Starting phenix.real_space_refine
on Fri Aug 22 18:36:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rlb_19337/08_2025/8rlb_19337.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rlb_19337/08_2025/8rlb_19337.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rlb_19337/08_2025/8rlb_19337.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rlb_19337/08_2025/8rlb_19337.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rlb_19337/08_2025/8rlb_19337.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rlb_19337/08_2025/8rlb_19337.cif"
  }
  resolution = 2.99
  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=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2231      2.51       5
     N     614      2.21       5
     O     696      1.98       5
     H    3337      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6894
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 3450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 3450
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 10, 'TRANS': 214}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 1699
          Classifications: {'peptide': 114}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "K"
      Number of atoms: 1745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1745
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
  Time building chain proxies: 1.42, per 1000 atoms: 0.21
  Number of scatterers: 6894
  At special positions: 0
  Unit cell: (63.08, 84.66, 78.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     O     696      8.00
     N     614      7.00
     C    2231      6.00
     H    3337      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  11 " - pdb=" SG  CYS K  11 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  92 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 212.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  832

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 6 sheets defined
      6.9% alpha, 43.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 9
    Processing helix  chain 'B' and resid 56 through 65
      removed outlier: 3.816A  pdb=" N   LEU B  60 " --> pdb=" O   PRO B  56 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   THR B  62 " --> pdb=" O   PRO B  58 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   THR B  63 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 81
    Processing helix  chain 'B' and resid 82 through 88
    Processing helix  chain 'D' and resid 83 through 88
      removed outlier: 4.464A  pdb=" N   ALA D  88 " --> pdb=" O   GLU D  85 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 22
      removed outlier: 5.496A  pdb=" N   ASN B 149 " --> pdb=" O   LYS B 166 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   LYS B 166 " --> pdb=" O   ASN B 149 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE B 161 " --> pdb=" O   ASN B 185 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 59
      removed outlier: 5.145A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'K' and resid 30 through 31
      removed outlier: 3.881A  pdb=" N   SER K  30 " --> pdb=" O   TYR K 101 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR K 101 " --> pdb=" O   SER K  30 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ARG K  33 " --> pdb=" O   TYR K  98 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   MET K  34 " --> pdb=" O   ALA K  50 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ALA K  50 " --> pdb=" O   MET K  34 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   TRP K  36 " --> pdb=" O   VAL K  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 30 through 31
      removed outlier: 3.881A  pdb=" N   SER K  30 " --> pdb=" O   TYR K 101 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   TYR K 101 " --> pdb=" O   SER K  30 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   TYR K  98 " --> pdb=" O   TYR K 114 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   TYR K 114 " --> pdb=" O   TYR K  98 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   THR K 100 " --> pdb=" O   ASP K 112 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ASP K 112 " --> pdb=" O   THR K 100 " (cutoff:3.500A)

    156 hydrogen bonds defined for protein.
    396 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: 1.39

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3335
        1.03 -     1.23: 3
        1.23 -     1.42: 1583
        1.42 -     1.62: 2025
        1.62 -     1.81: 26
  Bond restraints: 6972
  Sorted by residual:
  bond pdb=" N   VAL B 206 "
       pdb=" CA  VAL B 206 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.032 1.17e-02 7.31e+03 7.70e+00
  bond pdb=" N   LEU B 207 "
       pdb=" CA  LEU B 207 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.19e-02 7.06e+03 6.81e+00
  bond pdb=" N   THR B 203 "
       pdb=" H   THR B 203 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.64e+00
  bond pdb=" N   SER B 205 "
       pdb=" H   SER B 205 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.43e+00
  bond pdb=" N   VAL B 206 "
       pdb=" H   VAL B 206 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.43e+00
  ... (remaining 6967 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.90: 11489
        0.90 -     1.80: 936
        1.80 -     2.70: 45
        2.70 -     3.60: 23
        3.60 -     4.50: 10
  Bond angle restraints: 12503
  Sorted by residual:
  angle pdb=" CA  THR B 203 "
        pdb=" C   THR B 203 "
        pdb=" O   THR B 203 "
