Starting phenix.real_space_refine
on Tue Feb  3 13:14:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kyz_62650/02_2026/9kyz_62650.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kyz_62650/02_2026/9kyz_62650.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kyz_62650/02_2026/9kyz_62650.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kyz_62650/02_2026/9kyz_62650.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kyz_62650/02_2026/9kyz_62650.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kyz_62650/02_2026/9kyz_62650.map"
  }
  resolution = 3.2
  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=   0.002 sd=   0.024
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      13      5.16       5
     C    1859      2.51       5
     N     496      2.21       5
     O     598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 2966
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 598
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 649
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
    Chain: "A"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 925
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
    Chain: "B"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 794
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 8, 'TRANS': 96}
  Time building chain proxies: 0.80, per 1000 atoms: 0.27
  Number of scatterers: 2966
  At special positions: 0
  Unit cell: (61.198, 76.084, 66.16, 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      13     16.00
     O     598      8.00
     N     496      7.00
     C    1859      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 100 " - pdb=" SG  CYS C 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 126 " - pdb=" SG  CYS C 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 100 " - pdb=" SG  CYS D 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 126 " - pdb=" SG  CYS D 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  89 " distance=2.04

  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: 0.16
  Conformation dependent library (CDL) restraints added in 108.7 milliseconds
  

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  706

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 8 sheets defined
      14.8% alpha, 26.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'C' and resid 118 through 130
    Processing helix  chain 'C' and resid 135 through 141
      removed outlier: 3.659A  pdb=" N   VAL C 139 " --> pdb=" O   ASN C 135 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   THR C 141 " --> pdb=" O   SER C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 143 through 149
      removed outlier: 3.958A  pdb=" N   TYR C 147 " --> pdb=" O   TRP C 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 129
    Processing helix  chain 'D' and resid 135 through 140
    Processing helix  chain 'D' and resid 143 through 149
      removed outlier: 4.238A  pdb=" N   TYR D 147 " --> pdb=" O   TRP D 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 33
    Processing sheet with id=AA1, first strand: chain 'C' and resid 103 through 105
      removed outlier: 3.949A  pdb=" N   TYR C 178 " --> pdb=" O   HIS C 113 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASP C 115 " --> pdb=" O   ARG C 176 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   ARG C 176 " --> pdb=" O   ASP C 115 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 103 through 105
      removed outlier: 3.772A  pdb=" N   TYR D 178 " --> pdb=" O   HIS D 113 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ASP D 115 " --> pdb=" O   ARG D 176 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ARG D 176 " --> pdb=" O   ASP D 115 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.562A  pdb=" N   GLN A   5 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 59
      removed outlier: 5.809A  pdb=" N   TRP A  37 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   GLU A  51 " --> pdb=" O   TRP A  35 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   TRP A  35 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA A  92 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 47
      removed outlier: 3.709A  pdb=" N   TYR B  88 " --> pdb=" O   TYR B  37 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50
    Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91
      removed outlier: 3.690A  pdb=" N   THR B  98 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)

    93 hydrogen bonds defined for protein.
