Starting phenix.real_space_refine
on Fri May  9 19:06:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xwn_38739/05_2025/8xwn_38739.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xwn_38739/05_2025/8xwn_38739.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xwn_38739/05_2025/8xwn_38739.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xwn_38739/05_2025/8xwn_38739.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xwn_38739/05_2025/8xwn_38739.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xwn_38739/05_2025/8xwn_38739.cif"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   1.000
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      24      5.16       5
     C    2296      2.51       5
     N     586      2.21       5
     O     590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3496
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "R"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2421
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 291}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 575
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 68}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "E"
      Number of atoms: 500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 500
          Classifications: {'peptide': 65}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 60}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 3.11, per 1000 atoms: 0.89
  Number of scatterers: 3496
  At special positions: 0
  Unit cell: (69.5125, 74.7, 104.787, 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      24     16.00
     O     590      8.00
     N     586      7.00
     C    2296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  39 " - pdb=" SG  CYS R 286 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 119 " - pdb=" SG  CYS R 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  14 " - pdb=" SG  CYS D  41 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  16 " - pdb=" SG  CYS D  57 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  14 " - pdb=" SG  CYS E  41 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  16 " - pdb=" SG  CYS E  57 " 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: 0.76
  Conformation dependent library (CDL) restraints added in 404.8 milliseconds
  

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  848

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 2 sheets defined
      64.6% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'R' and resid 45 through 76
      removed outlier: 4.415A  pdb=" N   SER R  76 " --> pdb=" O   VAL R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 111
      Proline residue:  R 102  - end of helix
    Processing helix  chain 'R' and resid 115 through 149
    Processing helix  chain 'R' and resid 154 through 160
      removed outlier: 3.877A  pdb=" N   TYR R 160 " --> pdb=" O   GLN R 157 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 177
    Processing helix  chain 'R' and resid 177 through 183
      removed outlier: 3.542A  pdb=" N   LEU R 181 " --> pdb=" O   ALA R 177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 203 through 212
    Processing helix  chain 'R' and resid 212 through 218
    Processing helix  chain 'R' and resid 220 through 241
      removed outlier: 3.587A  pdb=" N   LYS R 240 " --> pdb=" O   ARG R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 279
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 285 through 304
    Processing helix  chain 'R' and resid 305 through 315
      Proline residue:  R 311  - end of helix
    Processing helix  chain 'R' and resid 318 through 329
    Processing helix  chain 'D' and resid 25 through 27
      No H-bonds generated for 'chain 'D' and resid 25 through 27'
    Processing helix  chain 'D' and resid 62 through 78
      removed outlier: 3.815A  pdb=" N   GLN D  66 " --> pdb=" O   GLU D  62 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 25 through 27
      No H-bonds generated for 'chain 'E' and resid 25 through 27'
    Processing helix  chain 'E' and resid 62 through 77
    Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 187
    Processing sheet with id=AA2, first strand: chain 'D' and resid 55 through 58
      removed outlier: 4.364A  pdb=" N   ILE D  46 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLU D  31 " --> pdb=" O   LYS D  49 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE E  46 " --> pdb=" O   LEU E  58 " (cutoff:3.500A)

    230 hydrogen bonds defined for protein.
