Starting phenix.real_space_refine
on Tue Mar  3 12:11:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d4g_30573/03_2026/7d4g_30573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d4g_30573/03_2026/7d4g_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_2026/7d4g_30573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d4g_30573/03_2026/7d4g_30573.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d4g_30573/03_2026/7d4g_30573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d4g_30573/03_2026/7d4g_30573.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.97, per 1000 atoms: 0.25
  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: 0.31
  Conformation dependent library (CDL) restraints added in 158.1 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: 0.13
  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: 0.55

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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:             2.720
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     5.660
  Find NCS groups from input model:        0.020
  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:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.140
-------------------------------------------------------------------------------
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   4033  Z= 0.381
  Angle     :  1.065  18.058   5493  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.003   0.001   ARG B 190 
 TYR   0.018   0.002   TYR N  28 
 PHE   0.027   0.003   PHE B 106 
 TRP   0.028   0.004   TRP B  64 
 HIS   0.007   0.002   HIS N  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 4029)
  covalent geometry    : angle       1.06489 ( 5485)
  SS BOND              : bond        0.00451 (    4)
  SS BOND              : angle       0.94424 (    8)
  hydrogen bonds       : bond        0.29692 (  104)
  hydrogen bonds       : angle      12.40971 (  264)

*********************** 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  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   78 ARG cc_start: 0.6915 (mmt90) cc_final: 0.6524 (tmm-80)
REVERT: N   39 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7175 (mtp180)
REVERT: N   55 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7103 (mt-10)
REVERT: N   82 MET cc_start: 0.7286 (ttp) cc_final: 0.7072 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0751
  time to fit residues: 13.2548
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  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
B  66 HIS
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 GLN
** 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.217869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.154143 restraints weight = 4354.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.158285 restraints weight = 3429.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.160835 restraints weight = 2854.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.162205 restraints weight = 2504.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.164252 restraints weight = 2294.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4033  Z= 0.206
  Angle     :  0.859  11.126   5493  Z= 0.444
  Chirality :  0.048   0.229    603
  Planarity :  0.006   0.047    703
  Dihedral  :  7.521  46.257    541
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 18.17
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.50 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 14.12 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.30 (0.31), residues: 494
  helix:  None (None), residues: 0
  sheet: -1.15 (0.38), residues: 142
  loop : -2.87 (0.27), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 214 
 TYR   0.027   0.003   TYR G  37 
 PHE   0.029   0.003   PHE B 106 
 TRP   0.042   0.003   TRP N 112 
 HIS   0.006   0.002   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 4029)
  covalent geometry    : angle       0.85514 ( 5485)
  SS BOND              : bond        0.00241 (    4)
  SS BOND              : angle       2.28952 (    8)
  hydrogen bonds       : bond        0.04860 (  104)
  hydrogen bonds       : angle       8.47522 (  264)

*********************** 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
  121 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 PHE cc_start: 0.8121 (m-10) cc_final: 0.7746 (m-10)
REVERT: B   80 ASP cc_start: 0.7298 (t0) cc_final: 0.7048 (t0)
REVERT: B  177 MET cc_start: 0.6008 (ppp) cc_final: 0.5363 (mtp)
REVERT: G   48 LEU cc_start: 0.8709 (mt) cc_final: 0.8272 (mp)
REVERT: G   59 ILE cc_start: 0.8060 (mm) cc_final: 0.7846 (mp)
REVERT: G   74 LEU cc_start: 0.8987 (tp) cc_final: 0.8529 (tt)
REVERT: N   39 ARG cc_start: 0.8395 (mtp180) cc_final: 0.7698 (mtp180)
REVERT: N   53 ASP cc_start: 0.8077 (t0) cc_final: 0.7741 (t0)
REVERT: N   55 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7176 (mt-10)
  outliers start: 17
  outliers final: 11
  residues processed: 114
  average time/residue: 0.0736
  time to fit residues: 10.1755
Evaluate side-chains
  92 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
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 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  101 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0370
   chunk 19 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 34 optimal weight:   20.0000
   chunk 39 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0050
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4672