    228 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: 0.32

  Time building geometry restraints manager: 0.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 949
        1.35 -     1.47: 817
        1.47 -     1.59: 1259
        1.59 -     1.71: 0
        1.71 -     1.83: 14
  Bond restraints: 3039
  Sorted by residual:
  bond pdb=" N   SER C 164 "
       pdb=" CA  SER C 164 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.27e+00
  bond pdb=" N   CYS D 100 "
       pdb=" CA  CYS D 100 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.13e+00
  bond pdb=" N   CYS C 100 "
       pdb=" CA  CYS C 100 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.75e+00
  bond pdb=" N   VAL A   2 "
       pdb=" CA  VAL A   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.65e+00
  bond pdb=" N   GLU B   1 "
       pdb=" CA  GLU B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.62e+00
  ... (remaining 3034 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 3899
        1.03 -     2.06: 186
        2.06 -     3.09: 28
        3.09 -     4.13: 18
        4.13 -     5.16: 2
  Bond angle restraints: 4133
  Sorted by residual:
  angle pdb=" N   GLY A  50 "
        pdb=" CA  GLY A  50 "
        pdb=" C   GLY A  50 "
      ideal   model   delta    sigma   weight residual
     111.63  115.04   -3.41 1.15e+00 7.56e-01 8.80e+00
  angle pdb=" CA  GLU C 120 "
        pdb=" CB  GLU C 120 "
        pdb=" CG  GLU C 120 "
      ideal   model   delta    sigma   weight residual
     114.10  118.65   -4.55 2.00e+00 2.50e-01 5.18e+00
  angle pdb=" CB  GLU C 120 "
        pdb=" CG  GLU C 120 "
        pdb=" CD  GLU C 120 "
      ideal   model   delta    sigma   weight residual
     112.60  116.05   -3.45 1.70e+00 3.46e-01 4.12e+00
  angle pdb=" C   SER B   7 "
        pdb=" CA  SER B   7 "
        pdb=" CB  SER B   7 "
      ideal   model   delta    sigma   weight residual
     113.57  110.81    2.76 1.57e+00 4.06e-01 3.09e+00
  angle pdb=" C   THR B  73 "
        pdb=" N   LEU B  74 "
        pdb=" CA  LEU B  74 "
      ideal   model   delta    sigma   weight residual
     122.87  125.45   -2.58 1.61e+00 3.86e-01 2.57e+00
  ... (remaining 4128 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 1534
       17.71 -    35.43: 188
       35.43 -    53.14: 53
       53.14 -    70.85: 17
       70.85 -    88.57: 3
  Dihedral angle restraints: 1795
    sinusoidal: 688
      harmonic: 1107
  Sorted by residual:
  dihedral pdb=" CB  CYS C 126 "
           pdb=" SG  CYS C 126 "
           pdb=" SG  CYS C 180 "
           pdb=" CB  CYS C 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.65  -74.65     1      1.00e+01 1.00e-02 7.06e+01
  dihedral pdb=" CA  CYS D 126 "
           pdb=" CB  CYS D 126 "
           pdb=" SG  CYS D 126 "
           pdb=" SG  CYS D 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -10.07  -62.93     1      2.00e+01 2.50e-03 1.31e+01
  dihedral pdb=" CA  TYR A  95 "
           pdb=" C   TYR A  95 "
           pdb=" N   CYS A  96 "
           pdb=" CA  CYS A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.56   17.44     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 1792 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 264
       0.027 -    0.053: 124
       0.053 -    0.080: 39
       0.080 -    0.107: 10
       0.107 -    0.133: 12
  Chirality restraints: 449
  Sorted by residual:
  chirality pdb=" CA  ILE B  76 "
            pdb=" N   ILE B  76 "
            pdb=" C   ILE B  76 "
            pdb=" CB  ILE B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CA  ILE D 111 "
            pdb=" N   ILE D 111 "
            pdb=" C   ILE D 111 "
            pdb=" CB  ILE D 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  VAL A  12 "
            pdb=" N   VAL A  12 "
            pdb=" C   VAL A  12 "
            pdb=" CB  VAL A  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 446 not shown)

  Planarity restraints: 528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 105 "    0.006 2.00e-02 2.50e+03   1.05e-02 2.21e+00
        pdb=" CG  TYR C 105 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 105 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 105 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 105 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 105 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 105 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 105 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  44 "   -0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO B  45 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B  45 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  45 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  61 "    0.015 5.00e-02 4.00e+02   2.29e-02 8.42e-01
        pdb=" N   PRO A  62 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A  62 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A  62 "    0.013 5.00e-02 4.00e+02
  ... (remaining 525 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 950
        2.81 -     3.33: 2743
        3.33 -     3.86: 4757
        3.86 -     4.38: 5673
        4.38 -     4.90: 9762
  Nonbonded interactions: 23885
  Sorted by model distance:
  nonbonded pdb=" O   ASN C 101 "
            pdb=" OD1 ASN C 101 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER C 118 "
            pdb=" OE1 GLU C 120 "
     model   vdw
     2.519 3.040
  nonbonded pdb=" O   SER A  19 "