    672 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: 0.89

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1091
        1.35 -     1.47: 830
        1.47 -     1.58: 1623
        1.58 -     1.70: 0
        1.70 -     1.82: 31
  Bond restraints: 3575
  Sorted by residual:
  bond pdb=" CA  LEU R  99 "
       pdb=" C   LEU R  99 "
    ideal  model  delta    sigma   weight residual
    1.522  1.506  0.017 1.36e-02 5.41e+03 1.48e+00
  bond pdb=" CA  GLU R  45 "
       pdb=" CB  GLU R  45 "
    ideal  model  delta    sigma   weight residual
    1.534  1.521  0.013 1.45e-02 4.76e+03 8.09e-01
  bond pdb=" CB  ASP R  35 "
       pdb=" CG  ASP R  35 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 2.50e-02 1.60e+03 6.03e-01
  bond pdb=" CA  LEU R 101 "
       pdb=" C   LEU R 101 "
    ideal  model  delta    sigma   weight residual
    1.521  1.530 -0.009 1.17e-02 7.31e+03 5.65e-01
  bond pdb=" CA  LYS E  18 "
       pdb=" CB  LYS E  18 "
    ideal  model  delta    sigma   weight residual
    1.536  1.521  0.014 2.08e-02 2.31e+03 4.68e-01
  ... (remaining 3570 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 4626
        0.91 -     1.83: 190
        1.83 -     2.74: 24
        2.74 -     3.66: 15
        3.66 -     4.57: 5
  Bond angle restraints: 4860
  Sorted by residual:
  angle pdb=" N   HIS D  40 "
        pdb=" CA  HIS D  40 "
        pdb=" C   HIS D  40 "
      ideal   model   delta    sigma   weight residual
     111.14  113.08   -1.94 1.08e+00 8.57e-01 3.22e+00
  angle pdb=" N   ILE R 113 "
        pdb=" CA  ILE R 113 "
        pdb=" C   ILE R 113 "
      ideal   model   delta    sigma   weight residual
     112.90  111.37    1.53 9.60e-01 1.09e+00 2.54e+00
  angle pdb=" N   ASN R 110 "
        pdb=" CA  ASN R 110 "
        pdb=" C   ASN R 110 "
      ideal   model   delta    sigma   weight residual
     111.56  113.68   -2.12 1.38e+00 5.25e-01 2.35e+00
  angle pdb=" N   GLY R 244 "
        pdb=" CA  GLY R 244 "
        pdb=" C   GLY R 244 "
      ideal   model   delta    sigma   weight residual
     115.66  113.27    2.39 1.56e+00 4.11e-01 2.34e+00
  angle pdb=" C   ALA R  98 "
        pdb=" N   LEU R  99 "
        pdb=" CA  LEU R  99 "
      ideal   model   delta    sigma   weight residual
     120.28  122.41   -2.13 1.44e+00 4.82e-01 2.19e+00
  ... (remaining 4855 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 1950
       17.77 -    35.54: 167
       35.54 -    53.31: 26
       53.31 -    71.08: 13
       71.08 -    88.85: 3
  Dihedral angle restraints: 2159
    sinusoidal: 859
      harmonic: 1300
  Sorted by residual:
  dihedral pdb=" CB  CYS E  14 "
           pdb=" SG  CYS E  14 "
           pdb=" SG  CYS E  41 "
           pdb=" CB  CYS E  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.87   55.87     1      1.00e+01 1.00e-02 4.21e+01
  dihedral pdb=" CA  LEU R 182 "
           pdb=" C   LEU R 182 "
           pdb=" N   PHE R 183 "
           pdb=" CA  PHE R 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.46  -15.54     0      5.00e+00 4.00e-02 9.65e+00
  dihedral pdb=" CA  LYS D  71 "
           pdb=" CB  LYS D  71 "
           pdb=" CG  LYS D  71 "
           pdb=" CD  LYS D  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.25  -58.75     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 2156 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 350
       0.024 -    0.048: 127
       0.048 -    0.071: 59
       0.071 -    0.095: 27
       0.095 -    0.119: 19
  Chirality restraints: 582
  Sorted by residual:
  chirality pdb=" CA  ILE D  35 "
            pdb=" N   ILE D  35 "
            pdb=" C   ILE D  35 "
            pdb=" CB  ILE D  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.53e-01
  chirality pdb=" CA  ILE E  47 "
            pdb=" N   ILE E  47 "
            pdb=" C   ILE E  47 "
            pdb=" CB  ILE E  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.39e-01
  chirality pdb=" CA  ILE E  35 "
            pdb=" N   ILE E  35 "
            pdb=" C   ILE E  35 "
            pdb=" CB  ILE E  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.37e-01
  ... (remaining 579 not shown)

  Planarity restraints: 596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D  25 "    0.018 5.00e-02 4.00e+02   2.65e-02 1.12e+00
