Starting phenix.real_space_refine
on Tue Feb  3 15:31:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uev_64093/02_2026/9uev_64093_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uev_64093/02_2026/9uev_64093.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uev_64093/02_2026/9uev_64093_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uev_64093/02_2026/9uev_64093_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uev_64093/02_2026/9uev_64093.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uev_64093/02_2026/9uev_64093.map"
  }
  resolution = 3.62
  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=  -0.006 sd=   0.293
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      37      5.16       5
     C    2681      2.51       5
     N     738      2.21       5
     O     841      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 4297
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2469
          Classifications: {'peptide': 321}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 302}
    Chain: "B"
      Number of atoms: 890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 890
          Classifications: {'peptide': 115}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 112}
    Chain: "C"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 938
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
  Time building chain proxies: 1.02, per 1000 atoms: 0.24
  Number of scatterers: 4297
  At special positions: 0
  Unit cell: (58.025, 74.905, 109.72, 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      37     16.00
     O     841      8.00
     N     738      7.00
     C    2681      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  49 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 143 " - pdb=" SG  CYS A 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 180 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 206 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 258 " - pdb=" SG  CYS A 305 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 303 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 280 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 287 " - pdb=" SG  CYS A 292 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " 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: 0.42
  Conformation dependent library (CDL) restraints added in 234.1 milliseconds
  

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  996

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 11 sheets defined
      19.0% alpha, 29.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 53
    Processing helix  chain 'A' and resid 54 through 65
    Processing helix  chain 'A' and resid 97 through 104
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 4.344A  pdb=" N   SER A 164 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 187 through 202
    Processing helix  chain 'A' and resid 252 through 254
      No H-bonds generated for 'chain 'A' and resid 252 through 254'
    Processing helix  chain 'A' and resid 267 through 278
      removed outlier: 3.590A  pdb=" N   GLY A 278 " --> pdb=" O   CYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 290
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.618A  pdb=" N   ASN B  31 " --> pdb=" O   THR B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 56
      removed outlier: 3.874A  pdb=" N   GLY B  56 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 53 through 56'
    Processing helix  chain 'B' and resid 88 through 92
      removed outlier: 3.576A  pdb=" N   THR B  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.633A  pdb=" N   SER C  31 " --> pdb=" O   THR C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 65
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.749A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83
      removed outlier: 6.522A  pdb=" N   SER A  81 " --> pdb=" O   TRP A 174 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   PHE A 129 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   ILE A 175 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   GLU A 131 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   LYS A 110 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   GLY A 142 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 149
    Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 180
      removed outlier: 6.548A  pdb=" N   MET A 334 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ILE A 208 " --> pdb=" O   MET A 334 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   THR A 336 " --> pdb=" O   CYS A 206 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 180
      removed outlier: 3.686A  pdb=" N   SER A 331 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   LEU A 221 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA A 228 " --> pdb=" O   MET A 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 248
      removed outlier: 3.713A  pdb=" N   LYS A 244 " --> pdb=" O   SER A 317 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 259
    Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 4
      removed outlier: 3.529A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 4
      removed outlier: 3.529A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR B  79 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   ASP B  74 " --> pdb=" O   THR B  79 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE B  72 " --> pdb=" O   TYR B  81 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.668A  pdb=" N   ALA B  49 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   ARG B  38 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   LEU B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 60
      removed outlier: 3.535A  pdb=" N   TYR C  59 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   ALA C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   MET C  34 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)

    137 hydrogen bonds defined for protein.
    342 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: 0.75

