Starting phenix.real_space_refine
on Sat Apr 26 21:37:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xwn_38739/04_2025/8xwn_38739.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xwn_38739/04_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_38739/04_2025/8xwn_38739.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xwn_38739/04_2025/8xwn_38739.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xwn_38739/04_2025/8xwn_38739.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xwn_38739/04_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-5669/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: 2.92, per 1000 atoms: 0.84
  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: 0.92
  Conformation dependent library (CDL) restraints added in 440.2 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: 0.41
  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: 0.91

  Time building geometry restraints manager: 1.08 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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.960
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.340
-------------------------------------------------------------------------------
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  : 0.405 
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: 0.2107
  time to fit residues: 36.4585
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  : 0.406 
-------------------------------------------------------------------------------
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 = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.094338 restraints weight = 6007.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.28
r_work: 0.3032 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
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        0.00243 (    6)
  SS BOND              : angle       1.53901 (   12)
  covalent geometry    : bond        0.00380 ( 3575)
  covalent geometry    : angle       0.55675 ( 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  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  203 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7784 (t0)
REVERT: R  280 GLN cc_start: 0.8741 (mm110) cc_final: 0.8532 (mt0)
REVERT: D   27 LYS cc_start: 0.9386 (ptmt) cc_final: 0.8948 (ttpp)
REVERT: D   31 GLU cc_start: 0.8171 (tt0) cc_final: 0.7936 (tt0)
REVERT: D   43 ASN cc_start: 0.9141 (m-40) cc_final: 0.8506 (p0)
REVERT: D   59 ASP cc_start: 0.8218 (t0) cc_final: 0.7969 (t70)
REVERT: E   49 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8096 (mttp)
  outliers start: 16
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2039
  time to fit residues: 29.3360
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  : 0.392 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   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:    1.1186

-------------------------------------------------------------------------------
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 = 0.3551 r_free = 0.3551 target = 0.120563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.093542 restraints weight = 6058.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.27
r_work: 0.3022 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.3187

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= 0.166
  Angle     :  0.544   5.503   4872  Z= 0.292
  Chirality :  0.042   0.165    582
  Planarity :  0.005   0.058    596
  Dihedral  :  3.842  16.127    476
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 12.01 %
    Favored  : 83.03 %
  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:  2.08 (0.39), residues: 435
  helix:  2.59 (0.31), residues: 270
  sheet: -1.05 (1.16), residues: 20
  loop : -0.64 (0.45), residues: 145

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   0.019   0.001   PHE D  72 
 TYR   0.009   0.001   TYR D  20 
 ARG   0.003   0.001   ARG R 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05044 (  230)
  hydrogen bonds       : angle       4.11905 (  672)
  SS BOND              : bond        0.00170 (    6)
  SS BOND              : angle       1.11089 (   12)
  covalent geometry    : bond        0.00396 ( 3575)
  covalent geometry    : angle       0.54231 ( 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
  127 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9122 (ttmm) cc_final: 0.8752 (mttp)
REVERT: D   28 PHE cc_start: 0.8422 (m-80) cc_final: 0.8122 (m-10)
REVERT: D   54 ARG cc_start: 0.8340 (ptp90) cc_final: 0.7951 (ptp90)
REVERT: D   59 ASP cc_start: 0.8183 (t0) cc_final: 0.7881 (t70)
REVERT: E   15 GLN cc_start: 0.8070 (mp10) cc_final: 0.7791 (mp10)
REVERT: E   49 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8106 (mttp)
REVERT: E   77 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7432 (mm-30)
  outliers start: 19
  outliers final: 15
  residues processed: 119
  average time/residue: 0.1993
  time to fit residues: 27.7567
Evaluate side-chains
  122 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
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  302 LEU
Chi-restraints excluded: chain R residue  304 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0570
   chunk 13 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0270
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3569 r_free = 0.3569 target = 0.122132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.095310 restraints weight = 6065.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.26
r_work: 0.3037 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.3437