        pdb=" N   PRO D  26 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO D  26 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO D  26 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY E  38 "   -0.014 5.00e-02 4.00e+02   2.04e-02 6.69e-01
        pdb=" N   PRO E  39 "    0.035 5.00e-02 4.00e+02
        pdb=" CA  PRO E  39 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO E  39 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 119 "    0.004 2.00e-02 2.50e+03   8.15e-03 6.64e-01
        pdb=" C   CYS R 119 "   -0.014 2.00e-02 2.50e+03
        pdb=" O   CYS R 119 "    0.005 2.00e-02 2.50e+03
        pdb=" N   LYS R 120 "    0.005 2.00e-02 2.50e+03
  ... (remaining 593 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 550
        2.76 -     3.30: 3369
        3.30 -     3.83: 5666
        3.83 -     4.37: 6074
        4.37 -     4.90: 11181
  Nonbonded interactions: 26840
  Sorted by model distance:
  nonbonded pdb=" O   GLY R 201 "
            pdb=" OG1 THR R 204 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OD1 ASP R 143 "
            pdb=" NH1 ARG R 159 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" O   LEU R 125 "
            pdb=" ND2 ASN R 129 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" OE2 GLU D  31 "
            pdb=" NE  ARG E  33 "
     model   vdw
     2.460 3.120
  nonbonded pdb=" O   LEU R  34 "
            pdb=" OD1 ASP R  35 "
     model   vdw
     2.469 3.040
  ... (remaining 26835 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'D' and (resid 14 through 17 or (resid 18 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 19 through 26 or (resid 27 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 28 through 60 or (resid 61 throu \ 
gh 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throu \ 
gh 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 72 through 77 or (resid 78 and (name N or name CA or name C or name O or na \ 
me CB ))))
  selection = (chain 'E' and (resid 14 through 61 or (resid 62 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 63 through 78))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.810
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.870
  Find NCS groups from input model:        0.070
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
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   0.021   3581  Z= 0.123
  Angle     :  0.476   4.569   4872  Z= 0.270
  Chirality :  0.037   0.119    582
  Planarity :  0.003   0.026    596
  Dihedral  : 14.065  88.855   1293
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.40), residues: 435
  helix:  2.86 (0.31), residues: 264
  sheet:  0.35 (0.82), residues: 41
  loop : -0.45 (0.49), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  64 
 HIS   0.002   0.001   HIS R 150 
 PHE   0.006   0.001   PHE D  72 
 TYR   0.010   0.001   TYR R  49 
 ARG   0.002   0.000   ARG D  13 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12909 (  230)
  hydrogen bonds       : angle       4.54908 (  672)
  SS BOND              : bond        0.00158 (    6)
  SS BOND              : angle       1.04269 (   12)
  covalent geometry    : bond        0.00235 ( 3575)
  covalent geometry    : angle       0.47363 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   84 ASP cc_start: 0.8606 (m-30) cc_final: 0.8282 (m-30)
REVERT: R  141 SER cc_start: 0.9031 (t) cc_final: 0.8807 (p)
REVERT: R  300 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7935 (mt-10)
REVERT: R  325 LEU cc_start: 0.9105 (tp) cc_final: 0.8870 (tp)
REVERT: R  327 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8631 (tptt)
REVERT: D   27 LYS cc_start: 0.9247 (ptmt) cc_final: 0.8782 (ttpp)
REVERT: D   31 GLU cc_start: 0.7413 (tt0) cc_final: 0.7197 (tt0)
REVERT: D   43 ASN cc_start: 0.8826 (m-40) cc_final: 0.8236 (p0)
REVERT: D   59 ASP cc_start: 0.7987 (t0) cc_final: 0.7638 (t70)
REVERT: D   66 GLN cc_start: 0.8567 (mt0) cc_final: 0.7990 (mm-40)
REVERT: D   75 ARG cc_start: 0.8997 (ttp-170) cc_final: 0.8744 (ttp-110)
REVERT: E   49 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7454 (mttp)
REVERT: E   57 CYS cc_start: 0.6149 (m) cc_final: 0.5922 (m)
REVERT: E   59 ASP cc_start: 0.9117 (t0) cc_final: 0.8507 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.2041
  time to fit residues: 35.2179
