Starting phenix.real_space_refine
on Wed Mar  5 22:43:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d4g_30573/03_2025/7d4g_30573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d4g_30573/03_2025/7d4g_30573.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d4g_30573/03_2025/7d4g_30573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d4g_30573/03_2025/7d4g_30573.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d4g_30573/03_2025/7d4g_30573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d4g_30573/03_2025/7d4g_30573.cif"
  }
  resolution = 3.9
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2510      2.51       5
     N     648      2.21       5
     O     752      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3925
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 2206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2206
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 14, 'TRANS': 258}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 788
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 6, 'TRANS': 102}
    Chain: "N"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 931
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 6, 'TRANS': 113}
  Time building chain proxies: 3.42, per 1000 atoms: 0.87
  Number of scatterers: 3925
  At special positions: 0
  Unit cell: (60.32, 99.84, 90.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     752      8.00
     N     648      7.00
     C    2510      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  15 " - pdb=" SG  CYS B 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  97 " 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: 0.82
  Conformation dependent library (CDL) restraints added in 507.2 milliseconds
  

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  920

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 11 sheets defined
      2.6% alpha, 35.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'B' and resid 156 through 158
      No H-bonds generated for 'chain 'B' and resid 156 through 158'
    Processing helix  chain 'G' and resid 80 through 84
      removed outlier: 4.334A  pdb=" N   GLU G  84 " --> pdb=" O   THR G  81 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 29 through 33
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31
      removed outlier: 4.087A  pdb=" N   SER B  31 " --> pdb=" O   SER B  60 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER B  60 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU B 191 " --> pdb=" O   LYS B 206 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS B 195 " --> pdb=" O   LYS B 202 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   PHE B 201 " --> pdb=" O   ASP B 228 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   ASP B 228 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ILE B 203 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER B 205 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU B 224 " --> pdb=" O   SER B 205 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55
      removed outlier: 3.918A  pdb=" N   THR B  51 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85
    Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 104
      removed outlier: 6.015A  pdb=" N   ILE B 101 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ALA B 243 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   GLY B 103 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 120
      removed outlier: 3.813A  pdb=" N   VAL B 127 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   GLU B 132 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   CYS B 166 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   GLN B 134 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 8.964A  pdb=" N   ASN B 164 " --> pdb=" O   GLN B 134 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 9 through 12
      removed outlier: 3.689A  pdb=" N   ASP G  86 " --> pdb=" O   GLN G  39 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL G  34 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   TYR G  50 " --> pdb=" O   VAL G  34 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   TRP G  36 " --> pdb=" O   LEU G  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 9 through 12
      removed outlier: 3.734A  pdb=" N   THR G  91 " --> pdb=" O   VAL G 100 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL G 100 " --> pdb=" O   THR G  91 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 20 through 23
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 4
      removed outlier: 3.836A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 22 through 23
      removed outlier: 3.602A  pdb=" N   ALA N  80 " --> pdb=" O   CYS N  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 46 through 49

    109 hydrogen bonds defined for protein.