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= 0.133
  Angle     :  0.535   5.450   4872  Z= 0.285
  Chirality :  0.041   0.199    582
  Planarity :  0.004   0.049    596
  Dihedral  :  3.851  16.524    476
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 14.10 %
    Favored  : 81.98 %
  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:  2.19 (0.40), residues: 435
  helix:  2.64 (0.31), residues: 270
  sheet: -0.20 (0.90), residues: 30
  loop : -0.68 (0.49), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 112 
 HIS   0.006   0.001   HIS D  25 
 PHE   0.018   0.001   PHE D  72 
 TYR   0.008   0.001   TYR D  20 
 ARG   0.005   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04505 (  230)
  hydrogen bonds       : angle       4.04720 (  672)
  SS BOND              : bond        0.00126 (    6)
  SS BOND              : angle       1.25157 (   12)
  covalent geometry    : bond        0.00305 ( 3575)
  covalent geometry    : angle       0.53235 ( 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
  127 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  323 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.7141 (t-90)
REVERT: R  327 LYS cc_start: 0.9091 (ttmm) cc_final: 0.8724 (mttp)
REVERT: D   28 PHE cc_start: 0.8348 (m-80) cc_final: 0.8060 (m-10)
REVERT: D   43 ASN cc_start: 0.9182 (m-40) cc_final: 0.8551 (p0)
REVERT: D   54 ARG cc_start: 0.8385 (ptp90) cc_final: 0.8013 (ptp90)
REVERT: D   59 ASP cc_start: 0.8149 (t0) cc_final: 0.7850 (t70)
REVERT: E   15 GLN cc_start: 0.8107 (mp10) cc_final: 0.7758 (mp10)
REVERT: E   49 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8172 (mttp)
  outliers start: 15
  outliers final: 11
  residues processed: 120
  average time/residue: 0.1879
  time to fit residues: 26.6160
Evaluate side-chains
  118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
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  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   50 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.119766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.092712 restraints weight = 6103.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.27
r_work: 0.3008 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3581  Z= 0.183
  Angle     :  0.597  11.895   4872  Z= 0.307
  Chirality :  0.043   0.200    582
  Planarity :  0.004   0.050    596
  Dihedral  :  4.084  17.186    476
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 15.40 %
    Favored  : 79.37 %
  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:  2.58 (0.31), residues: 268
  sheet: -0.37 (0.78), residues: 42
  loop : -0.75 (0.51), 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   0.015   0.002   PHE D  72 
 TYR   0.010   0.001   TYR E  20 
 ARG   0.003   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04948 (  230)
  hydrogen bonds       : angle       4.18388 (  672)
  SS BOND              : bond        0.00252 (    6)
  SS BOND              : angle       1.65470 (   12)
  covalent geometry    : bond        0.00444 ( 3575)
  covalent geometry    : angle       0.59168 ( 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
  131 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  284 GLU cc_start: 0.8165 (tt0) cc_final: 0.7916 (tt0)
REVERT: R  327 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8687 (mttp)
REVERT: D   28 PHE cc_start: 0.8424 (m-80) cc_final: 0.8150 (m-10)
REVERT: D   54 ARG cc_start: 0.8348 (ptp90) cc_final: 0.8004 (ptp90)
REVERT: D   59 ASP cc_start: 0.8159 (t0) cc_final: 0.7854 (t70)
REVERT: E   49 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8236 (mttp)
  outliers start: 20
  outliers final: 15
  residues processed: 124
  average time/residue: 0.1700
  time to fit residues: 25.2151
Evaluate side-chains
  121 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 38 optimal weight:    0.1980
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.121489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.094558 restraints weight = 6162.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.28
r_work: 0.3037 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3581  Z= 0.135
  Angle     :  0.539   7.473   4872  Z= 0.284
  Chirality :  0.041   0.203    582
  Planarity :  0.004   0.049    596
  Dihedral  :  4.033  18.372    476
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 16.45 %
    Favored  : 79.63 %
  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:  2.19 (0.40), residues: 435
  helix:  2.67 (0.31), residues: 268
  sheet: -0.39 (0.78), residues: 42
  loop : -0.63 (0.52), residues: 125