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

Flipped N/Q/H residues before XYZ refinement:
B  69 HIS
** 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**
N  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.217864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.156547 restraints weight = 4391.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.160537 restraints weight = 3479.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.162882 restraints weight = 2875.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.164044 restraints weight = 2510.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.166772 restraints weight = 2302.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6717
moved from start:          0.5697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4033  Z= 0.160
  Angle     :  0.793  13.108   5493  Z= 0.401
  Chirality :  0.047   0.194    603
  Planarity :  0.005   0.041    703
  Dihedral  :  6.800  41.936    541
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.73 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.52 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.34), residues: 494
  helix:  None (None), residues: 0
  sheet: -1.05 (0.35), residues: 190
  loop : -2.71 (0.32), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 214 
 TYR   0.020   0.002   TYR B 248 
 PHE   0.026   0.002   PHE B 135 
 TRP   0.038   0.004   TRP N 112 
 HIS   0.004   0.001   HIS B  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4029)
  covalent geometry    : angle       0.78568 ( 5485)
  SS BOND              : bond        0.00398 (    4)
  SS BOND              : angle       2.94693 (    8)
  hydrogen bonds       : bond        0.04204 (  104)
  hydrogen bonds       : angle       7.99892 (  264)

*********************** 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
  110 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   80 ASP cc_start: 0.6870 (t0) cc_final: 0.6549 (t0)
REVERT: B  116 SER cc_start: 0.7185 (m) cc_final: 0.6824 (p)
REVERT: B  177 MET cc_start: 0.6073 (ppp) cc_final: 0.5470 (mtp)
REVERT: G   48 LEU cc_start: 0.8831 (mt) cc_final: 0.8457 (mp)
REVERT: N   39 ARG cc_start: 0.8562 (mtp180) cc_final: 0.7847 (mtp180)
REVERT: N   53 ASP cc_start: 0.8167 (t0) cc_final: 0.7961 (t0)
REVERT: N   55 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7253 (mt-10)
REVERT: N  114 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7833 (pp30)
  outliers start: 16
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0636
  time to fit residues: 8.3506
Evaluate side-chains
  96 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   64 TRP
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B  69 HIS
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 HIS
** G  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   7 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.223530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.140566 restraints weight = 4720.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.145832 restraints weight = 3365.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.149228 restraints weight = 2661.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.152687 restraints weight = 2261.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.154917 restraints weight = 2000.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
moved from start:          0.6651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4033  Z= 0.207
  Angle     :  0.799  14.542   5493  Z= 0.400
  Chirality :  0.046   0.198    603
  Planarity :  0.005   0.048    703
  Dihedral  :  6.493  33.906    541
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.13 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 17.82 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.72 (0.35), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.66 (0.37), residues: 183
  loop : -2.70 (0.32), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  78 
 TYR   0.025   0.002   TYR B 248 
 PHE   0.018   0.003   PHE N 109 
 TRP   0.058   0.004   TRP N 112 
 HIS   0.007   0.002   HIS B  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 4029)
  covalent geometry    : angle       0.79174 ( 5485)
  SS BOND              : bond        0.00918 (    4)
  SS BOND              : angle       2.83143 (    8)
  hydrogen bonds       : bond        0.03802 (  104)
  hydrogen bonds       : angle       7.73555 (  264)

*********************** 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: 26
    poor density    : 93
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 THR cc_start: 0.6375 (OUTLIER) cc_final: 0.6159 (t)
REVERT: B  116 SER cc_start: 0.7503 (m) cc_final: 0.7043 (p)
REVERT: B  177 MET cc_start: 0.5935 (ppp) cc_final: 0.5423 (mtp)
REVERT: B  224 GLU cc_start: 0.8192 (pm20) cc_final: 0.7783 (pm20)
REVERT: G   36 TRP cc_start: 0.8037 (m100) cc_final: 0.7608 (m100)
REVERT: G   48 LEU cc_start: 0.8776 (mt) cc_final: 0.8540 (mt)
REVERT: G   54 LYS cc_start: 0.7735 (mmtp) cc_final: 0.7465 (mmtp)
REVERT: G  106 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7980 (mmtm)
REVERT: N   39 ARG cc_start: 0.8857 (mtp180) cc_final: 0.8217 (mtp180)
REVERT: N   53 ASP cc_start: 0.8351 (t0) cc_final: 0.8029 (t0)
REVERT: N   55 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7300 (mt-10)
REVERT: N   83 GLU cc_start: 0.8053 (tp30) cc_final: 0.7469 (tp30)
  outliers start: 26
  outliers final: 18
  residues processed: 111
  average time/residue: 0.0663
  time to fit residues: 9.0694
Evaluate side-chains
  105 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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  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   49 ILE
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 1 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 121 ASN
** G  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.219817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.137722 restraints weight = 4716.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.143319 restraints weight = 3358.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.147464 restraints weight = 2631.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.150173 restraints weight = 2209.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.151915 restraints weight = 1960.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.7219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4033  Z= 0.189
  Angle     :  0.786  10.193   5493  Z= 0.396
  Chirality :  0.046   0.184    603
  Planarity :  0.005   0.052    703
  Dihedral  :  6.380  26.760    541
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.93 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 18.75 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.35), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.44 (0.39), residues: 171
  loop : -2.62 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  62 
 TYR   0.023   0.002   TYR B 248 
 PHE   0.020   0.003   PHE B  79 
 TRP   0.037   0.003   TRP N 112 
 HIS   0.013   0.003   HIS B  69 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 4029)
  covalent geometry    : angle       0.78059 ( 5485)
  SS BOND              : bond        0.00751 (    4)
  SS BOND              : angle       2.62077 (    8)
  hydrogen bonds       : bond        0.03707 (  104)
  hydrogen bonds       : angle       7.29960 (  264)