    264 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1217
        1.34 -     1.46: 914
        1.46 -     1.58: 1876
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 4029
  Sorted by residual:
  bond pdb=" C   LEU B 229 "
       pdb=" N   PRO B 230 "
    ideal  model  delta    sigma   weight residual
    1.334  1.431 -0.097 2.34e-02 1.83e+03 1.72e+01
  bond pdb=" N   VAL B  47 "
       pdb=" CA  VAL B  47 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.11e-02 8.12e+03 1.11e+01
  bond pdb=" N   ILE B 285 "
       pdb=" CA  ILE B 285 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.040 1.19e-02 7.06e+03 1.10e+01
  bond pdb=" N   ILE B 203 "
       pdb=" CA  ILE B 203 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.20e-02 6.94e+03 9.50e+00
  bond pdb=" N   VAL B  42 "
       pdb=" CA  VAL B  42 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.32e+00
  ... (remaining 4024 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.61: 5426
        3.61 -     7.22: 52
        7.22 -    10.83: 6
       10.83 -    14.45: 0
       14.45 -    18.06: 1
  Bond angle restraints: 5485
  Sorted by residual:
  angle pdb=" N   ALA B 123 "
        pdb=" CA  ALA B 123 "
        pdb=" C   ALA B 123 "
      ideal   model   delta    sigma   weight residual
     107.57  125.63  -18.06 1.94e+00 2.66e-01 8.66e+01
  angle pdb=" N   THR B 124 "
        pdb=" CA  THR B 124 "
        pdb=" C   THR B 124 "
      ideal   model   delta    sigma   weight residual
     111.71  102.70    9.01 1.15e+00 7.56e-01 6.14e+01
  angle pdb=" C   ALA B 123 "
        pdb=" N   THR B 124 "
        pdb=" CA  THR B 124 "
      ideal   model   delta    sigma   weight residual
     120.28  109.69   10.59 1.44e+00 4.82e-01 5.41e+01
  angle pdb=" N   GLY B  72 "
        pdb=" CA  GLY B  72 "
        pdb=" C   GLY B  72 "
      ideal   model   delta    sigma   weight residual
     110.97  118.64   -7.67 1.56e+00 4.11e-01 2.42e+01
  angle pdb=" N   THR N 101 "
        pdb=" CA  THR N 101 "
        pdb=" C   THR N 101 "
      ideal   model   delta    sigma   weight residual
     109.64  115.61   -5.97 1.27e+00 6.20e-01 2.21e+01
  ... (remaining 5480 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.12: 2256
       16.12 -    32.23: 72
       32.23 -    48.35: 19
       48.35 -    64.46: 1
       64.46 -    80.58: 4
  Dihedral angle restraints: 2352
    sinusoidal: 908
      harmonic: 1444
  Sorted by residual:
  dihedral pdb=" CA  TYR B 248 "
           pdb=" C   TYR B 248 "
           pdb=" N   LEU B 249 "
           pdb=" CA  LEU B 249 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.81  -38.19     0      5.00e+00 4.00e-02 5.83e+01
  dihedral pdb=" CA  SER N   8 "
           pdb=" C   SER N   8 "
           pdb=" N   GLY N   9 "
           pdb=" CA  GLY N   9 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.92  -35.08     0      5.00e+00 4.00e-02 4.92e+01
  dihedral pdb=" CA  ALA B 123 "
           pdb=" C   ALA B 123 "
           pdb=" N   THR B 124 "
           pdb=" CA  THR B 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.99   30.01     0      5.00e+00 4.00e-02 3.60e+01
  ... (remaining 2349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 544
       0.095 -    0.190: 56
       0.190 -    0.285: 1
       0.285 -    0.380: 0
       0.380 -    0.476: 2
  Chirality restraints: 603
  Sorted by residual:
  chirality pdb=" CA  SER N 104 "
            pdb=" N   SER N 104 "
            pdb=" C   SER N 104 "
            pdb=" CB  SER N 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.65e+00
  chirality pdb=" CA  ALA B 123 "
            pdb=" N   ALA B 123 "
            pdb=" C   ALA B 123 "
            pdb=" CB  ALA B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.04    0.45 2.00e-01 2.50e+01 5.02e+00
  chirality pdb=" CA  LEU B 276 "
            pdb=" N   LEU B 276 "
            pdb=" C   LEU B 276 "
            pdb=" CB  LEU B 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 600 not shown)

  Planarity restraints: 703
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 122 "    0.015 2.00e-02 2.50e+03   3.16e-02 9.96e+00
        pdb=" C   ASN B 122 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASN B 122 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ALA B 123 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 120 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.23e+00
