Starting phenix.real_space_refine
on Sat May  2 09:19:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/11or_75892/05_2026/11or_75892.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/11or_75892/05_2026/11or_75892.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/11or_75892/05_2026/11or_75892.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/11or_75892/05_2026/11or_75892.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/11or_75892/05_2026/11or_75892.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/11or_75892/05_2026/11or_75892.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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      15      5.16       5
     C    2588      2.51       5
     N     708      2.21       5
     O     817      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4128
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 1606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1606
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 1610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1610
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 198}
    Chain: "K"
      Number of atoms: 912
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 120, 909
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 16
      Conformer: "B"
        Number of residues, atoms: 120, 909
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 16
          bond proxies already assigned to first conformer: 924
  Time building chain proxies: 1.30, per 1000 atoms: 0.31
  Number of scatterers: 4128
  At special positions: 0
  Unit cell: (56.166, 75.9, 94.622, 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      15     16.00
     O     817      8.00
     N     708      7.00
     C    2588      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 143 " - pdb=" SG  CYS H 199 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " 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: 0.30
  Conformation dependent library (CDL) restraints added in 175.0 milliseconds
  

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  994

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 12 sheets defined
      7.7% alpha, 43.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.529A  pdb=" N   THR H  91 " --> pdb=" O   VAL H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 159 through 161
      No H-bonds generated for 'chain 'H' and resid 159 through 161'
    Processing helix  chain 'H' and resid 189 through 195
    Processing helix  chain 'H' and resid 204 through 207
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.211A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 123 through 129
      removed outlier: 3.755A  pdb=" N   SER L 129 " --> pdb=" O   GLU L 125 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 185 through 190
    Processing helix  chain 'K' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.973A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  51 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.935A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 123 through 127
      removed outlier: 3.835A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP H 147 " --> pdb=" O   TYR H 179 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 123 through 127
      removed outlier: 3.835A  pdb=" N   GLY H 142 " --> pdb=" O   LEU H 127 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP H 147 " --> pdb=" O   TYR H 179 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   TYR H 179 " --> pdb=" O   ASP H 147 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 154 through 157
      removed outlier: 3.509A  pdb=" N   THR H 154 " --> pdb=" O   ASN H 202 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   TYR H 197 " --> pdb=" O   VAL H 214 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.454A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 107 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL L  86 " --> pdb=" O   GLN L  39 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.454A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 107 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 116 through 120
      removed outlier: 5.859A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 146 through 152
    Processing sheet with id=AB2, first strand: chain 'K' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'K' and resid 45 through 51
      removed outlier: 5.599A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ALA K  33 " --> pdb=" O   ASP K  99 " (cutoff:3.500A)

    176 hydrogen bonds defined for protein.
    440 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: 0.60

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1341
        1.34 -     1.46: 957
        1.46 -     1.58: 1907
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 4225
  Sorted by residual:
  bond pdb=" C   LYS H 204 "
       pdb=" N   PRO H 205 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.28e-02 6.10e+03 2.25e+00
  bond pdb=" C   GLN K  39 "
       pdb=" O   GLN K  39 "
    ideal  model  delta    sigma   weight residual
    1.235  1.222  0.013 1.14e-02 7.69e+03 1.39e+00
  bond pdb=" N   GLN K  39 "
       pdb=" CA  GLN K  39 "
    ideal  model  delta    sigma   weight residual
    1.462  1.447  0.015 1.28e-02 6.10e+03 1.33e+00
  bond pdb=" CA  ASN L 212 "