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 264 
 HIS   0.005   0.001   HIS D  25 
 PHE   0.016   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        0.04472 (  230)
  hydrogen bonds       : angle       4.09386 (  672)
  SS BOND              : bond        0.00144 (    6)
  SS BOND              : angle       1.35615 (   12)
  covalent geometry    : bond        0.00315 ( 3575)
  covalent geometry    : angle       0.53582 ( 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
  120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8532 (mptt)
REVERT: D   28 PHE cc_start: 0.8433 (m-80) cc_final: 0.8177 (m-10)
REVERT: D   54 ARG cc_start: 0.8417 (ptp90) cc_final: 0.8004 (ptp90)
REVERT: D   59 ASP cc_start: 0.8060 (t0) cc_final: 0.7736 (t70)
REVERT: E   15 GLN cc_start: 0.8085 (mp10) cc_final: 0.7750 (mp10)
REVERT: E   49 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8258 (mttp)
  outliers start: 15
  outliers final: 11
  residues processed: 116
  average time/residue: 0.1820
  time to fit residues: 25.1859
Evaluate side-chains
  113 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
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 D residue   50 LEU
Chi-restraints excluded: chain E residue   49 LYS
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:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 216 GLN
R 319 GLN
D  43 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.121866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.094629 restraints weight = 6041.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.24
r_work: 0.3036 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3581  Z= 0.141
  Angle     :  0.551   8.119   4872  Z= 0.287
  Chirality :  0.041   0.151    582
  Planarity :  0.004   0.047    596
  Dihedral  :  3.991  18.407    476
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 4.94
  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:  2.16 (0.40), residues: 435
  helix:  2.60 (0.31), residues: 270
  sheet: -0.38 (0.78), residues: 42
  loop : -0.60 (0.52), residues: 123

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   0.015   0.001   TYR E  20 
 ARG   0.003   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04464 (  230)
  hydrogen bonds       : angle       4.05679 (  672)
  SS BOND              : bond        0.00182 (    6)
  SS BOND              : angle       1.39213 (   12)
  covalent geometry    : bond        0.00329 ( 3575)
  covalent geometry    : angle       0.54690 ( 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
  116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8538 (mptt)
REVERT: D   28 PHE cc_start: 0.8432 (m-80) cc_final: 0.8185 (m-10)
REVERT: D   43 ASN cc_start: 0.9219 (m-40) cc_final: 0.8555 (p0)
REVERT: D   54 ARG cc_start: 0.8437 (ptp90) cc_final: 0.8038 (ptp90)
REVERT: D   59 ASP cc_start: 0.8039 (t0) cc_final: 0.7739 (t70)
REVERT: E   49 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8210 (mttp)
REVERT: E   57 CYS cc_start: 0.6976 (m) cc_final: 0.6560 (m)
  outliers start: 14
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1814
  time to fit residues: 24.3524
Evaluate side-chains
  113 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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  216 GLN
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   50 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain E residue   49 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 17 optimal weight:    0.3980
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN
R 216 GLN
R 319 GLN
E  25 HIS
E  66 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.122538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.095340 restraints weight = 6012.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.27
r_work: 0.3049 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.4015

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= 0.134
  Angle     :  0.547   6.926   4872  Z= 0.288
  Chirality :  0.041   0.161    582
  Planarity :  0.004   0.047    596
  Dihedral  :  3.974  18.878    476
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.28 %
    Favored  : 77.81 %
  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:  2.16 (0.40), residues: 435
  helix:  2.61 (0.31), residues: 270
  sheet: -0.36 (0.79), residues: 42
  loop : -0.62 (0.52), residues: 123

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   0.015   0.001   PHE D  72 
 TYR   0.006   0.001   TYR D  20 
 ARG   0.002   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04352 (  230)
  hydrogen bonds       : angle       4.02739 (  672)
  SS BOND              : bond        0.00150 (    6)
  SS BOND              : angle       1.29352 (   12)
  covalent geometry    : bond        0.00304 ( 3575)
  covalent geometry    : angle       0.54346 ( 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
  120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9038 (ttmm) cc_final: 0.8685 (mptt)
REVERT: D   28 PHE cc_start: 0.8456 (m-80) cc_final: 0.8204 (m-10)
REVERT: D   43 ASN cc_start: 0.9221 (m-40) cc_final: 0.8536 (p0)
REVERT: D   54 ARG cc_start: 0.8438 (ptp90) cc_final: 0.8045 (ptp90)
REVERT: D   59 ASP cc_start: 0.8035 (t0) cc_final: 0.7737 (t70)
REVERT: E   15 GLN cc_start: 0.8106 (mp10) cc_final: 0.7813 (mp10)
REVERT: E   57 CYS cc_start: 0.6978 (m) cc_final: 0.6574 (m)
  outliers start: 15
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1822
  time to fit residues: 25.1187
Evaluate side-chains
  116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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  325 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   69 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:   10.9990
   chunk 5 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN
R 216 GLN
R 319 GLN
E  66 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.121326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.093942 restraints weight = 6011.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 2.29
r_work: 0.3032 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.4134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3581  Z= 0.151
  Angle     :  0.565   5.810   4872  Z= 0.300
  Chirality :  0.042   0.157    582
  Planarity :  0.004   0.047    596
  Dihedral  :  4.013  18.591    476
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 18.02 %
    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:  2.51 (0.31), residues: 270
  sheet: -0.59 (0.75), residues: 42
  loop : -0.70 (0.51), residues: 123