        pdb=" C   VAL B 120 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL B 120 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASN B 121 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO N 102 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.95e+00
        pdb=" C   PRO N 102 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   PRO N 102 "    0.015 2.00e-02 2.50e+03
        pdb=" N   PHE N 103 "    0.013 2.00e-02 2.50e+03
  ... (remaining 700 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 56
        2.51 -     3.11: 3143
        3.11 -     3.71: 6126
        3.71 -     4.30: 8710
        4.30 -     4.90: 14193
  Nonbonded interactions: 32228
  Sorted by model distance:
  nonbonded pdb=" O   GLU N  32 "
            pdb=" CG  PRO N 102 "
     model   vdw
     1.917 3.440
  nonbonded pdb=" O   ASP N  91 "
            pdb=" OH  TYR N  95 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" O   GLU N  32 "
            pdb=" CB  PRO N 102 "
     model   vdw
     2.123 3.440
  nonbonded pdb=" NH1 ARG B 273 "
            pdb=" OD2 ASP B 290 "
     model   vdw
     2.126 3.120
  nonbonded pdb=" CB  PRO N  54 "
            pdb=" CB  SER N 104 "
     model   vdw
     2.132 3.840
  ... (remaining 32223 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.450
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.500
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5098
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      :  0.006   0.097   4029  Z= 0.395
  Angle     :  1.065  18.058   5485  Z= 0.654
  Chirality :  0.061   0.476    603
  Planarity :  0.006   0.044    703
  Dihedral  :  9.868  80.579   1420
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 36.47
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  : 10.73 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.64 %

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: -3.84 (0.29), residues: 494
  helix: -4.21 (0.49), residues: 6
  sheet: -1.91 (0.36), residues: 126
  loop : -3.00 (0.26), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP B  64 
 HIS   0.007   0.002   HIS N  36 
 PHE   0.027   0.003   PHE B 106 
 TYR   0.018   0.002   TYR N  28 
 ARG   0.003   0.001   ARG B 190 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   78 ARG cc_start: 0.6915 (mmt90) cc_final: 0.6522 (tmm-80)
REVERT: B   80 ASP cc_start: 0.7559 (t70) cc_final: 0.7359 (t0)
REVERT: N   39 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7178 (mtp180)
REVERT: N   55 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7106 (mt-10)
REVERT: N   82 MET cc_start: 0.7286 (ttp) cc_final: 0.7071 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1843
  time to fit residues: 32.5096
Evaluate side-chains
  95 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 282 ASN
G   6 GLN
G  39 GLN
G  80 GLN
** N   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.223303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.161064 restraints weight = 4274.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.165416 restraints weight = 3352.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.168581 restraints weight = 2709.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6615
moved from start:          0.4351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4029  Z= 0.249
  Angle     :  0.836  11.545   5485  Z= 0.432
  Chirality :  0.048   0.229    603
  Planarity :  0.005   0.042    703
  Dihedral  :  7.412  45.207    541
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.91 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 13.66 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -3.28 (0.31), residues: 494
  helix:  None (None), residues: 0
  sheet: -1.22 (0.37), residues: 143
  loop : -2.81 (0.27), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP N 112 
 HIS   0.005   0.002   HIS B  49 
 PHE   0.030   0.003   PHE B 106 
 TYR   0.024   0.002   TYR G  88 
 ARG   0.004   0.001   ARG B  44 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  168 PHE cc_start: 0.7480 (t80) cc_final: 0.7255 (t80)
REVERT: B  177 MET cc_start: 0.5888 (ppp) cc_final: 0.5321 (mtp)
REVERT: G   48 LEU cc_start: 0.8695 (mt) cc_final: 0.8356 (mp)
REVERT: G   74 LEU cc_start: 0.9007 (tp) cc_final: 0.8550 (tt)
REVERT: N   53 ASP cc_start: 0.7983 (t0) cc_final: 0.7757 (t0)
REVERT: N   55 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7274 (mt-10)
REVERT: N   60 MET cc_start: 0.5991 (mmp) cc_final: 0.5688 (mmm)