  Time building geometry restraints manager: 0.59 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: 1419
        1.35 -     1.46: 1095
        1.46 -     1.58: 1827
        1.58 -     1.70: 0
        1.70 -     1.82: 53
  Bond restraints: 4394
  Sorted by residual:
  bond pdb=" CB  GLU C   1 "
       pdb=" CG  GLU C   1 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.58e+00
  bond pdb=" CB  GLU B  44 "
       pdb=" CG  GLU B  44 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CB  LYS A 302 "
       pdb=" CG  LYS A 302 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.82e-01
  bond pdb=" CB  GLU C 111 "
       pdb=" CG  GLU C 111 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.72e-01
  bond pdb=" CB  GLN A  66 "
       pdb=" CG  GLN A  66 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.84e-01
  ... (remaining 4389 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 5838
        2.07 -     4.13: 88
        4.13 -     6.20: 6
        6.20 -     8.27: 3
        8.27 -    10.33: 1
  Bond angle restraints: 5936
  Sorted by residual:
  angle pdb=" CB  GLU C   1 "
        pdb=" CG  GLU C   1 "
        pdb=" CD  GLU C   1 "
      ideal   model   delta    sigma   weight residual
     112.60  118.42   -5.82 1.70e+00 3.46e-01 1.17e+01
  angle pdb=" CA  GLU C   1 "
        pdb=" CB  GLU C   1 "
        pdb=" CG  GLU C   1 "
      ideal   model   delta    sigma   weight residual
     114.10  120.44   -6.34 2.00e+00 2.50e-01 1.01e+01
  angle pdb=" CA  LEU C   4 "
        pdb=" CB  LEU C   4 "
        pdb=" CG  LEU C   4 "
      ideal   model   delta    sigma   weight residual
     116.30  126.63  -10.33 3.50e+00 8.16e-02 8.72e+00
  angle pdb=" CA  GLN A 215 "
        pdb=" CB  GLN A 215 "
        pdb=" CG  GLN A 215 "
      ideal   model   delta    sigma   weight residual
     114.10  119.15   -5.05 2.00e+00 2.50e-01 6.38e+00
  angle pdb=" N   GLY C 114 "
        pdb=" CA  GLY C 114 "
        pdb=" C   GLY C 114 "
      ideal   model   delta    sigma   weight residual
     112.85  108.80    4.05 1.61e+00 3.86e-01 6.34e+00
  ... (remaining 5931 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 2231
       17.81 -    35.61: 303
       35.61 -    53.42: 74
       53.42 -    71.23: 14
       71.23 -    89.03: 4
  Dihedral angle restraints: 2626
    sinusoidal: 1050
      harmonic: 1576
  Sorted by residual:
  dihedral pdb=" CB  CYS A 274 "
           pdb=" SG  CYS A 274 "
           pdb=" SG  CYS A 280 "
           pdb=" CB  CYS A 280 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.55  -64.45     1      1.00e+01 1.00e-02 5.46e+01
  dihedral pdb=" CB  CYS A 287 "
           pdb=" SG  CYS A 287 "
           pdb=" SG  CYS A 292 "
           pdb=" CB  CYS A 292 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -124.56   38.56     1      1.00e+01 1.00e-02 2.09e+01
  dihedral pdb=" CB  CYS A  26 "
           pdb=" SG  CYS A  26 "
           pdb=" SG  CYS A  49 "
           pdb=" CB  CYS A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.75   31.75     1      1.00e+01 1.00e-02 1.44e+01
  ... (remaining 2623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 364
       0.029 -    0.057: 162
       0.057 -    0.086: 53
       0.086 -    0.115: 40
       0.115 -    0.143: 2
  Chirality restraints: 621
  Sorted by residual:
  chirality pdb=" CA  ILE A  30 "
            pdb=" N   ILE A  30 "
            pdb=" C   ILE A  30 "
            pdb=" CB  ILE A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.15e-01
  chirality pdb=" CA  ILE A  38 "
            pdb=" N   ILE A  38 "
            pdb=" C   ILE A  38 "
            pdb=" CB  ILE A  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  VAL B 111 "
            pdb=" N   VAL B 111 "
            pdb=" C   VAL B 111 "
            pdb=" CB  VAL B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.26e-01
  ... (remaining 618 not shown)

  Planarity restraints: 774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 121 "   -0.034 5.00e-02 4.00e+02   5.06e-02 4.10e+00
        pdb=" N   PRO A 122 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 122 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 122 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C  46 "   -0.010 2.00e-02 2.50e+03   1.95e-02 3.80e+00
        pdb=" CD  GLU C  46 "    0.034 2.00e-02 2.50e+03
        pdb=" OE1 GLU C  46 "   -0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU C  46 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 186 "   -0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO A 187 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 187 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 187 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 771 not shown)