            pdb=" OG  SER A  19 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" O   ASP C 115 "
            pdb=" OD1 ASP C 115 "
     model   vdw
     2.556 3.040
  nonbonded pdb=" OE1 GLN B   6 "
            pdb=" OG1 THR B 103 "
     model   vdw
     2.561 3.040
  ... (remaining 23880 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = (chain 'D' and (resid 100 through 164 or resid 171 through 181))
}

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:             2.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.370
  Find NCS groups from input model:        0.030
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3045  Z= 0.151
  Angle     :  0.548   5.157   4145  Z= 0.297
  Chirality :  0.038   0.133    449
  Planarity :  0.003   0.030    528
  Dihedral  : 17.326  88.565   1071
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 30.21 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.94 (0.44), residues: 374
  helix:  0.24 (0.93), residues: 32
  sheet: -0.73 (0.53), residues: 94
  loop : -0.67 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  67 
 TYR   0.024   0.001   TYR C 105 
 PHE   0.011   0.001   PHE B  84 
 TRP   0.008   0.001   TRP C 143 
 HIS   0.002   0.001   HIS B  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3039)
  covalent geometry    : angle       0.54568 ( 4133)
  SS BOND              : bond        0.00260 (    6)
  SS BOND              : angle       1.01224 (   12)
  hydrogen bonds       : bond        0.20487 (   93)
  hydrogen bonds       : angle       8.65259 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.6955 (pt0) cc_final: 0.6352 (pt0)
REVERT: B   27 GLN cc_start: 0.7943 (mt0) cc_final: 0.7043 (mt0)
  outliers start: 4
  outliers final: 3
  residues processed: 115
  average time/residue: 0.0762
  time to fit residues: 10.3075
Evaluate side-chains
  71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  140 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
D 125 ASN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.049599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.040903 restraints weight = 16524.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 5.02
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3045  Z= 0.182
  Angle     :  0.681   5.400   4145  Z= 0.361
  Chirality :  0.046   0.162    449
  Planarity :  0.004   0.026    528
  Dihedral  :  6.039  49.462    421
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 27.49 %
    Favored  : 66.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.44), residues: 374
  helix:  2.41 (1.00), residues: 26
  sheet: -0.59 (0.51), residues: 113
  loop : -0.58 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  24 
 TYR   0.018   0.002   TYR D 105 
 PHE   0.019   0.003   PHE B  84 
 TRP   0.018   0.002   TRP A 110 
 HIS   0.003   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 3039)
  covalent geometry    : angle       0.68084 ( 4133)
  SS BOND              : bond        0.00351 (    6)
  SS BOND              : angle       0.87406 (   12)
  hydrogen bonds       : bond        0.03646 (   93)
  hydrogen bonds       : angle       6.62828 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  123 LYS cc_start: 0.9598 (ttmt) cc_final: 0.9288 (tppt)
REVERT: C  136 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9134 (tttp)
REVERT: C  174 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8232 (mp0)
REVERT: D  166 TYR cc_start: 0.7868 (p90) cc_final: 0.7457 (p90)
REVERT: A   11 LEU cc_start: 0.9148 (mm) cc_final: 0.8537 (tp)
  outliers start: 19
  outliers final: 10
  residues processed: 91
  average time/residue: 0.0713
  time to fit residues: 7.7873
Evaluate side-chains
  73 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A  33 ASN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.047910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.039794 restraints weight = 16487.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 4.68
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.4233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3045  Z= 0.188
  Angle     :  0.719   9.032   4145  Z= 0.364
  Chirality :  0.043   0.149    449
  Planarity :  0.004   0.022    528
  Dihedral  :  5.797  50.967    418
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 29.00 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.44), residues: 374
  helix:  2.88 (1.05), residues: 26
  sheet: -0.53 (0.49), residues: 113
  loop : -0.53 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  24 
 TYR   0.016   0.002   TYR D 105 
 PHE   0.016   0.002   PHE B  84 
 TRP   0.012   0.001   TRP A 110 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 3039)
  covalent geometry    : angle       0.71871 ( 4133)
  SS BOND              : bond        0.00427 (    6)
  SS BOND              : angle       0.90765 (   12)
  hydrogen bonds       : bond        0.03420 (   93)
  hydrogen bonds       : angle       6.38771 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  136 LYS cc_start: 0.9598 (OUTLIER) cc_final: 0.9368 (tttp)
REVERT: C  145 ILE cc_start: 0.8643 (tp) cc_final: 0.7788 (tp)
REVERT: C  149 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8161 (mt-10)
REVERT: D  150 ASP cc_start: 0.8891 (t0) cc_final: 0.8627 (t0)
REVERT: A   11 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8502 (tp)
REVERT: B   24 ARG cc_start: 0.8710 (mtm110) cc_final: 0.8496 (mtm-85)
REVERT: B   30 SER cc_start: 0.8378 (m) cc_final: 0.8072 (t)
  outliers start: 20