*********************** 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
  127 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  177 MET cc_start: 0.6062 (ppp) cc_final: 0.5769 (mtt)
REVERT: B  224 GLU cc_start: 0.8216 (pm20) cc_final: 0.7842 (pm20)
REVERT: G   48 LEU cc_start: 0.8895 (mt) cc_final: 0.8492 (mp)
REVERT: G   54 LYS cc_start: 0.7677 (mmtp) cc_final: 0.7351 (mmtm)
REVERT: G   74 LEU cc_start: 0.8761 (tp) cc_final: 0.8483 (tp)
REVERT: G  106 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7972 (mmtm)
REVERT: N   37 TRP cc_start: 0.8647 (m100) cc_final: 0.8189 (m100)
REVERT: N   39 ARG cc_start: 0.8913 (mtp180) cc_final: 0.8304 (mtp180)
REVERT: N   53 ASP cc_start: 0.8379 (t0) cc_final: 0.7980 (t0)
REVERT: N   55 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7442 (mt-10)
  outliers start: 26
  outliers final: 21
  residues processed: 119
  average time/residue: 0.0594
  time to fit residues: 8.8897
Evaluate side-chains
  107 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
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  166 CYS
Chi-restraints excluded: chain B residue  200 TYR
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   49 ILE
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 29 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 164 ASN
G  32 ASN
G  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.204342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.135390 restraints weight = 4441.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.139169 restraints weight = 3365.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.142430 restraints weight = 2758.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.144260 restraints weight = 2382.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.145077 restraints weight = 2145.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.7740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4033  Z= 0.162
  Angle     :  0.764   9.208   5493  Z= 0.384
  Chirality :  0.046   0.165    603
  Planarity :  0.006   0.060    703
  Dihedral  :  6.095  26.755    541
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.13 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 20.14 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.49 (0.39), residues: 177
  loop : -2.36 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  55 
 TYR   0.018   0.002   TYR B 248 
 PHE   0.022   0.002   PHE B  58 
 TRP   0.043   0.004   TRP G  36 
 HIS   0.003   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4029)
  covalent geometry    : angle       0.75765 ( 5485)
  SS BOND              : bond        0.00448 (    4)
  SS BOND              : angle       2.67440 (    8)
  hydrogen bonds       : bond        0.03533 (  104)
  hydrogen bonds       : angle       7.30231 (  264)

*********************** 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
  125 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  177 MET cc_start: 0.6064 (ppp) cc_final: 0.5793 (mtt)
REVERT: B  215 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.5377 (p0)
REVERT: B  221 SER cc_start: 0.7301 (m) cc_final: 0.7045 (m)
REVERT: B  224 GLU cc_start: 0.8099 (pm20) cc_final: 0.7707 (pm20)
REVERT: G   32 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.8107 (m-40)
REVERT: G   48 LEU cc_start: 0.8948 (mt) cc_final: 0.8535 (mp)
REVERT: G   55 ARG cc_start: 0.8259 (mtp180) cc_final: 0.8038 (mtp85)
REVERT: G  106 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7912 (mmtm)
REVERT: N   37 TRP cc_start: 0.8500 (m100) cc_final: 0.8043 (m100)
REVERT: N   39 ARG cc_start: 0.8716 (mtp180) cc_final: 0.8155 (mtp180)
REVERT: N   53 ASP cc_start: 0.8224 (t0) cc_final: 0.7976 (t0)
REVERT: N   55 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7624 (mt-10)
REVERT: N   61 TYR cc_start: 0.7445 (m-80) cc_final: 0.7107 (m-80)
REVERT: N   71 MET cc_start: 0.8656 (ppp) cc_final: 0.8107 (ppp)
REVERT: N   96 TYR cc_start: 0.8294 (m-80) cc_final: 0.7997 (m-10)
  outliers start: 27
  outliers final: 19
  residues processed: 112
  average time/residue: 0.0538
  time to fit residues: 7.6645
Evaluate side-chains
  102 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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   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 G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   32 ASN
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   49 ILE
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   69 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 34 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.4481 r_free = 0.4481 target = 0.201306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.131754 restraints weight = 4560.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.135499 restraints weight = 3492.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.137841 restraints weight = 2884.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.140286 restraints weight = 2518.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.141512 restraints weight = 2278.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.8103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4033  Z= 0.189
  Angle     :  0.799   9.206   5493  Z= 0.404
  Chirality :  0.046   0.171    603
  Planarity :  0.005   0.045    703
  Dihedral  :  6.103  25.782    541
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.13 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 22.92 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.40 (0.39), residues: 178
  loop : -2.40 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  55 
 TYR   0.031   0.002   TYR G  37 
 PHE   0.030   0.003   PHE B 275 
 TRP   0.040   0.003   TRP G  36 
 HIS   0.004   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 4029)
  covalent geometry    : angle       0.79085 ( 5485)
  SS BOND              : bond        0.00597 (    4)
  SS BOND              : angle       3.12202 (    8)
  hydrogen bonds       : bond        0.03871 (  104)
  hydrogen bonds       : angle       7.53464 (  264)