  Histogram of nonbonded interaction distances:
        2.47 -     2.96: 2010
        2.96 -     3.44: 4131
        3.44 -     3.93: 6916
        3.93 -     4.41: 8085
        4.41 -     4.90: 13182
  Nonbonded interactions: 34324
  Sorted by model distance:
  nonbonded pdb=" N   GLU C   1 "
            pdb=" OE1 GLU C   1 "
     model   vdw
     2.472 3.120
  nonbonded pdb=" N   ASP A 204 "
            pdb=" OD1 ASP A 204 "
     model   vdw
     2.518 3.120
  nonbonded pdb=" N   GLU B  44 "
            pdb=" OE1 GLU B  44 "
     model   vdw
     2.540 3.120
  nonbonded pdb=" N   GLU C  46 "
            pdb=" OE1 GLU C  46 "
     model   vdw
     2.566 3.120
  nonbonded pdb=" O   GLU C 111 "
            pdb=" O   TYR C 112 "
     model   vdw
     2.579 3.040
  ... (remaining 34319 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.730
  Set stop_for_unknowns flag:              0.010
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.400
  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:2.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
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      :  0.004   0.038   4404  Z= 0.171
  Angle     :  0.624  10.333   5956  Z= 0.326
  Chirality :  0.041   0.143    621
  Planarity :  0.004   0.051    774
  Dihedral  : 16.836  89.033   1600
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 24.57 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 (0.36), residues: 553
  helix:  1.06 (0.65), residues: 65
  sheet: -0.39 (0.47), residues: 133
  loop : -0.55 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 241 
 TYR   0.023   0.002   TYR C 112 
 PHE   0.014   0.002   PHE C  29 
 TRP   0.014   0.001   TRP C 113 
 HIS   0.003   0.001   HIS A 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 4394)
  covalent geometry    : angle       0.62115 ( 5936)
  SS BOND              : bond        0.00343 (   10)
  SS BOND              : angle       1.20596 (   20)
  hydrogen bonds       : bond        0.22754 (  132)
  hydrogen bonds       : angle       8.76385 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  106 MET cc_start: 0.9289 (mtt) cc_final: 0.8916 (mtt)
REVERT: A  208 ILE cc_start: 0.9111 (mt) cc_final: 0.8833 (mm)
REVERT: B    2 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9090 (p)
REVERT: B   71 MET cc_start: 0.8488 (ttt) cc_final: 0.8208 (ttt)
REVERT: B   92 THR cc_start: 0.8749 (m) cc_final: 0.8522 (t)
REVERT: C   67 ARG cc_start: 0.7711 (ptt180) cc_final: 0.7418 (ptt-90)
REVERT: C   80 TYR cc_start: 0.8710 (m-10) cc_final: 0.8477 (m-10)
  outliers start: 10
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0556
  time to fit residues: 6.2603
Evaluate side-chains
  89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   79 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0010
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS
A  68 GLN
C  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.051228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.045016 restraints weight = 15632.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.046503 restraints weight = 7445.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.047491 restraints weight = 4321.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.048160 restraints weight = 2889.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.048596 restraints weight = 2137.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4404  Z= 0.129
  Angle     :  0.550  11.141   5956  Z= 0.282
  Chirality :  0.040   0.135    621
  Planarity :  0.004   0.054    774
  Dihedral  :  5.982  53.699    624
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 22.86 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.41 (0.36), residues: 553
  helix:  1.23 (0.66), residues: 66
  sheet: -0.59 (0.44), residues: 142
  loop : -0.37 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  67 
 TYR   0.010   0.001   TYR C  59 
 PHE   0.011   0.002   PHE A 130 
 TRP   0.006   0.001   TRP B 105 
 HIS   0.002   0.001   HIS A 236 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4394)
  covalent geometry    : angle       0.54681 ( 5936)
  SS BOND              : bond        0.00293 (   10)
  SS BOND              : angle       1.13923 (   20)
  hydrogen bonds       : bond        0.03574 (  132)
  hydrogen bonds       : angle       5.97943 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  106 MET cc_start: 0.9298 (mtt) cc_final: 0.8889 (mtt)
REVERT: B    4 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8836 (mt)
REVERT: C    5 VAL cc_start: 0.8413 (t) cc_final: 0.8196 (m)
  outliers start: 24
  outliers final: 10
  residues processed: 101
  average time/residue: 0.0777
  time to fit residues: 9.7363
Evaluate side-chains
  91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  213 PHE
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.2804 r_free = 0.2804 target = 0.050277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.044072 restraints weight = 15470.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.045585 restraints weight = 7408.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.046557 restraints weight = 4331.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.047217 restraints weight = 2918.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.047650 restraints weight = 2164.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   4404  Z= 0.158
  Angle     :  0.572  10.349   5956  Z= 0.294
  Chirality :  0.041   0.139    621
  Planarity :  0.004   0.054    774
  Dihedral  :  5.608  52.364    616
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 21.79 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.54 (0.35), residues: 553
  helix:  1.25 (0.65), residues: 66
  sheet: -0.69 (0.43), residues: 138
  loop : -0.49 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  74 
 TYR   0.011   0.001   TYR B 104 
 PHE   0.011   0.002   PHE A 130 
 TRP   0.010   0.001   TRP B 105 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4394)
  covalent geometry    : angle       0.56864 ( 5936)
  SS BOND              : bond        0.00347 (   10)
  SS BOND              : angle       1.22358 (   20)
  hydrogen bonds       : bond        0.03277 (  132)
  hydrogen bonds       : angle       5.48596 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.171 
Fit side-chains
REVERT: B   60 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8196 (tt0)
REVERT: B   61 TYR cc_start: 0.8974 (m-80) cc_final: 0.8755 (m-10)
REVERT: C    5 VAL cc_start: 0.8487 (t) cc_final: 0.8258 (m)
REVERT: C   89 GLU cc_start: 0.7958 (pp20) cc_final: 0.7743 (pp20)
  outliers start: 25
  outliers final: 18
  residues processed: 102
  average time/residue: 0.0822
  time to fit residues: 10.2633
Evaluate side-chains
  98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  213 PHE
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   60 GLU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0000
   chunk 0 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.2810 r_free = 0.2810 target = 0.050474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.044314 restraints weight = 15304.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.045786 restraints weight = 7349.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.046762 restraints weight = 4300.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.047425 restraints weight = 2890.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.047871 restraints weight = 2140.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4404  Z= 0.143
  Angle     :  0.554  10.062   5956  Z= 0.286
  Chirality :  0.041   0.139    621
  Planarity :  0.004   0.051    774
  Dihedral  :  5.556  51.761    616
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 22.44 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.40 (0.36), residues: 553
  helix:  1.34 (0.65), residues: 66
  sheet: -0.65 (0.41), residues: 154
  loop : -0.33 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  74 
 TYR   0.010   0.001   TYR B 104 
 PHE   0.010   0.002   PHE C  47 
 TRP   0.007   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4394)
  covalent geometry    : angle       0.55053 ( 5936)
  SS BOND              : bond        0.00326 (   10)
  SS BOND              : angle       1.16087 (   20)
  hydrogen bonds       : bond        0.02993 (  132)
  hydrogen bonds       : angle       5.26718 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.175 
Fit side-chains
REVERT: B   60 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8192 (tt0)
REVERT: B   61 TYR cc_start: 0.8952 (m-80) cc_final: 0.8720 (m-10)
REVERT: C    5 VAL cc_start: 0.8495 (t) cc_final: 0.8279 (m)
REVERT: C   89 GLU cc_start: 0.7959 (pp20) cc_final: 0.7740 (pp20)
  outliers start: 23
  outliers final: 15
  residues processed: 96
  average time/residue: 0.0587
  time to fit residues: 7.1016
Evaluate side-chains
  94 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   60 GLU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  107 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    0.0040
   chunk 18 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.0998