      ideal   model   delta    sigma   weight residual
     120.70  116.93    3.77 1.08e+00 8.57e-01 1.22e+01
  angle pdb=" CA  VAL B 206 "
        pdb=" C   VAL B 206 "
        pdb=" O   VAL B 206 "
      ideal   model   delta    sigma   weight residual
     120.39  117.29    3.10 1.05e+00 9.07e-01 8.73e+00
  angle pdb=" CA  GLN B 204 "
        pdb=" C   GLN B 204 "
        pdb=" O   GLN B 204 "
      ideal   model   delta    sigma   weight residual
     120.30  117.21    3.09 1.07e+00 8.73e-01 8.34e+00
  angle pdb=" CA  LEU B 207 "
        pdb=" C   LEU B 207 "
        pdb=" O   LEU B 207 "
      ideal   model   delta    sigma   weight residual
     121.16  118.05    3.11 1.13e+00 7.83e-01 7.55e+00
  angle pdb=" CA  SER B 205 "
        pdb=" C   SER B 205 "
        pdb=" O   SER B 205 "
      ideal   model   delta    sigma   weight residual
     120.36  117.60    2.76 1.08e+00 8.57e-01 6.53e+00
  ... (remaining 12498 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.58: 2994
       15.58 -    31.16: 228
       31.16 -    46.74: 68
       46.74 -    62.31: 31
       62.31 -    77.89: 4
  Dihedral angle restraints: 3325
    sinusoidal: 1759
      harmonic: 1566
  Sorted by residual:
  dihedral pdb=" CB  CYS D  11 "
           pdb=" SG  CYS D  11 "
           pdb=" SG  CYS K  11 "
           pdb=" CB  CYS K  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.55   50.55     1      1.00e+01 1.00e-02 3.50e+01
  dihedral pdb=" CB  MET B 218 "
           pdb=" CG  MET B 218 "
           pdb=" SD  MET B 218 "
           pdb=" CE  MET B 218 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -105.65   45.65     3      1.50e+01 4.44e-03 8.21e+00
  dihedral pdb=" CB  GLU D  46 "
           pdb=" CG  GLU D  46 "
           pdb=" CD  GLU D  46 "
           pdb=" OE1 GLU D  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   76.55  -76.55     1      3.00e+01 1.11e-03 8.19e+00
  ... (remaining 3322 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 374
       0.038 -    0.077: 97
       0.077 -    0.115: 48
       0.115 -    0.153: 8
       0.153 -    0.192: 2
  Chirality restraints: 529
  Sorted by residual:
  chirality pdb=" CA  VAL B 206 "
            pdb=" N   VAL B 206 "
            pdb=" C   VAL B 206 "
            pdb=" CB  VAL B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CA  ILE B 152 "
            pdb=" N   ILE B 152 "
            pdb=" C   ILE B 152 "
            pdb=" CB  ILE B 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  GLN B 204 "
            pdb=" N   GLN B 204 "
            pdb=" C   GLN B 204 "
            pdb=" CB  GLN B 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.37e-01
  ... (remaining 526 not shown)

  Planarity restraints: 1093
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 204 "    0.076 2.00e-02 2.50e+03   8.00e-02 9.61e+01
        pdb=" CD  GLN B 204 "   -0.007 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 204 "   -0.072 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 204 "   -0.000 2.00e-02 2.50e+03
        pdb="HE21 GLN B 204 "   -0.116 2.00e-02 2.50e+03
        pdb="HE22 GLN B 204 "    0.118 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 210 "    0.023 5.00e-02 4.00e+02   3.49e-02 1.94e+00
        pdb=" N   PRO B 211 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 211 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 211 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 181 "    0.003 2.00e-02 2.50e+03   8.42e-03 1.59e+00
        pdb=" CG  HIS B 181 "   -0.019 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 181 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 181 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 181 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 181 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 HIS B 181 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 HIS B 181 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 HIS B 181 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1090 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 597
        2.22 -     2.82: 14619
        2.82 -     3.41: 17841
        3.41 -     4.01: 24749
        4.01 -     4.60: 36891
  Nonbonded interactions: 94697
  Sorted by model distance:
  nonbonded pdb=" O   CYS B  70 "
            pdb=" HZ1 LYS B  85 "
     model   vdw
     1.626 2.450
  nonbonded pdb=" HZ2 LYS B 166 "
            pdb=" OD1 ASP B 180 "
     model   vdw
     1.649 2.450
  nonbonded pdb=" O   PRO B  56 "
            pdb=" HG1 THR B  59 "
     model   vdw
     1.733 2.450
  nonbonded pdb=" O   GLU B 213 "
            pdb=" HE2 HIS B 217 "
     model   vdw
     1.734 2.450
  nonbonded pdb=" OE2 GLU B 115 "
            pdb="HH12 ARG B 122 "
     model   vdw
     1.756 2.450
  ... (remaining 94692 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=0.00 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:             4.520
  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:             0.030
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.420
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
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      :  0.002   0.032   3637  Z= 0.135
  Angle     :  0.485   4.500   4934  Z= 0.277
  Chirality :  0.045   0.192    529
  Planarity :  0.003   0.035    650
  Dihedral  : 12.441  77.892   1297
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  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 aren not related in a simple way.