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0702
  time to fit residues: 7.4899
Evaluate side-chains
  72 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
B   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.045332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.037084 restraints weight = 17040.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 4.66
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.5046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   3045  Z= 0.299
  Angle     :  0.745   7.484   4145  Z= 0.390
  Chirality :  0.044   0.146    449
  Planarity :  0.004   0.024    528
  Dihedral  :  6.069  49.436    418
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  7.85 %
    Allowed  : 26.28 %
    Favored  : 65.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.43), residues: 374
  helix:  1.62 (1.01), residues: 32
  sheet: -0.90 (0.48), residues: 112
  loop : -0.60 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  18 
 TYR   0.018   0.002   TYR D 104 
 PHE   0.013   0.002   PHE B  84 
 TRP   0.014   0.002   TRP A  35 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00648 ( 3039)
  covalent geometry    : angle       0.74281 ( 4133)
  SS BOND              : bond        0.00456 (    6)
  SS BOND              : angle       1.23352 (   12)
  hydrogen bonds       : bond        0.03884 (   93)
  hydrogen bonds       : angle       6.58463 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 60
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: C  123 LYS cc_start: 0.9583 (ttmm) cc_final: 0.9012 (mtpp)
REVERT: C  136 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9308 (tttp)
REVERT: D  150 ASP cc_start: 0.9147 (t0) cc_final: 0.8917 (t0)
REVERT: A   25 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8177 (p)
REVERT: B   30 SER cc_start: 0.8467 (m) cc_final: 0.7903 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0588
  time to fit residues: 6.1871
Evaluate side-chains
  70 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  136 LYS
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain D residue  130 SER
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   84 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 30 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
B   6 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.046976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.038753 restraints weight = 16467.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 4.65
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3045  Z= 0.145
  Angle     :  0.741  10.176   4145  Z= 0.373
  Chirality :  0.045   0.149    449
  Planarity :  0.004   0.025    528
  Dihedral  :  5.245  18.184    416
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  6.04 %
    Allowed  : 29.91 %
    Favored  : 64.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.43), residues: 374
  helix:  1.52 (1.00), residues: 32
  sheet: -0.68 (0.46), residues: 118
  loop : -0.46 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  18 
 TYR   0.021   0.002   TYR D 105 
 PHE   0.014   0.002   PHE B  84 
 TRP   0.011   0.001   TRP A  35 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3039)
  covalent geometry    : angle       0.74101 ( 4133)
  SS BOND              : bond        0.00263 (    6)
  SS BOND              : angle       0.88201 (   12)
  hydrogen bonds       : bond        0.03308 (   93)
  hydrogen bonds       : angle       6.41414 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  123 LYS cc_start: 0.9563 (ttmm) cc_final: 0.8946 (mtpp)
REVERT: D  150 ASP cc_start: 0.8968 (t0) cc_final: 0.8626 (t0)
REVERT: A   25 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8346 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 84
  average time/residue: 0.0561
  time to fit residues: 5.7458
Evaluate side-chains
  71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  126 CYS
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain D residue  130 SER
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0980
   chunk 6 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 28 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.046139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.038061 restraints weight = 16892.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 4.60
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.5492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3045  Z= 0.207
  Angle     :  0.752   9.186   4145  Z= 0.393
  Chirality :  0.043   0.140    449
  Planarity :  0.004   0.034    528
  Dihedral  :  5.361  20.371    416
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 30.51 %
    Favored  : 63.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.43), residues: 374
  helix:  2.99 (1.05), residues: 26
  sheet: -0.73 (0.46), residues: 118
  loop : -0.46 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  24 
 TYR   0.037   0.002   TYR D 105 
 PHE   0.014   0.002   PHE B  84 
 TRP   0.011   0.002   TRP A 114 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 3039)
  covalent geometry    : angle       0.75095 ( 4133)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       1.09158 (   12)
  hydrogen bonds       : bond        0.03443 (   93)
  hydrogen bonds       : angle       6.34898 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 56
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  177 LYS cc_start: 0.9355 (mtpt) cc_final: 0.8924 (mttp)
REVERT: D  150 ASP cc_start: 0.9045 (t0) cc_final: 0.8692 (t0)