Evaluate side-chains
  118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0060
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
R  47 ASN
R 203 ASN
R 216 GLN
R 245 GLN
R 323 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.121464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.094341 restraints weight = 6007.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.28
r_work: 0.3032 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3581  Z= 0.160
  Angle     :  0.561   5.073   4872  Z= 0.295
  Chirality :  0.042   0.181    582
  Planarity :  0.004   0.031    596
  Dihedral  :  3.803  17.424    476
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 12.53 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.39), residues: 435
  helix:  2.74 (0.30), residues: 270
  sheet:  0.17 (0.86), residues: 34
  loop : -0.71 (0.47), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 264 
 HIS   0.003   0.001   HIS R 247 
 PHE   0.016   0.001   PHE D  72 
 TYR   0.011   0.001   TYR D  20 
 ARG   0.003   0.000   ARG R 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05158 (  230)
  hydrogen bonds       : angle       4.11965 (  672)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       1.53889 (   12)
  covalent geometry    : bond        0.00380 ( 3575)
  covalent geometry    : angle       0.55676 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  203 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7785 (t0)
REVERT: R  280 GLN cc_start: 0.8738 (mm110) cc_final: 0.8531 (mt0)
REVERT: D   27 LYS cc_start: 0.9381 (ptmt) cc_final: 0.8949 (ttpp)
REVERT: D   31 GLU cc_start: 0.8171 (tt0) cc_final: 0.7939 (tt0)
REVERT: D   43 ASN cc_start: 0.9148 (m-40) cc_final: 0.8513 (p0)
REVERT: D   59 ASP cc_start: 0.8222 (t0) cc_final: 0.7975 (t70)
REVERT: E   49 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8104 (mttp)
  outliers start: 16
  outliers final: 13
  residues processed: 123
  average time/residue: 0.1838
  time to fit residues: 26.4625
Evaluate side-chains
  118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  203 ASN
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  237 THR
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain R residue  323 HIS
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   63 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
R 323 HIS
E  66 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.121543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.094649 restraints weight = 6045.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.28
r_work: 0.3040 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3581  Z= 0.145
  Angle     :  0.530   5.310   4872  Z= 0.286
  Chirality :  0.041   0.165    582
  Planarity :  0.004   0.059    596
  Dihedral  :  3.783  16.077    476
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 12.01 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.40), residues: 435
  helix:  2.67 (0.31), residues: 270
  sheet: -0.97 (1.17), residues: 20
  loop : -0.61 (0.45), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 264 
 HIS   0.008   0.001   HIS D  25 
 PHE   0.018   0.001   PHE D  72 
 TYR   0.009   0.001   TYR D  20 
 ARG   0.004   0.001   ARG R 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04851 (  230)
  hydrogen bonds       : angle       4.06891 (  672)
  SS BOND              : bond        0.00155 (    6)
  SS BOND              : angle       1.05363 (   12)
  covalent geometry    : bond        0.00337 ( 3575)
  covalent geometry    : angle       0.52838 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8603 (mptt)
REVERT: D   28 PHE cc_start: 0.8409 (m-80) cc_final: 0.8121 (m-10)
REVERT: D   43 ASN cc_start: 0.9145 (m-40) cc_final: 0.8504 (p0)
REVERT: D   54 ARG cc_start: 0.8359 (ptp90) cc_final: 0.7965 (ptp90)
REVERT: D   59 ASP cc_start: 0.8126 (t0) cc_final: 0.7848 (t70)
REVERT: E   15 GLN cc_start: 0.7993 (mp10) cc_final: 0.7672 (mp10)
REVERT: E   36 GLU cc_start: 0.7594 (tt0) cc_final: 0.7250 (tp30)
REVERT: E   49 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8110 (mttp)
  outliers start: 18
  outliers final: 16
  residues processed: 121
  average time/residue: 0.1884
  time to fit residues: 26.6506
Evaluate side-chains
  122 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain R residue  323 HIS