*********************** 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
  118 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.7007 (mm110) cc_final: 0.6015 (pt0)
REVERT: B   83 VAL cc_start: 0.8994 (t) cc_final: 0.8659 (m)
REVERT: B  177 MET cc_start: 0.6145 (ppp) cc_final: 0.5816 (mtt)
REVERT: B  215 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.5569 (p0)
REVERT: B  224 GLU cc_start: 0.8172 (pm20) cc_final: 0.7717 (pm20)
REVERT: G   36 TRP cc_start: 0.7928 (m100) cc_final: 0.6766 (m100)
REVERT: G   48 LEU cc_start: 0.8915 (mt) cc_final: 0.8489 (mp)
REVERT: G   55 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7800 (mtp85)
REVERT: N   37 TRP cc_start: 0.8571 (m100) cc_final: 0.8091 (m100)
REVERT: N   39 ARG cc_start: 0.8850 (mtp180) cc_final: 0.8251 (mtp180)
REVERT: N   53 ASP cc_start: 0.8302 (t0) cc_final: 0.7976 (t0)
REVERT: N   55 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7585 (mt-10)
REVERT: N   61 TYR cc_start: 0.7562 (m-80) cc_final: 0.7078 (m-80)
REVERT: N   71 MET cc_start: 0.8649 (ppp) cc_final: 0.8111 (ppp)
REVERT: N  114 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8169 (pp30)
  outliers start: 24
  outliers final: 20
  residues processed: 108
  average time/residue: 0.0604
  time to fit residues: 8.2173
Evaluate side-chains
  102 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
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  111 ASP
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 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 N residue    2 VAL
Chi-restraints excluded: chain N residue   69 VAL
Chi-restraints excluded: chain N residue   99 THR
Chi-restraints excluded: chain N residue  101 THR
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 1 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 16 optimal weight:    0.1980
   chunk 48 optimal weight:    0.4980
   chunk 43 optimal weight:    0.3980
   chunk 44 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 ** 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 = 0.4634 r_free = 0.4634 target = 0.216645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.156773 restraints weight = 4594.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.159903 restraints weight = 3819.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.161123 restraints weight = 3330.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.161122 restraints weight = 3073.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.161122 restraints weight = 3073.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.8446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4033  Z= 0.149
  Angle     :  0.765   9.376   5493  Z= 0.387
  Chirality :  0.047   0.191    603
  Planarity :  0.005   0.061    703
  Dihedral  :  5.908  26.201    541
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.93 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 24.07 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.59 (0.37), residues: 191
  loop : -2.24 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  55 
 TYR   0.016   0.002   TYR G  37 
 PHE   0.025   0.003   PHE B  58 
 TRP   0.048   0.003   TRP G  36 
 HIS   0.002   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4029)
  covalent geometry    : angle       0.76147 ( 5485)
  SS BOND              : bond        0.00709 (    4)
  SS BOND              : angle       2.16632 (    8)
  hydrogen bonds       : bond        0.03745 (  104)
  hydrogen bonds       : angle       7.06649 (  264)