       pdb=" CB  ASN L 212 "
    ideal  model  delta    sigma   weight residual
    1.526  1.540 -0.014 1.53e-02 4.27e+03 8.59e-01
  bond pdb=" C   VAL K  64 "
       pdb=" O   VAL K  64 "
    ideal  model  delta    sigma   weight residual
    1.240  1.226  0.014 1.49e-02 4.50e+03 8.22e-01
  ... (remaining 4220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 5395
        1.04 -     2.09: 286
        2.09 -     3.13: 49
        3.13 -     4.18: 13
        4.18 -     5.22: 2
  Bond angle restraints: 5745
  Sorted by residual:
  angle pdb=" N   VAL K 119 "
        pdb=" CA  VAL K 119 "
        pdb=" C   VAL K 119 "
      ideal   model   delta    sigma   weight residual
     113.10  109.29    3.81 9.70e-01 1.06e+00 1.54e+01
  angle pdb=" N   ILE K  29 "
        pdb=" CA  ILE K  29 "
        pdb=" C   ILE K  29 "
      ideal   model   delta    sigma   weight residual
     113.47  109.63    3.84 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" CA  VAL H 187 "
        pdb=" C   VAL H 187 "
        pdb=" N   PRO H 188 "
      ideal   model   delta    sigma   weight residual
     116.57  119.20   -2.63 9.80e-01 1.04e+00 7.22e+00
  angle pdb=" N   GLY K  26 "
        pdb=" CA  GLY K  26 "
        pdb=" C   GLY K  26 "
      ideal   model   delta    sigma   weight residual
     110.20  113.08   -2.88 1.32e+00 5.74e-01 4.75e+00
  angle pdb=" CA  ILE K  29 "
        pdb=" C   ILE K  29 "
        pdb=" N   SER K  30 "
      ideal   model   delta    sigma   weight residual
     118.94  116.40    2.54 1.22e+00 6.72e-01 4.32e+00
  ... (remaining 5740 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2232
       17.95 -    35.89: 209
       35.89 -    53.84: 52
       53.84 -    71.78: 8
       71.78 -    89.73: 8
  Dihedral angle restraints: 2509
    sinusoidal: 944
      harmonic: 1565
  Sorted by residual:
  dihedral pdb=" CB  CYS H 143 "
           pdb=" SG  CYS H 143 "
           pdb=" SG  CYS H 199 "
           pdb=" CB  CYS H 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.01  -38.01     1      1.00e+01 1.00e-02 2.04e+01
  dihedral pdb=" CB  CYS L 136 "
           pdb=" SG  CYS L 136 "
           pdb=" SG  CYS L 196 "
           pdb=" CB  CYS L 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   64.72   28.28     1      1.00e+01 1.00e-02 1.15e+01
  dihedral pdb=" CB  GLU H 215 "
           pdb=" CG  GLU H 215 "
           pdb=" CD  GLU H 215 "
           pdb=" OE1 GLU H 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 2506 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 335
       0.024 -    0.048: 178
       0.048 -    0.073: 60
       0.073 -    0.097: 31
       0.097 -    0.121: 29
  Chirality restraints: 633
  Sorted by residual:
  chirality pdb=" CA  VAL H 145 "
            pdb=" N   VAL H 145 "
            pdb=" C   VAL H 145 "
            pdb=" CB  VAL H 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.66e-01
  chirality pdb=" CA  ILE L  59 "
            pdb=" N   ILE L  59 "
            pdb=" C   ILE L  59 "
            pdb=" CB  ILE L  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.56e-01
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.41e-01
  ... (remaining 630 not shown)

  Planarity restraints: 744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 204 "   -0.034 5.00e-02 4.00e+02   5.17e-02 4.27e+00
        pdb=" N   PRO H 205 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO H 205 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO H 205 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K  87 "   -0.032 5.00e-02 4.00e+02   4.91e-02 3.85e+00
        pdb=" N   PRO K  88 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO K  88 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO K  88 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 151 "   -0.028 5.00e-02 4.00e+02   4.29e-02 2.94e+00
        pdb=" N   PRO H 152 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO H 152 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 152 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 741 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 2
        2.62 -     3.19: 3441
        3.19 -     3.76: 6146
        3.76 -     4.33: 9098
        4.33 -     4.90: 14988
  Nonbonded interactions: 33675
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN K  39 "
            pdb=" O   LYS K  43 "
     model   vdw
     2.049 3.040
  nonbonded pdb=" N   VAL K 119 "
            pdb=" N   SER K 120 "
     model   vdw
     2.606 2.560
  nonbonded pdb=" N   SER K   7 "
            pdb=" OG ASER K   7 "
     model   vdw
     2.623 2.496
  nonbonded pdb=" N   SER K   7 "
            pdb=" OG BSER K   7 "
     model   vdw
     2.627 2.496
  nonbonded pdb=" N   ILE K  29 "
            pdb=" N   SER K  30 "
     model   vdw
     2.630 2.560
  ... (remaining 33670 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=0.36 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:             5.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.500
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4230  Z= 0.136
  Angle     :  0.551   5.221   5755  Z= 0.319
  Chirality :  0.041   0.121    633
  Planarity :  0.005   0.052    744
  Dihedral  : 15.594  89.729   1500
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 16.00 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.31 (0.39), residues: 538