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue   63 ASN
Chi-restraints excluded: chain E residue   73 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
E  66 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.119337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.092125 restraints weight = 6091.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.24
r_work: 0.3002 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3581  Z= 0.205
  Angle     :  0.585   5.964   4872  Z= 0.312
  Chirality :  0.043   0.196    582
  Planarity :  0.004   0.053    596
  Dihedral  :  4.005  16.254    476
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 13.32 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.39), residues: 435
  helix:  2.51 (0.31), residues: 268
  sheet: -1.24 (1.19), residues: 20
  loop : -0.68 (0.45), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 264 
 HIS   0.007   0.002   HIS D  25 
 PHE   0.018   0.002   PHE D  72 
 TYR   0.008   0.001   TYR D  20 
 ARG   0.006   0.001   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05111 (  230)
  hydrogen bonds       : angle       4.11744 (  672)
  SS BOND              : bond        0.00158 (    6)
  SS BOND              : angle       1.42448 (   12)
  covalent geometry    : bond        0.00494 ( 3575)
  covalent geometry    : angle       0.58191 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8665 (mptt)
REVERT: D   28 PHE cc_start: 0.8445 (m-80) cc_final: 0.8158 (m-10)
REVERT: D   31 GLU cc_start: 0.8192 (tt0) cc_final: 0.7984 (tt0)
REVERT: D   54 ARG cc_start: 0.8403 (ptp90) cc_final: 0.8033 (ptp90)
REVERT: D   59 ASP cc_start: 0.8143 (t0) cc_final: 0.7843 (t70)
REVERT: D   66 GLN cc_start: 0.8710 (mt0) cc_final: 0.8139 (mm-40)
REVERT: E   15 GLN cc_start: 0.8023 (mp10) cc_final: 0.7694 (mp10)
REVERT: E   49 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8236 (mttp)
  outliers start: 20
  outliers final: 17
  residues processed: 120
  average time/residue: 0.1739
  time to fit residues: 24.7672
Evaluate side-chains
  120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain R residue  323 HIS
Chi-restraints excluded: chain D residue   10 LYS
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue   63 ASN
Chi-restraints excluded: chain E residue   73 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
R 323 HIS
D  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.119599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.092204 restraints weight = 6126.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.30
r_work: 0.3002 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3581  Z= 0.181
  Angle     :  0.592  11.689   4872  Z= 0.306
  Chirality :  0.042   0.193    582
  Planarity :  0.004   0.052    596
  Dihedral  :  4.116  17.866    476
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 14.10 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.40), residues: 435
  helix:  2.53 (0.31), residues: 268
  sheet: -0.49 (0.78), residues: 42
  loop : -0.78 (0.50), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 264 
 HIS   0.006   0.001   HIS D  25 
 PHE   0.016   0.001   PHE D  72 
 TYR   0.011   0.001   TYR E  20 
 ARG   0.003   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04987 (  230)
  hydrogen bonds       : angle       4.13743 (  672)
  SS BOND              : bond        0.00186 (    6)
  SS BOND              : angle       1.42554 (   12)
  covalent geometry    : bond        0.00435 ( 3575)
  covalent geometry    : angle       0.58809 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  284 GLU cc_start: 0.8229 (tt0) cc_final: 0.7982 (tt0)
REVERT: R  327 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8672 (tptt)
REVERT: D   28 PHE cc_start: 0.8472 (m-80) cc_final: 0.8197 (m-10)
REVERT: D   54 ARG cc_start: 0.8377 (ptp90) cc_final: 0.8054 (ptp90)
REVERT: D   59 ASP cc_start: 0.8078 (t0) cc_final: 0.7767 (t70)
REVERT: E   15 GLN cc_start: 0.8003 (mp10) cc_final: 0.7601 (mp10)
REVERT: E   49 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8254 (mttp)
  outliers start: 20
  outliers final: 15
  residues processed: 122
  average time/residue: 0.1760
  time to fit residues: 25.7429
Evaluate side-chains
  119 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain R residue  323 HIS