-------------------------------------------------------------------------------
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 = 0.2776 r_free = 0.2776 target = 0.049385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.043215 restraints weight = 15675.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.044705 restraints weight = 7541.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.045682 restraints weight = 4438.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.046344 restraints weight = 2995.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.046772 restraints weight = 2223.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4404  Z= 0.198
  Angle     :  0.604   9.715   5956  Z= 0.314
  Chirality :  0.042   0.144    621
  Planarity :  0.005   0.056    774
  Dihedral  :  5.628  50.023    615
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 22.22 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.50 (0.35), residues: 553
  helix:  1.15 (0.64), residues: 66
  sheet: -0.59 (0.43), residues: 141
  loop : -0.46 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  74 
 TYR   0.010   0.002   TYR B 104 
 PHE   0.014   0.002   PHE C  47 
 TRP   0.009   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 4394)
  covalent geometry    : angle       0.60040 ( 5936)
  SS BOND              : bond        0.00363 (   10)
  SS BOND              : angle       1.29725 (   20)
  hydrogen bonds       : bond        0.03191 (  132)
  hydrogen bonds       : angle       5.23448 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8679 (t0)
REVERT: B   60 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8092 (tt0)
REVERT: B   61 TYR cc_start: 0.8958 (m-80) cc_final: 0.8712 (m-10)
  outliers start: 25
  outliers final: 17
  residues processed: 95
  average time/residue: 0.0490
  time to fit residues: 5.8945
Evaluate side-chains
  96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   37 ASP
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   60 GLU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0670
   overall best weight:    0.9322