  whole:  0.25 (0.40), residues: 457
  helix: -0.71 (1.32), residues: 19
  sheet:  0.47 (0.36), residues: 207
  loop :  0.08 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  19 
 TYR   0.011   0.001   TYR K  37 
 PHE   0.011   0.001   PHE D  67 
 TRP   0.005   0.001   TRP D 101 
 HIS   0.015   0.002   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 3635)
  covalent geometry    : angle       0.48447 ( 4930)
  SS BOND              : bond        0.00101 (    2)
  SS BOND              : angle       1.08925 (    4)
  hydrogen bonds       : bond        0.10021 (  156)
  hydrogen bonds       : angle       6.80497 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   67 PHE cc_start: 0.6260 (m-10) cc_final: 0.5750 (m-10)
REVERT: D   82 MET cc_start: 0.7550 (mmm) cc_final: 0.7293 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.8403
  time to fit residues: 90.2632
Evaluate side-chains
  93 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0770
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.145865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.133821 restraints weight = 17287.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.92
r_work: 0.3834 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3637  Z= 0.178
  Angle     :  0.579   5.957   4934  Z= 0.306
  Chirality :  0.047   0.141    529
  Planarity :  0.005   0.041    650
  Dihedral  :  4.117  13.807    505
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.24 %
    Favored  : 84.86 %
  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 aren not related in a simple way.
  whole:  0.26 (0.41), residues: 457
  helix:  0.02 (1.57), residues: 13
  sheet:  0.37 (0.36), residues: 211
  loop :  0.13 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  71 
 TYR   0.012   0.002   TYR B 143 
 PHE   0.013   0.002   PHE B  84 
 TRP   0.004   0.001   TRP D  36 
 HIS   0.005   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 3635)
  covalent geometry    : angle       0.57778 ( 4930)
  SS BOND              : bond        0.01486 (    2)
  SS BOND              : angle       1.33211 (    4)
  hydrogen bonds       : bond        0.03394 (  156)
  hydrogen bonds       : angle       6.15375 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 3
  residues processed: 111
  average time/residue: 0.7334
  time to fit residues: 84.5112
Evaluate side-chains
  100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 HIS
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain D residue   58 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0470
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.136276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.124135 restraints weight = 17353.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 2.80
r_work: 0.3682 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3637  Z= 0.220
  Angle     :  0.603   5.651   4934  Z= 0.325
  Chirality :  0.048   0.167    529
  Planarity :  0.005   0.053    650
  Dihedral  :  4.754  16.292    505
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 15.68 %
    Favored  : 81.35 %
  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 aren not related in a simple way.