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   49 LYS
Chi-restraints excluded: chain E residue   73 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 35 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 29 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
D  43 ASN
E  66 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.120731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.093435 restraints weight = 6196.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 2.32
r_work: 0.3022 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3581  Z= 0.149
  Angle     :  0.566   9.499   4872  Z= 0.297
  Chirality :  0.041   0.196    582
  Planarity :  0.004   0.052    596
  Dihedral  :  4.069  17.401    476
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 16.45 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.40), residues: 435
  helix:  2.59 (0.31), residues: 268
  sheet: -0.46 (0.79), residues: 42
  loop : -0.68 (0.52), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 264 
 HIS   0.007   0.001   HIS D  25 
 PHE   0.018   0.001   PHE D  72 
 TYR   0.007   0.001   TYR D  20 
 ARG   0.003   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04707 (  230)
  hydrogen bonds       : angle       4.11105 (  672)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       1.39272 (   12)
  covalent geometry    : bond        0.00350 ( 3575)
  covalent geometry    : angle       0.56226 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8584 (mptt)
REVERT: D   28 PHE cc_start: 0.8452 (m-80) cc_final: 0.8179 (m-10)
REVERT: D   54 ARG cc_start: 0.8417 (ptp90) cc_final: 0.8103 (ptp90)
REVERT: D   59 ASP cc_start: 0.8098 (t0) cc_final: 0.7783 (t70)
REVERT: E   15 GLN cc_start: 0.8000 (mp10) cc_final: 0.7603 (mp10)
  outliers start: 19
  outliers final: 15
  residues processed: 119
  average time/residue: 0.2043
  time to fit residues: 29.0616
Evaluate side-chains
  118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  109 VAL
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain R residue  323 HIS
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue   44 THR
Chi-restraints excluded: chain E residue   63 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 37 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
R 323 HIS
D  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.120392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.093215 restraints weight = 6078.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 2.26
r_work: 0.3014 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3581  Z= 0.168
  Angle     :  0.570   8.618   4872  Z= 0.298
  Chirality :  0.042   0.190    582
  Planarity :  0.004   0.052    596
  Dihedral  :  4.065  17.521    476
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 16.71 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.40), residues: 435
  helix:  2.56 (0.31), residues: 268
  sheet: -0.44 (0.78), residues: 42
  loop : -0.69 (0.52), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 264 
 HIS   0.006   0.001   HIS D  25 
 PHE   0.013   0.001   PHE D  72 
 TYR   0.014   0.001   TYR E  20 
 ARG   0.002   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04845 (  230)
  hydrogen bonds       : angle       4.13197 (  672)
  SS BOND              : bond        0.00188 (    6)
  SS BOND              : angle       1.33349 (   12)
  covalent geometry    : bond        0.00399 ( 3575)
  covalent geometry    : angle       0.56666 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8610 (mptt)
REVERT: D   28 PHE cc_start: 0.8463 (m-80) cc_final: 0.8184 (m-10)
REVERT: D   54 ARG cc_start: 0.8426 (ptp90) cc_final: 0.8025 (ptp90)
REVERT: D   59 ASP cc_start: 0.8124 (t0) cc_final: 0.7838 (t70)
REVERT: E   15 GLN cc_start: 0.7954 (mp10) cc_final: 0.7564 (mp10)
REVERT: E   57 CYS cc_start: 0.6845 (m) cc_final: 0.6401 (m)
  outliers start: 17
  outliers final: 14
  residues processed: 116
  average time/residue: 0.1809
  time to fit residues: 24.9318
Evaluate side-chains
  115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  109 VAL
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain R residue  323 HIS
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   69 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0980