  outliers start: 16
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1783
  time to fit residues: 22.7266
Evaluate side-chains
  86 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue  101 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 4 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0040
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8396

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

Flipped N/Q/H residues before XYZ refinement:
B  69 HIS
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.211015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.145824 restraints weight = 4410.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.150039 restraints weight = 3419.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.153063 restraints weight = 2826.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
moved from start:          0.5839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4029  Z= 0.279
  Angle     :  0.795  14.799   5485  Z= 0.403
  Chirality :  0.047   0.195    603
  Planarity :  0.005   0.037    703
  Dihedral  :  6.803  41.252    541
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 18.04
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.51 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.82 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -3.00 (0.34), residues: 494
  helix:  None (None), residues: 0
  sheet: -1.08 (0.36), residues: 187
  loop : -2.74 (0.31), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.004   TRP N 112 
 HIS   0.004   0.002   HIS B 207 
 PHE   0.024   0.003   PHE B 135 
 TYR   0.023   0.002   TYR B 248 
 ARG   0.008   0.001   ARG B 214 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 PHE cc_start: 0.7538 (m-10) cc_final: 0.7335 (m-10)
REVERT: B  116 SER cc_start: 0.7284 (m) cc_final: 0.6913 (p)
REVERT: B  177 MET cc_start: 0.6135 (ppp) cc_final: 0.5504 (mtp)
REVERT: B  215 ASP cc_start: 0.6275 (OUTLIER) cc_final: 0.5641 (p0)
REVERT: B  224 GLU cc_start: 0.7945 (pm20) cc_final: 0.7657 (pm20)
REVERT: G   48 LEU cc_start: 0.8841 (mt) cc_final: 0.8441 (mp)
REVERT: G   74 LEU cc_start: 0.8846 (tp) cc_final: 0.8304 (tp)
REVERT: N   39 ARG cc_start: 0.8555 (mtp180) cc_final: 0.7842 (mtp180)
REVERT: N   53 ASP cc_start: 0.8311 (t0) cc_final: 0.8071 (t0)
REVERT: N   55 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7279 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 112
  average time/residue: 0.1565
  time to fit residues: 21.5698
Evaluate side-chains
  98 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    5.9990
   chunk 4 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 HIS
** G  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.226337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.145065 restraints weight = 4752.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.150004 restraints weight = 3421.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.154299 restraints weight = 2724.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.6512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4029  Z= 0.240
  Angle     :  0.773  13.086   5485  Z= 0.383
  Chirality :  0.046   0.199    603
  Planarity :  0.005   0.036    703
  Dihedral  :  6.280  33.531    541
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.12 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 16.20 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -2.79 (0.35), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.96 (0.37), residues: 186
  loop : -2.57 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.004   TRP N 112 
 HIS   0.003   0.001   HIS B  69 
 PHE   0.021   0.003   PHE N 109 
 TYR   0.026   0.002   TYR G  37 
 ARG   0.008   0.001   ARG B  78 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   18 LEU cc_start: 0.8043 (pt) cc_final: 0.7758 (pt)
REVERT: B   79 PHE cc_start: 0.6695 (m-80) cc_final: 0.5943 (m-80)
REVERT: B  168 PHE cc_start: 0.7885 (t80) cc_final: 0.7665 (t80)
REVERT: B  177 MET cc_start: 0.5960 (ppp) cc_final: 0.5476 (mtp)
REVERT: B  224 GLU cc_start: 0.8091 (pm20) cc_final: 0.7745 (pm20)
REVERT: G   48 LEU cc_start: 0.8825 (mt) cc_final: 0.8412 (mp)
REVERT: G   74 LEU cc_start: 0.8927 (tp) cc_final: 0.8442 (tp)
REVERT: G  106 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7965 (mmtm)
REVERT: N   39 ARG cc_start: 0.8777 (mtp180) cc_final: 0.8132 (mtp180)