  whole: -0.24 (0.39), residues: 457
  helix: -0.58 (1.49), residues: 13
  sheet:  0.07 (0.36), residues: 212
  loop : -0.23 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K  71 
 TYR   0.019   0.002   TYR B 143 
 PHE   0.025   0.003   PHE K  67 
 TRP   0.009   0.002   TRP K 115 
 HIS   0.006   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 3635)
  covalent geometry    : angle       0.60137 ( 4930)
  SS BOND              : bond        0.00306 (    2)
  SS BOND              : angle       1.51643 (    4)
  hydrogen bonds       : bond        0.03788 (  156)
  hydrogen bonds       : angle       6.40645 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   17 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8459 (m)
REVERT: K   34 MET cc_start: 0.7713 (mmt) cc_final: 0.7387 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 105
  average time/residue: 0.8320
  time to fit residues: 90.4939
Evaluate side-chains
  107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain K residue   35 THR
Chi-restraints excluded: chain K residue   48 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 43 optimal weight:    0.4980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
** D  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
** K  76 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.135342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.123423 restraints weight = 17652.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.78
r_work: 0.3685 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3637  Z= 0.171
  Angle     :  0.560   5.915   4934  Z= 0.297
  Chirality :  0.046   0.157    529
  Planarity :  0.004   0.047    650
  Dihedral  :  4.545  15.965    505
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 19.73 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.40), residues: 457
  helix: -1.02 (1.49), residues: 13
  sheet:  0.03 (0.36), residues: 211
  loop : -0.24 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  19 
 TYR   0.022   0.002   TYR B 143 
 PHE   0.011   0.002   PHE K  67 
 TRP   0.008   0.001   TRP K 115 
 HIS   0.003   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 3635)
  covalent geometry    : angle       0.55956 ( 4930)
  SS BOND              : bond        0.00314 (    2)
  SS BOND              : angle       0.76593 (    4)
  hydrogen bonds       : bond        0.03281 (  156)
  hydrogen bonds       : angle       6.28142 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 GLN cc_start: 0.7723 (mt0) cc_final: 0.7402 (mp10)
REVERT: D   17 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8454 (m)
REVERT: K   34 MET cc_start: 0.7655 (mmt) cc_final: 0.7357 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 99
  average time/residue: 0.8249
  time to fit residues: 84.5961
Evaluate side-chains
  99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain K residue   35 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0470
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.3878

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

Flipped N/Q/H residues before XYZ refinement:
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
** D  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
** K  76 ASN ** 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 = 0.3944 r_free = 0.3944 target = 0.137387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.124844 restraints weight = 17402.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.90
r_work: 0.3677 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3637  Z= 0.145
  Angle     :  0.538   5.740   4934  Z= 0.287
  Chirality :  0.046   0.154    529
  Planarity :  0.004   0.047    650
  Dihedral  :  4.442  15.847    505
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 22.43 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.40), residues: 457
  helix: -1.01 (1.52), residues: 13
  sheet: -0.05 (0.36), residues: 212
  loop : -0.23 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  19 
 TYR   0.010   0.001   TYR B 143 
 PHE   0.009   0.001   PHE K  67 
 TRP   0.007   0.001   TRP K 115 
 HIS   0.002   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3635)
  covalent geometry    : angle       0.53795 ( 4930)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       0.60608 (    4)
  hydrogen bonds       : bond        0.03070 (  156)
  hydrogen bonds       : angle       6.23959 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LEU cc_start: 0.7672 (mm) cc_final: 0.7448 (mt)
REVERT: D   17 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8480 (m)
REVERT: K   34 MET cc_start: 0.7648 (mmt) cc_final: 0.7347 (mmm)
  outliers start: 4
  outliers final: 2
  residues processed: 98
  average time/residue: 0.8432
  time to fit residues: 85.7248
Evaluate side-chains
  100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain K residue   35 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0770
   chunk 41 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  32 ASN
** K  76 ASN ** 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 = 0.3907 r_free = 0.3907 target = 0.133719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.121378 restraints weight = 17437.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3743 rms_B_bonded: 2.85
r_work: 0.3650 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.4670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3637  Z= 0.190
  Angle     :  0.573   6.301   4934  Z= 0.305
  Chirality :  0.046   0.154    529
  Planarity :  0.005   0.049    650
  Dihedral  :  4.612  16.024    505
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.43 %
    Favored  : 75.95 %
  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 aren not related in a simple way.