  helix:  0.29 (1.13), residues: 20
  sheet:  0.03 (0.34), residues: 252
  loop :  0.60 (0.43), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K  31 
 TYR   0.009   0.001   TYR K  80 
 PHE   0.016   0.001   PHE H  59 
 TRP   0.009   0.001   TRP H 157 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4225)
  covalent geometry    : angle       0.55086 ( 5745)
  SS BOND              : bond        0.00111 (    5)
  SS BOND              : angle       0.64165 (   10)
  hydrogen bonds       : bond        0.14511 (  161)
  hydrogen bonds       : angle       7.39295 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.153 
Fit side-chains
REVERT: H  120 LYS cc_start: 0.7584 (ptpt) cc_final: 0.7113 (ptmm)
REVERT: K   31 ARG cc_start: 0.8272 (tpt90) cc_final: 0.8040 (tpt90)
  outliers start: 2
  outliers final: 2
  residues processed: 56
  average time/residue: 0.0648
  time to fit residues: 4.7571
Evaluate side-chains
  53 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   38 ARG
Chi-restraints excluded: chain K residue   39 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0170
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.173316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.141403 restraints weight = 10374.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 4.09
r_work: 0.3324 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3327 r_free = 0.3327    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.0542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4230  Z= 0.117
  Angle     :  0.495   5.574   5755  Z= 0.262
  Chirality :  0.041   0.135    633
  Planarity :  0.005   0.047    744
  Dihedral  :  5.465  72.137    605
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 13.78 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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 (0.39), residues: 538
  helix:  0.63 (1.16), residues: 21
  sheet:  0.11 (0.34), residues: 250
  loop :  0.62 (0.43), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K  31 
 TYR   0.008   0.001   TYR H 148 
 PHE   0.010   0.001   PHE L 141 
 TRP   0.009   0.001   TRP H 157 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4225)
  covalent geometry    : angle       0.49505 ( 5745)
  SS BOND              : bond        0.00137 (    5)
  SS BOND              : angle       0.61238 (   10)
  hydrogen bonds       : bond        0.03371 (  161)
  hydrogen bonds       : angle       5.90238 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.134 
Fit side-chains
REVERT: H  120 LYS cc_start: 0.7786 (ptpt) cc_final: 0.7211 (ptmm)
REVERT: K    6 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7457 (mp0)
REVERT: K   29 ILE cc_start: 0.6293 (OUTLIER) cc_final: 0.5922 (tp)
  outliers start: 18
  outliers final: 12
  residues processed: 70
  average time/residue: 0.0555
  time to fit residues: 5.1814
Evaluate side-chains
  65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue    6 GLU
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   39 GLN
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue  100 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0060
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.9198

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.169842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.134441 restraints weight = 9936.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 5.02
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.0882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4230  Z= 0.151
  Angle     :  0.521   5.706   5755  Z= 0.270
  Chirality :  0.042   0.145    633
  Planarity :  0.005   0.045    744
  Dihedral  :  4.775  49.975    601
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 14.44 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.33 (0.39), residues: 538
  helix:  0.72 (1.15), residues: 21
  sheet: -0.01 (0.32), residues: 260
  loop :  0.66 (0.44), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K  31 
 TYR   0.010   0.001   TYR H 148 
 PHE   0.011   0.001   PHE L 141 
 TRP   0.007   0.001   TRP H 157 
 HIS   0.005   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4225)
  covalent geometry    : angle       0.52091 ( 5745)
  SS BOND              : bond        0.00088 (    5)
  SS BOND              : angle       0.67479 (   10)
  hydrogen bonds       : bond        0.03239 (  161)
  hydrogen bonds       : angle       5.70100 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 54
  time to evaluate  : 0.149 
Fit side-chains
REVERT: H    6 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6697 (mm-30)
REVERT: H   59 PHE cc_start: 0.7975 (m-10) cc_final: 0.7771 (m-10)
REVERT: H  120 LYS cc_start: 0.7741 (ptpt) cc_final: 0.7346 (ptmm)
REVERT: K   29 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5928 (tp)
  outliers start: 22
  outliers final: 14
  residues processed: 71
  average time/residue: 0.0563
  time to fit residues: 5.3151
Evaluate side-chains
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  164 SER
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue  100 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
H 200 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.163276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.128661 restraints weight = 7749.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 3.10