   chunk 17 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN
D  43 ASN
E  25 HIS
E  66 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.119982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.092524 restraints weight = 6091.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.30
r_work: 0.2990 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3581  Z= 0.181
  Angle     :  0.584   7.617   4872  Z= 0.309
  Chirality :  0.042   0.190    582
  Planarity :  0.005   0.052    596
  Dihedral  :  4.094  17.855    476
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.23 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.39), residues: 435
  helix:  2.44 (0.30), residues: 268
  sheet: -0.46 (0.77), residues: 42
  loop : -0.86 (0.49), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 264 
 HIS   0.007   0.001   HIS D  25 
 PHE   0.016   0.002   PHE D  72 
 TYR   0.007   0.001   TYR D  20 
 ARG   0.004   0.000   ARG R 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04902 (  230)
  hydrogen bonds       : angle       4.15722 (  672)
  SS BOND              : bond        0.00164 (    6)
  SS BOND              : angle       1.38651 (   12)
  covalent geometry    : bond        0.00432 ( 3575)
  covalent geometry    : angle       0.58025 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   35 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6621 (p0)
REVERT: R  327 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8697 (mptt)
REVERT: D   28 PHE cc_start: 0.8476 (m-80) cc_final: 0.7856 (m-80)
REVERT: D   49 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8622 (mtmt)
REVERT: D   54 ARG cc_start: 0.8440 (ptp90) cc_final: 0.8117 (ptp90)
REVERT: D   59 ASP cc_start: 0.8139 (t0) cc_final: 0.7849 (t70)
REVERT: E   15 GLN cc_start: 0.7954 (mp10) cc_final: 0.7582 (mp10)
REVERT: E   57 CYS cc_start: 0.6800 (m) cc_final: 0.6365 (m)
  outliers start: 17
  outliers final: 16
  residues processed: 113
  average time/residue: 0.1806
  time to fit residues: 24.2793
Evaluate side-chains
  116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 ASP
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue   95 LEU
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  109 VAL
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  243 MET
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain R residue  323 HIS
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue   44 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0020
   chunk 11 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN
R 203 ASN
R 323 HIS
D  43 ASN
E  66 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.121681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.094858 restraints weight = 6046.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.25
r_work: 0.3040 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.4113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3581  Z= 0.136
  Angle     :  0.558   6.356   4872  Z= 0.296
  Chirality :  0.041   0.184    582
  Planarity :  0.004   0.051    596
  Dihedral  :  4.008  18.382    476
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.49 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.40), residues: 435
  helix:  2.57 (0.31), residues: 268
  sheet: -0.08 (0.87), residues: 32
  loop : -0.94 (0.48), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 264 
 HIS   0.007   0.001   HIS D  25 
 PHE   0.013   0.001   PHE D  72 
 TYR   0.017   0.001   TYR E  20 
 ARG   0.002   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  230)
  hydrogen bonds       : angle       4.07729 (  672)
  SS BOND              : bond        0.00110 (    6)
  SS BOND              : angle       1.25590 (   12)
  covalent geometry    : bond        0.00311 ( 3575)
  covalent geometry    : angle       0.55470 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   35 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6538 (p0)
REVERT: R  327 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8598 (mptt)
REVERT: D   28 PHE cc_start: 0.8478 (m-80) cc_final: 0.8212 (m-10)
REVERT: D   49 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8652 (mtmt)
REVERT: D   54 ARG cc_start: 0.8416 (ptp90) cc_final: 0.8015 (ptp90)
REVERT: D   59 ASP cc_start: 0.8066 (t0) cc_final: 0.7787 (t70)