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   0.013   0.001   PHE D  72 
 TYR   0.015   0.001   TYR E  20 
 ARG   0.002   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  230)
  hydrogen bonds       : angle       4.06596 (  672)
  SS BOND              : bond        0.00160 (    6)
  SS BOND              : angle       1.39381 (   12)
  covalent geometry    : bond        0.00353 ( 3575)
  covalent geometry    : angle       0.56154 ( 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
  115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8676 (mptt)
REVERT: D   28 PHE cc_start: 0.8480 (m-80) cc_final: 0.8235 (m-10)
REVERT: D   43 ASN cc_start: 0.9233 (m-40) cc_final: 0.8545 (p0)
REVERT: D   54 ARG cc_start: 0.8429 (ptp90) cc_final: 0.8034 (ptp90)
REVERT: D   59 ASP cc_start: 0.8084 (t0) cc_final: 0.7786 (t70)
REVERT: E   15 GLN cc_start: 0.8057 (mp10) cc_final: 0.7737 (mp10)
  outliers start: 15
  outliers final: 13
  residues processed: 112
  average time/residue: 0.1877
  time to fit residues: 24.9162
Evaluate side-chains
  112 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
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  325 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   69 VAL
Chi-restraints excluded: chain E residue   63 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0670
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
R 216 GLN
R 319 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.122333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.095259 restraints weight = 6026.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.26
r_work: 0.3044 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.4197

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= 0.131
  Angle     :  0.552   6.114   4872  Z= 0.293
  Chirality :  0.041   0.151    582
  Planarity :  0.004   0.050    596
  Dihedral  :  4.049  19.232    476
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 17.75 %
    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:  2.06 (0.40), residues: 435
  helix:  2.57 (0.31), residues: 270
  sheet: -0.63 (0.75), residues: 42
  loop : -0.66 (0.51), residues: 123

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04334 (  230)
  hydrogen bonds       : angle       4.02546 (  672)
  SS BOND              : bond        0.00150 (    6)
  SS BOND              : angle       1.35218 (   12)
  covalent geometry    : bond        0.00297 ( 3575)
  covalent geometry    : angle       0.54858 ( 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
  115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: R  327 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8688 (mptt)
REVERT: D   28 PHE cc_start: 0.8502 (m-80) cc_final: 0.8264 (m-10)
REVERT: D   54 ARG cc_start: 0.8412 (ptp90) cc_final: 0.8015 (ptp90)
REVERT: D   59 ASP cc_start: 0.7967 (t0) cc_final: 0.7680 (t70)
  outliers start: 15
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1860
  time to fit residues: 24.7137
Evaluate side-chains
  113 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
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  325 LEU
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   63 ASN
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:    0.6980
   chunk 23 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0570
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0040
   overall best weight:    0.3910

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

Flipped N/Q/H residues before XYZ refinement:
R 129 ASN
R 216 GLN
D  43 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.123687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.096565 restraints weight = 6025.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.30
r_work: 0.3070 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.4367

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= 0.122
  Angle     :  0.547   6.440   4872  Z= 0.291
  Chirality :  0.041   0.145    582
  Planarity :  0.004   0.049    596
  Dihedral  :  3.947  19.316    476
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.54 %
    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:  2.05 (0.40), residues: 435
  helix:  2.58 (0.31), residues: 270
  sheet: -0.19 (0.87), residues: 32
  loop : -0.88 (0.50), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP R 264 
 HIS   0.007   0.001   HIS D  25 
 PHE   0.013   0.001   PHE E  24 
 TYR   0.007   0.001   TYR D  20 
 ARG   0.003   0.000   ARG R 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04069 (  230)
  hydrogen bonds       : angle       3.97341 (  672)
  SS BOND              : bond        0.00142 (    6)
  SS BOND              : angle       1.28387 (   12)
  covalent geometry    : bond        0.00266 ( 3575)
  covalent geometry    : angle       0.54378 ( 4860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2505.33 seconds
wall clock time: 43 minutes 28.91 seconds (2608.91 seconds total)