r_work: 0.3272 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3282
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3282 r_free = 0.3282    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3282
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4230  Z= 0.255
  Angle     :  0.603   6.179   5755  Z= 0.315
  Chirality :  0.045   0.175    633
  Planarity :  0.005   0.047    744
  Dihedral  :  4.281  16.844    598
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 15.33 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.09 (0.38), residues: 538
  helix:  0.29 (1.08), residues: 21
  sheet:  0.01 (0.33), residues: 240
  loop :  0.27 (0.41), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K  31 
 TYR   0.014   0.002   TYR H 148 
 PHE   0.014   0.002   PHE H 169 
 TRP   0.010   0.002   TRP H  47 
 HIS   0.005   0.002   HIS H 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 4225)
  covalent geometry    : angle       0.60202 ( 5745)
  SS BOND              : bond        0.00400 (    5)
  SS BOND              : angle       1.06811 (   10)
  hydrogen bonds       : bond        0.03500 (  161)
  hydrogen bonds       : angle       6.01087 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.170 
Fit side-chains
REVERT: H    6 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.6832 (mm-30)
REVERT: H  120 LYS cc_start: 0.8303 (ptpt) cc_final: 0.7626 (ptmm)
REVERT: H  212 LYS cc_start: 0.8174 (tppt) cc_final: 0.7919 (tptp)
REVERT: K   29 ILE cc_start: 0.6436 (OUTLIER) cc_final: 0.6165 (tp)
  outliers start: 20
  outliers final: 15
  residues processed: 73
  average time/residue: 0.0900
  time to fit residues: 8.1284
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  164 SER
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue  100 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
H 195 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.167113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.131165 restraints weight = 13309.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 5.59
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4230  Z= 0.153
  Angle     :  0.532   5.586   5755  Z= 0.278
  Chirality :  0.042   0.143    633
  Planarity :  0.005   0.046    744
  Dihedral  :  4.131  15.586    598
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 14.67 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.19 (0.38), residues: 538
  helix:  0.37 (1.10), residues: 21
  sheet: -0.02 (0.34), residues: 235
  loop :  0.43 (0.42), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  62 
 TYR   0.013   0.001   TYR H  60 
 PHE   0.012   0.001   PHE L 141 
 TRP   0.011   0.001   TRP H 157 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4225)
  covalent geometry    : angle       0.53181 ( 5745)
  SS BOND              : bond        0.00070 (    5)
  SS BOND              : angle       0.77768 (   10)
  hydrogen bonds       : bond        0.03141 (  161)
  hydrogen bonds       : angle       5.76476 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.6909 (mm-30)
REVERT: H   89 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7264 (pm20)
REVERT: H  120 LYS cc_start: 0.8000 (ptpt) cc_final: 0.7519 (ptmm)
REVERT: H  159 SER cc_start: 0.7711 (m) cc_final: 0.7498 (p)
REVERT: H  212 LYS cc_start: 0.7782 (tppt) cc_final: 0.7547 (tptt)
REVERT: K   29 ILE cc_start: 0.6292 (OUTLIER) cc_final: 0.5982 (tp)
  outliers start: 22
  outliers final: 14
  residues processed: 75
  average time/residue: 0.0895
  time to fit residues: 8.2614
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  164 SER
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue  119 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    0.2980
   chunk 15 optimal weight:    0.0670
   chunk 45 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.171810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137329 restraints weight = 6224.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.94
r_work: 0.3376 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3396 r_free = 0.3396    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4230  Z= 0.109
  Angle     :  0.504   5.260   5755  Z= 0.262
  Chirality :  0.041   0.136    633
  Planarity :  0.004   0.045    744
  Dihedral  :  3.981  14.410    598
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.89 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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 (0.38), residues: 538
  helix:  0.74 (1.17), residues: 21
  sheet:  0.05 (0.34), residues: 240
  loop :  0.42 (0.42), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  67 
 TYR   0.009   0.001   TYR H 148 
 PHE   0.012   0.001   PHE L 141 
 TRP   0.011   0.001   TRP H 157 
 HIS   0.003   0.001   HIS L 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4225)
  covalent geometry    : angle       0.50389 ( 5745)
  SS BOND              : bond        0.00108 (    5)
  SS BOND              : angle       0.63100 (   10)
  hydrogen bonds       : bond        0.02854 (  161)
  hydrogen bonds       : angle       5.50450 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.6848 (mm-30)
REVERT: H   59 PHE cc_start: 0.8026 (m-10) cc_final: 0.7805 (m-10)
REVERT: H   89 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7301 (pm20)
REVERT: H  120 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7343 (ptmm)