REVERT: N   53 ASP cc_start: 0.8363 (t0) cc_final: 0.8123 (t0)
REVERT: N   55 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7344 (mt-10)
REVERT: N   71 MET cc_start: 0.9197 (ppp) cc_final: 0.8922 (ppp)
  outliers start: 23
  outliers final: 17
  residues processed: 112
  average time/residue: 0.1615
  time to fit residues: 22.1611
Evaluate side-chains
  103 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain N residue  107 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 1 optimal weight:    0.2980
   chunk 43 optimal weight:    0.0970
   chunk 35 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** B  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 GLN
G  32 ASN
N   7 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4584 r_free = 0.4584 target = 0.224995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.143695 restraints weight = 4913.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.149099 restraints weight = 3442.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.153418 restraints weight = 2702.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.7065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4029  Z= 0.208
  Angle     :  0.749   9.147   5485  Z= 0.375
  Chirality :  0.046   0.185    603
  Planarity :  0.005   0.038    703
  Dihedral  :  5.982  28.972    541
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.32 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 17.36 %
    Favored  : 76.85 %
  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: -2.64 (0.35), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.84 (0.37), residues: 189
  loop : -2.49 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP N 112 
 HIS   0.002   0.001   HIS B 245 
 PHE   0.015   0.002   PHE B 135 
 TYR   0.017   0.002   TYR B 248 
 ARG   0.007   0.001   ARG B 273 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 PHE cc_start: 0.6566 (m-80) cc_final: 0.6295 (m-80)
REVERT: B  177 MET cc_start: 0.5988 (ppp) cc_final: 0.5586 (mtt)
REVERT: G   36 TRP cc_start: 0.8041 (m100) cc_final: 0.7643 (m100)
REVERT: G   48 LEU cc_start: 0.8826 (mt) cc_final: 0.8420 (mp)
REVERT: G   54 LYS cc_start: 0.7684 (mmtp) cc_final: 0.7475 (mmtp)
REVERT: G   74 LEU cc_start: 0.8853 (tp) cc_final: 0.8471 (tp)
REVERT: G  106 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7908 (mmtm)
REVERT: N   37 TRP cc_start: 0.8610 (m100) cc_final: 0.8078 (m100)
REVERT: N   39 ARG cc_start: 0.8864 (mtp180) cc_final: 0.8212 (mtp180)
REVERT: N   53 ASP cc_start: 0.8281 (t0) cc_final: 0.7947 (t0)
REVERT: N   55 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7402 (mt-10)
REVERT: N   71 MET cc_start: 0.9067 (ppp) cc_final: 0.8616 (ppp)
REVERT: N   82 MET cc_start: 0.8560 (tmm) cc_final: 0.7895 (tmm)
REVERT: N   96 TYR cc_start: 0.8727 (m-80) cc_final: 0.8158 (m-10)
REVERT: N  112 TRP cc_start: 0.6186 (p90) cc_final: 0.5792 (p90)
  outliers start: 25
  outliers final: 21
  residues processed: 109
  average time/residue: 0.1626
  time to fit residues: 22.1440
Evaluate side-chains
  103 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain N residue  107 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0570
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
B  69 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.214369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.137275 restraints weight = 4580.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.137456 restraints weight = 3477.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.138903 restraints weight = 2932.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.7459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4029  Z= 0.238
  Angle     :  0.748   9.251   5485  Z= 0.377
  Chirality :  0.045   0.152    603
  Planarity :  0.005   0.039    703
  Dihedral  :  5.893  26.030    541
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.93 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 20.14 %
    Favored  : 73.84 %
  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: -2.42 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.60 (0.38), residues: 185
  loop : -2.39 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP N 112 
 HIS   0.003   0.001   HIS B 207 
 PHE   0.019   0.002   PHE N 109 
 TYR   0.022   0.002   TYR B 145 
 ARG   0.005   0.001   ARG G  55 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 PHE cc_start: 0.6637 (m-80) cc_final: 0.6395 (m-80)