  whole: -0.58 (0.39), residues: 457
  helix: -1.51 (1.41), residues: 13
  sheet: -0.14 (0.36), residues: 212
  loop : -0.43 (0.40), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  80 
 TYR   0.016   0.001   TYR B  92 
 PHE   0.010   0.002   PHE K  67 
 TRP   0.008   0.002   TRP K 115 
 HIS   0.002   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 3635)
  covalent geometry    : angle       0.57262 ( 4930)
  SS BOND              : bond        0.00364 (    2)
  SS BOND              : angle       0.86208 (    4)
  hydrogen bonds       : bond        0.03332 (  156)
  hydrogen bonds       : angle       6.33089 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LEU cc_start: 0.7822 (mm) cc_final: 0.7611 (mt)
REVERT: D   17 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8540 (m)
REVERT: K   34 MET cc_start: 0.7623 (mmt) cc_final: 0.7341 (mmm)
  outliers start: 6
  outliers final: 2
  residues processed: 104
  average time/residue: 0.8985
  time to fit residues: 96.5761
Evaluate side-chains
  102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain K residue   35 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 41 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.2980
   chunk 33 optimal weight:    0.1980
   chunk 0 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.136244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.123604 restraints weight = 17131.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.95
r_work: 0.3659 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.4729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3637  Z= 0.145
  Angle     :  0.554   6.082   4934  Z= 0.292
  Chirality :  0.046   0.154    529
  Planarity :  0.004   0.046    650
  Dihedral  :  4.518  17.272    505
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 22.70 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.39), residues: 457
  helix: -1.64 (1.36), residues: 13
  sheet: -0.19 (0.36), residues: 212
  loop : -0.40 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  19 
 TYR   0.013   0.001   TYR B  92 
 PHE   0.007   0.001   PHE B  46 
 TRP   0.008   0.001   TRP D 101 
 HIS   0.003   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3635)
  covalent geometry    : angle       0.55439 ( 4930)
  SS BOND              : bond        0.00276 (    2)
  SS BOND              : angle       0.58856 (    4)
  hydrogen bonds       : bond        0.03015 (  156)
  hydrogen bonds       : angle       6.29656 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LEU cc_start: 0.7831 (mm) cc_final: 0.7624 (mt)
REVERT: D   17 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8566 (m)
REVERT: K   34 MET cc_start: 0.7651 (mmt) cc_final: 0.7375 (mmm)
REVERT: K  117 GLN cc_start: 0.7686 (pm20) cc_final: 0.7391 (pm20)
  outliers start: 4
  outliers final: 1
  residues processed: 100
  average time/residue: 0.8503
  time to fit residues: 88.0418
Evaluate side-chains
  99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain K residue   35 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0570
   chunk 13 optimal weight:    0.9990
   chunk 42 optimal weight:    0.4980
   chunk 16 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 ASN ** 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 = 0.3902 r_free = 0.3902 target = 0.133301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.121091 restraints weight = 17466.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.79
r_work: 0.3651 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3637  Z= 0.179
  Angle     :  0.582   6.356   4934  Z= 0.306
  Chirality :  0.046   0.157    529
  Planarity :  0.005   0.047    650
  Dihedral  :  4.666  16.971    505
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 22.97 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.39), residues: 457
  helix: -1.66 (1.41), residues: 13
  sheet: -0.24 (0.36), residues: 212
  loop : -0.44 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  19 
 TYR   0.018   0.002   TYR B  92 
 PHE   0.009   0.002   PHE B 223 
 TRP   0.011   0.002   TRP D 101 
 HIS   0.002   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 3635)
  covalent geometry    : angle       0.58214 ( 4930)
  SS BOND              : bond        0.00461 (    2)
  SS BOND              : angle       0.77764 (    4)
  hydrogen bonds       : bond        0.03218 (  156)
  hydrogen bonds       : angle       6.34052 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   96 ARG cc_start: 0.6806 (mtp85) cc_final: 0.6364 (ttm-80)
REVERT: B  178 LEU cc_start: 0.7995 (mm) cc_final: 0.7782 (mt)
REVERT: K   34 MET cc_start: 0.7821 (mmt) cc_final: 0.7543 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 103
  average time/residue: 0.7970
  time to fit residues: 85.1089
Evaluate side-chains
  102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain K residue   35 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 23 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:
B  81 HIS
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
** D  95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  76 ASN ** 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 = 0.3884 r_free = 0.3884 target = 0.131689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.119333 restraints weight = 17390.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3716 rms_B_bonded: 2.78
r_work: 0.3627 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3637  Z= 0.220
  Angle     :  0.637   7.729   4934  Z= 0.334
  Chirality :  0.048   0.155    529
  Planarity :  0.005   0.052    650
  Dihedral  :  4.880  15.993    505
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 23.51 %
    Favored  : 75.41 %
  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 aren not related in a simple way.
