  SS BOND              : angle       0.68966 (    6)
  hydrogen bonds       : bond        0.02019 (   31)
  hydrogen bonds       : angle       4.60973 (   93)

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

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

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  456 Ramachandran restraints generated.
    228 Oldfield, 0 Emsley, 228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.045 
Fit side-chains
REVERT: C   62 ARG cc_start: 0.8496 (ttt180) cc_final: 0.7754 (ttt90)
REVERT: C   88 ASP cc_start: 0.8679 (p0) cc_final: 0.8278 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 51
  average time/residue: 0.2609
  time to fit residues: 13.6154
Evaluate side-chains
  49 residues out of total 213 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 0 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.111192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.092583 restraints weight = 2151.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.71
r_work: 0.3160 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8979
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   1857  Z= 0.217
  Angle     :  0.634   7.287   2520  Z= 0.344
  Chirality :  0.047   0.141    276
  Planarity :  0.003   0.015    327
  Dihedral  :  5.741  17.543    252
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 23.47 %
    Favored  : 76.06 %
  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: -3.51 (0.41), residues: 228
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.31), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  62 
 TYR   0.014   0.002   TYR B  89 
 PHE   0.011   0.002   PHE B  63 
 TRP   0.004   0.001   TRP B  36 
 HIS   0.001   0.001   HIS C   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 1854)
  covalent geometry    : angle       0.63426 ( 2514)
  SS BOND              : bond        0.00112 (    3)
  SS BOND              : angle       0.50969 (    6)
  hydrogen bonds       : bond        0.01824 (   31)
  hydrogen bonds       : angle       4.55813 (   93)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 823.42 seconds
wall clock time: 14 minutes 43.82 seconds (883.82 seconds total)