REVERT: B  177 MET cc_start: 0.6037 (ppp) cc_final: 0.5589 (mtt)
REVERT: B  224 GLU cc_start: 0.8151 (pm20) cc_final: 0.7688 (pm20)
REVERT: G   48 LEU cc_start: 0.8853 (mt) cc_final: 0.8453 (mp)
REVERT: G   55 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.8208 (mtp85)
REVERT: G   74 LEU cc_start: 0.8773 (tp) cc_final: 0.8501 (tp)
REVERT: G  106 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7897 (mmtm)
REVERT: N   37 TRP cc_start: 0.8609 (m100) cc_final: 0.8140 (m100)
REVERT: N   39 ARG cc_start: 0.8723 (mtp180) cc_final: 0.8165 (mtp180)
REVERT: N   53 ASP cc_start: 0.8245 (t0) cc_final: 0.8016 (t0)
REVERT: N   55 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7421 (mt-10)
REVERT: N   82 MET cc_start: 0.8227 (tmm) cc_final: 0.7807 (tmm)
REVERT: N   96 TYR cc_start: 0.8574 (m-80) cc_final: 0.8077 (m-10)
REVERT: N  112 TRP cc_start: 0.5956 (p90) cc_final: 0.5645 (p90)
  outliers start: 26
  outliers final: 24
  residues processed: 100
  average time/residue: 0.1446
  time to fit residues: 18.2441
Evaluate side-chains
  105 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  150 LYS
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   17 LYS
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   49 ILE
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  107 TYR
Chi-restraints excluded: chain N residue  109 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 34 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 0 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0070
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
G  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.213041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.129067 restraints weight = 4579.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.133475 restraints weight = 3362.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.136599 restraints weight = 2696.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.7785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4029  Z= 0.224
  Angle     :  0.725   9.049   5485  Z= 0.366
  Chirality :  0.045   0.148    603
  Planarity :  0.005   0.040    703
  Dihedral  :  5.721  26.575    541
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.93 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 20.37 %
    Favored  : 73.15 %
  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: -2.32 (0.37), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.52 (0.39), residues: 185
  loop : -2.32 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP G  36 
 HIS   0.003   0.001   HIS B 207 
 PHE   0.023   0.002   PHE B  58 
 TYR   0.016   0.002   TYR B 248 
 ARG   0.004   0.001   ARG G  55 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 92
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 PHE cc_start: 0.6786 (m-80) cc_final: 0.6573 (m-80)
REVERT: B  177 MET cc_start: 0.6076 (ppp) cc_final: 0.5617 (mtt)
REVERT: B  224 GLU cc_start: 0.8185 (pm20) cc_final: 0.7705 (pm20)
REVERT: G   36 TRP cc_start: 0.8005 (m100) cc_final: 0.7380 (m100)
REVERT: G   48 LEU cc_start: 0.8857 (mt) cc_final: 0.8458 (mp)
REVERT: G   74 LEU cc_start: 0.8851 (tp) cc_final: 0.8589 (tp)
REVERT: N   37 TRP cc_start: 0.8645 (m100) cc_final: 0.8100 (m100)
REVERT: N   39 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8320 (mtp180)
REVERT: N   53 ASP cc_start: 0.8329 (t0) cc_final: 0.8040 (t0)
REVERT: N   55 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7541 (mt-10)
REVERT: N   82 MET cc_start: 0.8550 (tmm) cc_final: 0.8091 (tmm)
REVERT: N   96 TYR cc_start: 0.8693 (m-80) cc_final: 0.8261 (m-10)
REVERT: N  112 TRP cc_start: 0.5862 (p90) cc_final: 0.5477 (p90)
  outliers start: 28
  outliers final: 22
  residues processed: 109
  average time/residue: 0.1483
  time to fit residues: 20.2349
Evaluate side-chains
  106 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   17 LYS
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue   99 THR
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain N residue  107 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    0.2980
   chunk 6 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.215814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.135581 restraints weight = 4509.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.136776 restraints weight = 3512.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.137535 restraints weight = 2822.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.8072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4029  Z= 0.229