REVERT: A   25 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8256 (p)
  outliers start: 21
  outliers final: 19
  residues processed: 75
  average time/residue: 0.0532
  time to fit residues: 4.9428
Evaluate side-chains
  73 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  126 CYS
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain D residue  130 SER
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.045741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.037653 restraints weight = 17576.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 4.65
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.5617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3045  Z= 0.206
  Angle     :  0.749   9.107   4145  Z= 0.390
  Chirality :  0.043   0.151    449
  Planarity :  0.004   0.034    528
  Dihedral  :  5.436  20.273    416
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  7.55 %
    Allowed  : 30.51 %
    Favored  : 61.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.43), residues: 374
  helix:  1.53 (0.99), residues: 32
  sheet: -0.73 (0.46), residues: 118
  loop : -0.54 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  24 
 TYR   0.032   0.002   TYR D 105 
 PHE   0.014   0.002   PHE B  84 
 TRP   0.011   0.002   TRP A  35 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 3039)
  covalent geometry    : angle       0.74856 ( 4133)
  SS BOND              : bond        0.00402 (    6)
  SS BOND              : angle       0.90265 (   12)
  hydrogen bonds       : bond        0.03400 (   93)
  hydrogen bonds       : angle       6.31263 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  177 LYS cc_start: 0.9335 (mtpt) cc_final: 0.8932 (mttp)
REVERT: D  150 ASP cc_start: 0.9061 (t0) cc_final: 0.8712 (t0)
REVERT: A   25 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8284 (p)
  outliers start: 25
  outliers final: 21
  residues processed: 79
  average time/residue: 0.0679
  time to fit residues: 6.4042
Evaluate side-chains
  74 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  126 CYS
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  130 SER
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  132 THR
Chi-restraints excluded: chain D residue  172 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue   98 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 32 optimal weight:    0.0010
   chunk 7 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7788

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

Flipped N/Q/H residues before XYZ refinement:
C 106 GLN
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 100 GLN
B   6 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.046599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.038434 restraints weight = 17832.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 4.81
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.5776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3045  Z= 0.150
  Angle     :  0.744   8.981   4145  Z= 0.385
  Chirality :  0.043   0.145    449
  Planarity :  0.004   0.032    528
  Dihedral  :  5.342  19.422    416
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  5.74 %
    Allowed  : 31.72 %
    Favored  : 62.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.43), residues: 374
  helix:  1.34 (0.98), residues: 32
  sheet: -0.57 (0.46), residues: 118
  loop : -0.50 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  24 
 TYR   0.029   0.002   TYR D 105 
 PHE   0.014   0.002   PHE B  84 
 TRP   0.012   0.001   TRP A  35 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3039)
  covalent geometry    : angle       0.74430 ( 4133)
  SS BOND              : bond        0.00352 (    6)
  SS BOND              : angle       0.74137 (   12)
  hydrogen bonds       : bond        0.03159 (   93)
  hydrogen bonds       : angle       6.19067 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  150 ASP cc_start: 0.8982 (t0) cc_final: 0.8608 (t0)
REVERT: A   22 CYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5738 (m)
REVERT: B   50 TYR cc_start: 0.7871 (p90) cc_final: 0.7605 (p90)
  outliers start: 19
  outliers final: 17
  residues processed: 75
  average time/residue: 0.0804
  time to fit residues: 7.1482
Evaluate side-chains
  71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 GLN
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  126 CYS
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  172 SER
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  130 SER
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   74 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.1980
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0040
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
C 106 GLN
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.046992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.038949 restraints weight = 17677.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 4.76
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.5856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   3045  Z= 0.150
  Angle     :  0.765   9.715   4145  Z= 0.393
  Chirality :  0.043   0.144    449
  Planarity :  0.004   0.035    528
  Dihedral  :  5.237  19.727    416
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 32.33 %
    Favored  : 62.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.43), residues: 374
  helix:  0.92 (0.97), residues: 32