-------------------------------------------------------------------------------
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 = 0.2783 r_free = 0.2783 target = 0.049677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.043489 restraints weight = 15658.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.044984 restraints weight = 7541.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.045982 restraints weight = 4413.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.046647 restraints weight = 2950.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.047073 restraints weight = 2180.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4404  Z= 0.175
  Angle     :  0.596   9.599   5956  Z= 0.309
  Chirality :  0.041   0.145    621
  Planarity :  0.005   0.056    774
  Dihedral  :  5.590  48.866    615
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 23.72 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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 (0.35), residues: 553
  helix:  1.31 (0.64), residues: 66
  sheet: -0.61 (0.42), residues: 141
  loop : -0.46 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  74 
 TYR   0.011   0.002   TYR C  32 
 PHE   0.013   0.002   PHE C  47 
 TRP   0.007   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 4394)
  covalent geometry    : angle       0.59246 ( 5936)
  SS BOND              : bond        0.00329 (   10)
  SS BOND              : angle       1.20820 (   20)
  hydrogen bonds       : bond        0.03014 (  132)
  hydrogen bonds       : angle       5.13289 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8129 (tt0)
REVERT: B   61 TYR cc_start: 0.8933 (m-80) cc_final: 0.8683 (m-10)
REVERT: C   38 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8683 (ptm160)
  outliers start: 20
  outliers final: 16
  residues processed: 91
  average time/residue: 0.0639
  time to fit residues: 7.2561
Evaluate side-chains
  95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   60 GLU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   38 ARG
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.048960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.042802 restraints weight = 15581.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.044276 restraints weight = 7540.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.045273 restraints weight = 4427.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.045912 restraints weight = 2962.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.046328 restraints weight = 2210.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4404  Z= 0.206
  Angle     :  0.630   9.605   5956  Z= 0.327
  Chirality :  0.042   0.151    621
  Planarity :  0.005   0.059    774
  Dihedral  :  5.342  45.151    613
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 23.08 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.54 (0.35), residues: 553
  helix:  1.16 (0.64), residues: 66
  sheet: -0.64 (0.42), residues: 141
  loop : -0.49 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  74 
 TYR   0.015   0.002   TYR C  32 
 PHE   0.012   0.002   PHE C  47 
 TRP   0.009   0.001   TRP A 141 
 HIS   0.004   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 4394)
  covalent geometry    : angle       0.62708 ( 5936)
  SS BOND              : bond        0.00379 (   10)
  SS BOND              : angle       1.28850 (   20)
  hydrogen bonds       : bond        0.03179 (  132)
  hydrogen bonds       : angle       5.16137 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8575 (t0)
REVERT: A  117 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8206 (mtt)
REVERT: B   60 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8124 (tt0)
REVERT: B   61 TYR cc_start: 0.8941 (m-80) cc_final: 0.8689 (m-10)
  outliers start: 25
  outliers final: 17
  residues processed: 93
  average time/residue: 0.0486
  time to fit residues: 5.6607
Evaluate side-chains
  96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   37 ASP
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   60 GLU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  102 THR
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   13 GLN
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue  107 MET
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0970
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.049907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2617 r_free = 0.2617 target = 0.043717 restraints weight = 15220.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.045210 restraints weight = 7313.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.046188 restraints weight = 4271.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.046846 restraints weight = 2871.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.047272 restraints weight = 2129.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4404  Z= 0.151
  Angle     :  0.609   9.492   5956  Z= 0.311
  Chirality :  0.041   0.145    621
  Planarity :  0.004   0.054    774
  Dihedral  :  4.815  38.439    611
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.57 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.48 (0.35), residues: 553
  helix:  1.37 (0.64), residues: 66
  sheet: -0.65 (0.40), residues: 152
  loop : -0.44 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 304 
 TYR   0.016   0.001   TYR C  32 
 PHE   0.011   0.001   PHE C  47 
 TRP   0.007   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 4394)
  covalent geometry    : angle       0.60686 ( 5936)
  SS BOND              : bond        0.00287 (   10)
  SS BOND              : angle       1.13323 (   20)
  hydrogen bonds       : bond        0.02890 (  132)
  hydrogen bonds       : angle       5.05668 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8101 (mtt)
REVERT: B   60 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8068 (tt0)
REVERT: B   61 TYR cc_start: 0.8932 (m-80) cc_final: 0.8685 (m-10)
  outliers start: 19
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0597
  time to fit residues: 6.6799
Evaluate side-chains
  94 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue  117 MET
Chi-restraints excluded: chain A residue  143 CYS
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   60 GLU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   13 GLN
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0170
   chunk 37 optimal weight:    0.3980
   chunk 16 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
B 107 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.050821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.044606 restraints weight = 15288.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.046112 restraints weight = 7328.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.047106 restraints weight = 4256.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.047777 restraints weight = 2852.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.048225 restraints weight = 2096.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4404  Z= 0.120
  Angle     :  0.598   9.267   5956  Z= 0.303
  Chirality :  0.041   0.140    621
  Planarity :  0.004   0.050    774
  Dihedral  :  4.628  38.051    611
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 25.64 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.29 (0.36), residues: 553
  helix:  1.47 (0.64), residues: 66
  sheet: -0.44 (0.42), residues: 159
  loop : -0.34 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 304 
 TYR   0.017   0.001   TYR C  32 
 PHE   0.010   0.001   PHE C  47 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4394)
  covalent geometry    : angle       0.59573 ( 5936)
  SS BOND              : bond        0.00237 (   10)
  SS BOND              : angle       1.02176 (   20)
  hydrogen bonds       : bond        0.02693 (  132)
  hydrogen bonds       : angle       4.94442 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8138 (tt0)
  outliers start: 15
  outliers final: 12
  residues processed: 87
  average time/residue: 0.0665
  time to fit residues: 6.9401
Evaluate side-chains
  87 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   60 GLU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue  107 GLN
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   13 GLN
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue   83 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0980
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0020
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.4388