REVERT: E   15 GLN cc_start: 0.7926 (mp10) cc_final: 0.7637 (mp10)
REVERT: E   57 CYS cc_start: 0.6935 (m) cc_final: 0.6597 (m)
  outliers start: 17
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1751
  time to fit residues: 24.2081
Evaluate side-chains
  115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 ASP
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue   44 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0970
   chunk 23 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
R 319 GLN
D  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.121782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.094635 restraints weight = 6057.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.28
r_work: 0.3037 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3581  Z= 0.138
  Angle     :  0.566   6.408   4872  Z= 0.300
  Chirality :  0.041   0.181    582
  Planarity :  0.004   0.051    596
  Dihedral  :  4.058  18.658    476
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.75 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.40), residues: 435
  helix:  2.50 (0.31), residues: 270
  sheet: -0.29 (0.80), residues: 42
  loop : -0.80 (0.50), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 264 
 HIS   0.007   0.001   HIS D  25 
 PHE   0.013   0.001   PHE E  24 
 TYR   0.008   0.001   TYR E  20 
 ARG   0.002   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04457 (  230)
  hydrogen bonds       : angle       4.08475 (  672)
  SS BOND              : bond        0.00097 (    6)
  SS BOND              : angle       1.26410 (   12)
  covalent geometry    : bond        0.00317 ( 3575)
  covalent geometry    : angle       0.56305 ( 4860)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R   35 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6561 (p0)
REVERT: R  327 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8696 (mptt)
REVERT: D   28 PHE cc_start: 0.8463 (m-80) cc_final: 0.8199 (m-10)
REVERT: D   43 ASN cc_start: 0.9212 (m-40) cc_final: 0.8548 (p0)
REVERT: D   49 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8658 (mtmt)
REVERT: D   54 ARG cc_start: 0.8414 (ptp90) cc_final: 0.8012 (ptp90)
REVERT: D   59 ASP cc_start: 0.7992 (t0) cc_final: 0.7736 (t70)
REVERT: E   15 GLN cc_start: 0.7930 (mp10) cc_final: 0.7636 (mp10)
  outliers start: 14
  outliers final: 12
  residues processed: 111
  average time/residue: 0.1797
  time to fit residues: 23.5551
Evaluate side-chains
  114 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   35 ASP
Chi-restraints excluded: chain R residue   61 LEU
Chi-restraints excluded: chain R residue   83 THR
Chi-restraints excluded: chain R residue  100 THR
Chi-restraints excluded: chain R residue  152 THR
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  221 ILE
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
Chi-restraints excluded: chain D residue   29 ILE
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue   44 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN
R 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.121744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.094531 restraints weight = 6090.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.28
r_work: 0.3001 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3581  Z= 0.143
  Angle     :  0.576   6.191   4872  Z= 0.305
  Chirality :  0.041   0.180    582
  Planarity :  0.004   0.051    596
  Dihedral  :  4.021  18.376    476
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 18.28 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.40), residues: 435
  helix:  2.50 (0.31), residues: 270
  sheet: -0.35 (0.80), residues: 42
  loop : -0.82 (0.49), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 264 
 HIS   0.007   0.002   HIS D  25 
 PHE   0.011   0.001   PHE E  24 
 TYR   0.007   0.001   TYR D  20 
 ARG   0.002   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04435 (  230)
  hydrogen bonds       : angle       4.06342 (  672)
  SS BOND              : bond        0.00110 (    6)
  SS BOND              : angle       1.27105 (   12)
  covalent geometry    : bond        0.00333 ( 3575)
  covalent geometry    : angle       0.57321 ( 4860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2342.94 seconds
wall clock time: 41 minutes 8.89 seconds (2468.89 seconds total)