  sheet: -0.51 (0.46), residues: 118
  loop : -0.56 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  24 
 TYR   0.028   0.002   TYR D 105 
 PHE   0.015   0.002   PHE B  84 
 TRP   0.012   0.001   TRP A  35 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3039)
  covalent geometry    : angle       0.76487 ( 4133)
  SS BOND              : bond        0.00369 (    6)
  SS BOND              : angle       0.65508 (   12)
  hydrogen bonds       : bond        0.03151 (   93)
  hydrogen bonds       : angle       6.13147 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  149 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8739 (tt0)
REVERT: C  177 LYS cc_start: 0.9294 (mtpt) cc_final: 0.9028 (mttp)
REVERT: D  150 ASP cc_start: 0.8901 (t0) cc_final: 0.8527 (t0)
REVERT: A   22 CYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5756 (m)
REVERT: A   25 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8405 (p)
REVERT: A   47 GLU cc_start: 0.8294 (pm20) cc_final: 0.8090 (pm20)
REVERT: A  116 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6885 (pp30)
REVERT: B   50 TYR cc_start: 0.7819 (p90) cc_final: 0.7561 (p90)
  outliers start: 17
  outliers final: 14
  residues processed: 72
  average time/residue: 0.0685
  time to fit residues: 5.9706
Evaluate side-chains
  71 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 GLN
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  126 CYS
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
C 106 GLN
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.046812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.038804 restraints weight = 17471.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 4.72
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.5938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3045  Z= 0.158
  Angle     :  0.750   8.864   4145  Z= 0.387
  Chirality :  0.043   0.143    449
  Planarity :  0.004   0.038    528
  Dihedral  :  5.180  19.737    416
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 32.63 %
    Favored  : 61.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.43), residues: 374
  helix:  0.95 (0.97), residues: 32
  sheet: -0.48 (0.46), residues: 118
  loop : -0.54 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  24 
 TYR   0.027   0.002   TYR D 105 
 PHE   0.014   0.002   PHE B  84 
 TRP   0.012   0.001   TRP A  35 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3039)
  covalent geometry    : angle       0.75035 ( 4133)
  SS BOND              : bond        0.00362 (    6)
  SS BOND              : angle       0.67720 (   12)
  hydrogen bonds       : bond        0.03174 (   93)
  hydrogen bonds       : angle       6.01598 (  228)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  149 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8715 (tt0)
REVERT: C  177 LYS cc_start: 0.9312 (mtpt) cc_final: 0.9014 (mttp)
REVERT: D  150 ASP cc_start: 0.8936 (t0) cc_final: 0.8545 (t0)
REVERT: A   22 CYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5791 (m)
REVERT: A   25 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8412 (p)
REVERT: A  116 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6851 (pp30)
REVERT: B   50 TYR cc_start: 0.7832 (p90) cc_final: 0.7566 (p90)
  outliers start: 18
  outliers final: 15
  residues processed: 73
  average time/residue: 0.0705
  time to fit residues: 6.1832
Evaluate side-chains
  73 residues out of total 331 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  106 GLN
Chi-restraints excluded: chain C residue  114 SER
Chi-restraints excluded: chain C residue  115 ASP
Chi-restraints excluded: chain C residue  126 CYS
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain C residue  154 SER
Chi-restraints excluded: chain C residue  180 CYS
Chi-restraints excluded: chain D residue  105 TYR
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   71 SER
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  116 GLN
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   59 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
C 106 GLN
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.045383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.037425 restraints weight = 17416.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 4.65
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.5981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   3045  Z= 0.257
  Angle     :  0.796   9.144   4145  Z= 0.414
  Chirality :  0.043   0.146    449
  Planarity :  0.004   0.045    528
  Dihedral  :  5.397  19.720    416
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 17.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 33.23 %
    Favored  : 61.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.43), residues: 374
  helix:  1.03 (0.97), residues: 32
  sheet: -0.50 (0.46), residues: 118
  loop : -0.48 (0.41), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  24 
 TYR   0.029   0.002   TYR D 178 
 PHE   0.013   0.002   PHE B  84 
 TRP   0.010   0.002   TRP A  35 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 ( 3039)
  covalent geometry    : angle       0.79549 ( 4133)
  SS BOND              : bond        0.00426 (    6)
  SS BOND              : angle       0.87203 (   12)
  hydrogen bonds       : bond        0.03571 (   93)
  hydrogen bonds       : angle       6.09067 (  228)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 788.39 seconds
wall clock time: 14 minutes 17.18 seconds (857.18 seconds total)