  whole: -0.77 (0.39), residues: 457
  helix: -1.80 (1.38), residues: 13
  sheet: -0.34 (0.35), residues: 213
  loop : -0.47 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  19 
 TYR   0.020   0.002   TYR B  92 
 PHE   0.011   0.002   PHE B 223 
 TRP   0.011   0.002   TRP D 101 
 HIS   0.003   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 3635)
  covalent geometry    : angle       0.63632 ( 4930)
  SS BOND              : bond        0.00465 (    2)
  SS BOND              : angle       0.94784 (    4)
  hydrogen bonds       : bond        0.03453 (  156)
  hydrogen bonds       : angle       6.47185 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LEU cc_start: 0.8113 (mm) cc_final: 0.7910 (mt)
REVERT: K   34 MET cc_start: 0.7886 (mmt) cc_final: 0.7597 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 105
  average time/residue: 0.7508
  time to fit residues: 81.6048
Evaluate side-chains
  104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain K residue   31 ILE
Chi-restraints excluded: chain K residue   35 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0070
   chunk 43 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
** K  76 ASN ** 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 = 0.3893 r_free = 0.3893 target = 0.132274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.119793 restraints weight = 17225.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.77
r_work: 0.3636 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.5404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3637  Z= 0.191
  Angle     :  0.637   9.186   4934  Z= 0.332
  Chirality :  0.047   0.158    529
  Planarity :  0.005   0.051    650
  Dihedral  :  4.861  15.781    505
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 25.14 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.39), residues: 457
  helix: -1.79 (1.40), residues: 13
  sheet: -0.33 (0.35), residues: 210
  loop : -0.47 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  19 
 TYR   0.017   0.002   TYR B  92 
 PHE   0.011   0.002   PHE B  71 
 TRP   0.014   0.002   TRP D 101 
 HIS   0.003   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 3635)
  covalent geometry    : angle       0.63699 ( 4930)
  SS BOND              : bond        0.00337 (    2)
  SS BOND              : angle       0.93209 (    4)
  hydrogen bonds       : bond        0.03270 (  156)
  hydrogen bonds       : angle       6.49146 (  396)

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   52 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  158 is missing expected H atoms. Skipping.
Residue SER  205 is missing expected H atoms. Skipping.
Residue VAL  206 is missing expected H atoms. Skipping.
Residue LYS  214 is missing expected H atoms. Skipping.
Residue VAL    5 is missing expected H atoms. Skipping.
Residue VAL   12 is missing expected H atoms. Skipping.
Residue LYS   13 is missing expected H atoms. Skipping.
Residue SER   17 is missing expected H atoms. Skipping.
Residue LEU   20 is missing expected H atoms. Skipping.
Residue SER   56 is missing expected H atoms. Skipping.
Evaluate side-chains
  102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 LEU cc_start: 0.8125 (mm) cc_final: 0.7916 (mt)
REVERT: K   34 MET cc_start: 0.7849 (mmt) cc_final: 0.7557 (mmm)
  outliers start: 2
  outliers final: 3
  residues processed: 102
  average time/residue: 0.8081
  time to fit residues: 85.1684
Evaluate side-chains
  104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain K residue   31 ILE
Chi-restraints excluded: chain K residue   35 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 34 optimal weight:    0.0770
   chunk 43 optimal weight:    0.1980
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 159 ASN
D   3 GLN
** D  95 ASN ** 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 = 0.3898 r_free = 0.3898 target = 0.132585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.120075 restraints weight = 17168.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.78
r_work: 0.3640 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3637  Z= 0.174
  Angle     :  0.644   9.111   4934  Z= 0.332
  Chirality :  0.047   0.158    529
  Planarity :  0.005   0.052    650
  Dihedral  :  4.856  15.693    505
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 26.22 %
    Favored  : 72.97 %
  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 aren not related in a simple way.
  whole: -0.78 (0.39), residues: 457
  helix: -1.82 (1.40), residues: 13
  sheet: -0.35 (0.35), residues: 210
  loop : -0.47 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  19 
 TYR   0.016   0.002   TYR B 143 
 PHE   0.008   0.001   PHE B 223 
 TRP   0.018   0.002   TRP D 101 
 HIS   0.003   0.001   HIS B 181 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 3635)
  covalent geometry    : angle       0.64325 ( 4930)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       1.11042 (    4)
  hydrogen bonds       : bond        0.03191 (  156)
  hydrogen bonds       : angle       6.47735 (  396)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2697.78 seconds
wall clock time: 46 minutes 20.78 seconds (2780.78 seconds total)