REVERT: H  159 SER cc_start: 0.7642 (m) cc_final: 0.7401 (p)
REVERT: H  212 LYS cc_start: 0.8086 (tppt) cc_final: 0.7793 (tptt)
REVERT: K   29 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.5998 (tp)
  outliers start: 13
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0883
  time to fit residues: 8.2590
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  164 SER
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
K  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.170291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.135188 restraints weight = 8034.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 3.10
r_work: 0.3330 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3334
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3334 r_free = 0.3334    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3334
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4230  Z= 0.132
  Angle     :  0.520   5.591   5755  Z= 0.269
  Chirality :  0.043   0.225    633
  Planarity :  0.004   0.044    744
  Dihedral  :  3.951  14.296    598
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 16.44 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.26 (0.38), residues: 538
  helix:  0.77 (1.17), residues: 21
  sheet:  0.05 (0.34), residues: 240
  loop :  0.43 (0.42), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  72 
 TYR   0.010   0.001   TYR L  37 
 PHE   0.012   0.001   PHE L 141 
 TRP   0.009   0.001   TRP H 157 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4225)
  covalent geometry    : angle       0.51962 ( 5745)
  SS BOND              : bond        0.00046 (    5)
  SS BOND              : angle       0.66293 (   10)
  hydrogen bonds       : bond        0.02898 (  161)
  hydrogen bonds       : angle       5.53726 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.6835 (mm-30)
REVERT: H   89 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7301 (pm20)
REVERT: H  120 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7410 (ptmm)
REVERT: H  159 SER cc_start: 0.7669 (m) cc_final: 0.7411 (p)
REVERT: H  212 LYS cc_start: 0.8053 (tppt) cc_final: 0.7730 (tptt)
REVERT: K   29 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.5993 (tp)
  outliers start: 20
  outliers final: 14
  residues processed: 76
  average time/residue: 0.0904
  time to fit residues: 8.4270
Evaluate side-chains
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  164 SER
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue  119 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 35 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 0 optimal weight:    0.6980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.168017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.133359 restraints weight = 8634.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 4.06
r_work: 0.3238 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4230  Z= 0.179
  Angle     :  0.556   5.947   5755  Z= 0.287
  Chirality :  0.043   0.147    633
  Planarity :  0.005   0.044    744
  Dihedral  :  4.100  15.358    598
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.00 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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 (0.38), residues: 538
  helix:  0.62 (1.14), residues: 21
  sheet:  0.21 (0.35), residues: 223
  loop :  0.29 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.012   0.001   TYR H 148 
 PHE   0.012   0.002   PHE L 141 
 TRP   0.007   0.001   TRP H 157 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 4225)
  covalent geometry    : angle       0.55505 ( 5745)
  SS BOND              : bond        0.00118 (    5)
  SS BOND              : angle       0.77239 (   10)
  hydrogen bonds       : bond        0.03097 (  161)
  hydrogen bonds       : angle       5.69178 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.6870 (mm-30)
REVERT: H   89 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7298 (pm20)
REVERT: H  120 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7527 (ptmm)
REVERT: H  159 SER cc_start: 0.7795 (m) cc_final: 0.7501 (p)
REVERT: H  212 LYS cc_start: 0.8019 (tppt) cc_final: 0.7750 (tptt)
REVERT: K   29 ILE cc_start: 0.6376 (OUTLIER) cc_final: 0.5981 (tp)
  outliers start: 17
  outliers final: 14
  residues processed: 72
  average time/residue: 0.0933
  time to fit residues: 8.2364
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  164 SER
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue  119 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 191 HIS
K  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.167021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.133490 restraints weight = 9019.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 3.77
r_work: 0.3269 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4230  Z= 0.154
  Angle     :  0.549   5.935   5755  Z= 0.281
  Chirality :  0.042   0.143    633
  Planarity :  0.004   0.044    744
  Dihedral  :  4.072  15.158    598
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 17.56 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.26 (0.38), residues: 538
  helix:  0.66 (1.15), residues: 21
  sheet:  0.17 (0.35), residues: 223
  loop :  0.28 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG K  72 
 TYR   0.010   0.001   TYR H 148 
 PHE   0.012   0.002   PHE L 141 