  Angle     :  0.758  10.674   5485  Z= 0.378
  Chirality :  0.045   0.177    603
  Planarity :  0.005   0.046    703
  Dihedral  :  5.624  26.353    541
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 15.06
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.93 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 21.30 %
    Favored  : 72.69 %
  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: -2.24 (0.37), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.49 (0.38), residues: 191
  loop : -2.28 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP G  36 
 HIS   0.003   0.001   HIS B 207 
 PHE   0.026   0.002   PHE B  58 
 TYR   0.015   0.002   TYR B 248 
 ARG   0.009   0.001   ARG B 273 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.6564 (mm-40) cc_final: 0.5773 (pt0)
REVERT: B   79 PHE cc_start: 0.6793 (m-80) cc_final: 0.6358 (m-80)
REVERT: B  150 LYS cc_start: 0.6660 (mmmt) cc_final: 0.6285 (tptp)
REVERT: B  177 MET cc_start: 0.6031 (ppp) cc_final: 0.5660 (mtt)
REVERT: B  224 GLU cc_start: 0.8140 (pm20) cc_final: 0.7682 (pm20)
REVERT: G   36 TRP cc_start: 0.7661 (m100) cc_final: 0.7435 (m100)
REVERT: G   48 LEU cc_start: 0.8800 (mt) cc_final: 0.8464 (mp)
REVERT: G   55 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7912 (ttt-90)
REVERT: G   74 LEU cc_start: 0.8698 (tp) cc_final: 0.8483 (tp)
REVERT: N   37 TRP cc_start: 0.8559 (m100) cc_final: 0.8129 (m100)
REVERT: N   39 ARG cc_start: 0.8664 (mtp180) cc_final: 0.8137 (mtp180)
REVERT: N   55 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7785 (mt-10)
REVERT: N   82 MET cc_start: 0.7970 (tmm) cc_final: 0.7597 (tmm)
  outliers start: 26
  outliers final: 23
  residues processed: 109
  average time/residue: 0.1426
  time to fit residues: 19.6654
Evaluate side-chains
  111 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue   99 THR
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain N residue  107 TYR
Chi-restraints excluded: chain N residue  109 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0970
   chunk 43 optimal weight:    0.0170
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
** B  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  32 ASN
N   7 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.209255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.144137 restraints weight = 4370.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.147461 restraints weight = 3503.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.149718 restraints weight = 2962.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6868
moved from start:          0.8317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4029  Z= 0.212
  Angle     :  0.778  10.891   5485  Z= 0.389
  Chirality :  0.046   0.237    603
  Planarity :  0.006   0.086    703
  Dihedral  :  5.741  26.649    541
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 15.84
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.34 %
    Favored  : 88.46 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 23.84 %
    Favored  : 71.76 %
  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 (0.38), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.44 (0.39), residues: 190
  loop : -2.25 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.003   TRP N 112 
 HIS   0.002   0.001   HIS B 245 
 PHE   0.023   0.002   PHE N 109 
 TYR   0.013   0.001   TYR N  81 
 ARG   0.009   0.001   ARG G  55 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.6951 (mm-40) cc_final: 0.5952 (pt0)
REVERT: B   79 PHE cc_start: 0.6816 (m-80) cc_final: 0.6290 (m-80)
REVERT: B  150 LYS cc_start: 0.6690 (mmmt) cc_final: 0.6286 (tptp)
REVERT: B  177 MET cc_start: 0.6046 (ppp) cc_final: 0.5746 (mtt)
REVERT: B  224 GLU cc_start: 0.8144 (pm20) cc_final: 0.7644 (pm20)
REVERT: G   36 TRP cc_start: 0.7883 (m100) cc_final: 0.7362 (m100)
REVERT: G   48 LEU cc_start: 0.8786 (mt) cc_final: 0.8416 (mp)
REVERT: N   37 TRP cc_start: 0.8632 (m100) cc_final: 0.8219 (m100)
REVERT: N   39 ARG cc_start: 0.8863 (mtp180) cc_final: 0.8251 (mtp180)
REVERT: N   61 TYR cc_start: 0.7338 (m-80) cc_final: 0.6582 (m-80)
REVERT: N   71 MET cc_start: 0.8637 (ppp) cc_final: 0.8007 (ppp)
REVERT: N   82 MET cc_start: 0.8253 (tmm) cc_final: 0.7777 (tmm)
  outliers start: 19
  outliers final: 17