-------------------------------------------------------------------------------
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 = 0.2828 r_free = 0.2828 target = 0.051178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.045008 restraints weight = 15114.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.046509 restraints weight = 7226.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.047506 restraints weight = 4198.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.048153 restraints weight = 2785.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.048609 restraints weight = 2066.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4404  Z= 0.122
  Angle     :  0.615   9.528   5956  Z= 0.312
  Chirality :  0.041   0.151    621
  Planarity :  0.004   0.050    774
  Dihedral  :  4.592  37.912    611
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 25.43 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.25 (0.36), residues: 553
  helix:  1.48 (0.64), residues: 66
  sheet: -0.36 (0.41), residues: 159
  loop : -0.34 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 281 
 TYR   0.017   0.001   TYR C  32 
 PHE   0.009   0.001   PHE C  47 
 TRP   0.006   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4394)
  covalent geometry    : angle       0.61300 ( 5936)
  SS BOND              : bond        0.00235 (   10)
  SS BOND              : angle       0.98887 (   20)
  hydrogen bonds       : bond        0.02670 (  132)
  hydrogen bonds       : angle       4.90957 (  342)

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

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

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1106 Ramachandran restraints generated.
    553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: B   60 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7994 (tt0)
  outliers start: 14
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0786
  time to fit residues: 8.3348
Evaluate side-chains
  88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   60 GLU
Chi-restraints excluded: chain B residue   77 ARG
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue   13 GLN
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain C residue   70 ILE
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  117 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.050037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.043792 restraints weight = 15249.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.045303 restraints weight = 7334.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.046301 restraints weight = 4290.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.046967 restraints weight = 2862.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.047405 restraints weight = 2114.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4404  Z= 0.169
  Angle     :  0.637   9.412   5956  Z= 0.326
  Chirality :  0.042   0.150    621
  Planarity :  0.004   0.051    774
  Dihedral  :  4.797  38.828    611
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.98 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 25.64 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    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: -0.49 (0.35), residues: 553
  helix:  1.32 (0.63), residues: 66
  sheet: -0.71 (0.40), residues: 152
  loop : -0.40 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 281 
 TYR   0.020   0.002   TYR B  61 
 PHE   0.010   0.001   PHE C  47 
 TRP   0.008   0.001   TRP A 141 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 4394)
  covalent geometry    : angle       0.63490 ( 5936)
  SS BOND              : bond        0.00323 (   10)
  SS BOND              : angle       1.14974 (   20)
  hydrogen bonds       : bond        0.02854 (  132)
  hydrogen bonds       : angle       4.97778 (  342)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 740.82 seconds
wall clock time: 13 minutes 31.10 seconds (811.10 seconds total)