 TRP   0.009   0.001   TRP H 157 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 4225)
  covalent geometry    : angle       0.54860 ( 5745)
  SS BOND              : bond        0.00079 (    5)
  SS BOND              : angle       0.70666 (   10)
  hydrogen bonds       : bond        0.03003 (  161)
  hydrogen bonds       : angle       5.64980 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    6 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6899 (mm-30)
REVERT: H   89 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7324 (pm20)
REVERT: H  120 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7534 (ptmm)
REVERT: H  159 SER cc_start: 0.7784 (m) cc_final: 0.7502 (p)
REVERT: H  212 LYS cc_start: 0.8043 (tppt) cc_final: 0.7777 (tptt)
REVERT: K   29 ILE cc_start: 0.6387 (OUTLIER) cc_final: 0.5988 (tp)
  outliers start: 19
  outliers final: 15
  residues processed: 75
  average time/residue: 0.0884
  time to fit residues: 8.1807
Evaluate side-chains
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   89 GLU
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  154 THR
Chi-restraints excluded: chain H residue  164 SER
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   20 LEU
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue  119 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0970
   chunk 52 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0370
   chunk 38 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.171447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.134835 restraints weight = 11890.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 5.46
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4230  Z= 0.120
  Angle     :  0.523   5.486   5755  Z= 0.269
  Chirality :  0.042   0.138    633
  Planarity :  0.004   0.043    744
  Dihedral  :  3.998  18.534    598
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 18.22 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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 (0.38), residues: 538
  helix:  0.82 (1.17), residues: 21
  sheet:  0.00 (0.34), residues: 235
  loop :  0.50 (0.42), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  62 
 TYR   0.014   0.001   TYR H  60 
 PHE   0.011   0.001   PHE L 141 
 TRP   0.010   0.001   TRP H 157 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4225)
  covalent geometry    : angle       0.52262 ( 5745)
  SS BOND              : bond        0.00088 (    5)
  SS BOND              : angle       0.62231 (   10)
  hydrogen bonds       : bond        0.02872 (  161)
  hydrogen bonds       : angle       5.50020 (  440)

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

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

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1076 Ramachandran restraints generated.
    538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.160 
Fit side-chains
REVERT: H    6 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6908 (mm-30)
REVERT: H  120 LYS cc_start: 0.7811 (ptpt) cc_final: 0.7351 (ptmm)
REVERT: H  159 SER cc_start: 0.7664 (m) cc_final: 0.7459 (p)
REVERT: K   29 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5893 (tp)
  outliers start: 18
  outliers final: 15
  residues processed: 70
  average time/residue: 0.0756
  time to fit residues: 6.7296
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain H residue  164 SER
Chi-restraints excluded: chain H residue  210 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   12 VAL
Chi-restraints excluded: chain K residue   20 LEU
Chi-restraints excluded: chain K residue   29 ILE
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue   69 THR
Chi-restraints excluded: chain K residue   84 ASN
Chi-restraints excluded: chain K residue  119 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0050
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 50 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.171702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.135407 restraints weight = 11898.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 5.40
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3582 r_free = 0.3582    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
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   0.026   4230  Z= 0.113
  Angle     :  0.518   5.472   5755  Z= 0.266
  Chirality :  0.041   0.136    633
  Planarity :  0.004   0.043    744
  Dihedral  :  3.934  16.327    598
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 18.22 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.86 %
    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:  0.34 (0.39), residues: 538
  helix:  0.88 (1.18), residues: 21
  sheet:  0.06 (0.34), residues: 235
  loop :  0.51 (0.41), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  53 
 TYR   0.008   0.001   TYR H 148 
 PHE   0.013   0.001   PHE H  59 
 TRP   0.009   0.001   TRP H 157 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4225)
  covalent geometry    : angle       0.51750 ( 5745)
  SS BOND              : bond        0.00094 (    5)
  SS BOND              : angle       0.62435 (   10)
  hydrogen bonds       : bond        0.02829 (  161)
  hydrogen bonds       : angle       5.45670 (  440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1296.47 seconds
wall clock time: 23 minutes 1.87 seconds (1381.87 seconds total)