  residues processed: 103
  average time/residue: 0.1417
  time to fit residues: 18.5967
Evaluate side-chains
  101 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   29 ILE
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue  107 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0770
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** B  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.199898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.126285 restraints weight = 4242.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.130320 restraints weight = 3252.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.132895 restraints weight = 2685.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.8574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4029  Z= 0.246
  Angle     :  0.794  11.171   5485  Z= 0.397
  Chirality :  0.046   0.179    603
  Planarity :  0.005   0.043    703
  Dihedral  :  5.758  25.752    541
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.35 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 23.61 %
    Favored  : 71.53 %
  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 (0.38), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.47 (0.39), residues: 190
  loop : -2.22 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.004   TRP N 112 
 HIS   0.003   0.001   HIS B 245 
 PHE   0.026   0.002   PHE N 109 
 TYR   0.016   0.002   TYR N  81 
 ARG   0.008   0.001   ARG G  55 

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.6927 (mm-40) cc_final: 0.5885 (pt0)
REVERT: B   79 PHE cc_start: 0.6789 (m-80) cc_final: 0.6250 (m-80)
REVERT: B  150 LYS cc_start: 0.7026 (mmmt) cc_final: 0.6535 (tptp)
REVERT: B  177 MET cc_start: 0.5986 (ppp) cc_final: 0.5775 (mtt)
REVERT: B  224 GLU cc_start: 0.8195 (pm20) cc_final: 0.7687 (pm20)
REVERT: G   48 LEU cc_start: 0.8894 (mt) cc_final: 0.8530 (mp)
REVERT: G   55 ARG cc_start: 0.7930 (mtp180) cc_final: 0.7688 (ttt-90)
REVERT: N    7 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6749 (mt0)
REVERT: N   37 TRP cc_start: 0.8630 (m100) cc_final: 0.8214 (m100)
REVERT: N   39 ARG cc_start: 0.8863 (mtp180) cc_final: 0.8278 (mtp180)
REVERT: N   71 MET cc_start: 0.8658 (ppp) cc_final: 0.8004 (ppp)
REVERT: N   82 MET cc_start: 0.8311 (tmm) cc_final: 0.8007 (tmm)
  outliers start: 21
  outliers final: 18
  residues processed: 103
  average time/residue: 0.1612
  time to fit residues: 21.0136
Evaluate side-chains
  102 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  211 ASN
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue    7 GLN
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain N residue  107 TYR
Chi-restraints excluded: chain N residue  109 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0570
   chunk 13 optimal weight:    0.0020
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 3 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0170
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.5146

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

Flipped N/Q/H residues before XYZ refinement:
** B  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   7 GLN
N  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.188400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.122911 restraints weight = 4125.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.127319 restraints weight = 2815.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.130440 restraints weight = 2161.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6821
moved from start:          0.8778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4029  Z= 0.223
  Angle     :  0.808  14.080   5485  Z= 0.397
  Chirality :  0.045   0.157    603
  Planarity :  0.005   0.045    703
  Dihedral  :  5.650  26.045    541
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.55 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.31 %
    Favored  : 71.53 %
  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: -2.12 (0.38), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.46 (0.38), residues: 197
  loop : -2.18 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP N 112 
 HIS   0.002   0.001   HIS B 245 
 PHE   0.022   0.002   PHE N 109 
 TYR   0.011   0.002   TYR N  81 
 ARG   0.006   0.001   ARG G  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2062.30 seconds
wall clock time: 36 minutes 17.39 seconds (2177.39 seconds total)