*********************** 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
  108 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.6996 (mm110) cc_final: 0.5866 (pt0)
REVERT: B   83 VAL cc_start: 0.8910 (t) cc_final: 0.8549 (m)
REVERT: B  177 MET cc_start: 0.6118 (ppp) cc_final: 0.5896 (mtt)
REVERT: B  215 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.5564 (p0)
REVERT: B  224 GLU cc_start: 0.8165 (pm20) cc_final: 0.7675 (pm20)
REVERT: G   48 LEU cc_start: 0.8619 (mt) cc_final: 0.8370 (mp)
REVERT: N   37 TRP cc_start: 0.8540 (m100) cc_final: 0.8046 (m100)
REVERT: N   39 ARG cc_start: 0.8897 (mtp180) cc_final: 0.8257 (mtp180)
REVERT: N   53 ASP cc_start: 0.8246 (t0) cc_final: 0.7952 (t0)
REVERT: N   55 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7888 (mt-10)
REVERT: N   61 TYR cc_start: 0.7432 (m-80) cc_final: 0.7203 (m-80)
REVERT: N  114 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8272 (pp30)
  outliers start: 19
  outliers final: 15
  residues processed: 100
  average time/residue: 0.0512
  time to fit residues: 6.8121
Evaluate side-chains
  100 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  111 ASP
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  124 THR
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   35 SER
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain N residue   69 VAL
Chi-restraints excluded: chain N residue  107 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.200830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.135190 restraints weight = 4601.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.133640 restraints weight = 3931.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.135832 restraints weight = 3513.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.137123 restraints weight = 2957.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.137528 restraints weight = 2803.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.8679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4033  Z= 0.183
  Angle     :  0.784   9.023   5493  Z= 0.394
  Chirality :  0.047   0.203    603
  Planarity :  0.005   0.045    703
  Dihedral  :  6.189  27.518    541
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.55 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 23.61 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.57 (0.38), residues: 177
  loop : -2.24 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  55 
 TYR   0.020   0.002   TYR G  37 
 PHE   0.029   0.003   PHE B  58 
 TRP   0.037   0.003   TRP G  36 
 HIS   0.003   0.001   HIS B 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 4029)
  covalent geometry    : angle       0.78008 ( 5485)
  SS BOND              : bond        0.00848 (    4)
  SS BOND              : angle       2.15003 (    8)
  hydrogen bonds       : bond        0.03603 (  104)
  hydrogen bonds       : angle       6.98381 (  264)

*********************** 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
  113 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.6971 (mm110) cc_final: 0.5880 (pt0)
REVERT: B   83 VAL cc_start: 0.8923 (t) cc_final: 0.8519 (m)
REVERT: B  177 MET cc_start: 0.6077 (ppp) cc_final: 0.5844 (mtt)
REVERT: B  215 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.5576 (p0)
REVERT: B  224 GLU cc_start: 0.8156 (pm20) cc_final: 0.7693 (pm20)
REVERT: G   32 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8048 (m-40)
REVERT: G   46 LYS cc_start: 0.8246 (tttt) cc_final: 0.7832 (ttpp)
REVERT: G   48 LEU cc_start: 0.8800 (mt) cc_final: 0.8576 (mp)
REVERT: G   55 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7378 (ttm-80)
REVERT: N   28 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7313 (m-80)
REVERT: N   37 TRP cc_start: 0.8503 (m100) cc_final: 0.8027 (m100)
REVERT: N   39 ARG cc_start: 0.8797 (mtp180) cc_final: 0.8224 (mtp180)
REVERT: N   53 ASP cc_start: 0.8306 (t0) cc_final: 0.8034 (t0)
REVERT: N   55 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7952 (mt-10)
  outliers start: 23
  outliers final: 17
  residues processed: 104
  average time/residue: 0.0510
  time to fit residues: 6.9363
Evaluate side-chains
  105 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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  111 ASP
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  124 THR
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 G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   32 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   28 TYR
Chi-restraints excluded: chain N residue   69 VAL
Chi-restraints excluded: chain N residue   99 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 42 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 5 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0470
   chunk 3 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.6480

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.213456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.154280 restraints weight = 4619.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.156958 restraints weight = 3889.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.158137 restraints weight = 3448.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.158461 restraints weight = 3182.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.158461 restraints weight = 3043.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.8819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4033  Z= 0.159
  Angle     :  0.788  10.612   5493  Z= 0.391
  Chirality :  0.046   0.197    603
  Planarity :  0.005   0.048    703
  Dihedral  :  6.174  26.604    541
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.15 %
    Favored  : 87.65 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 23.84 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.62 (0.38), residues: 177
  loop : -2.20 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  55 
 TYR   0.016   0.002   TYR G  37 
 PHE   0.029   0.003   PHE B  58 
 TRP   0.040   0.003   TRP G  36 
 HIS   0.003   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 4029)
  covalent geometry    : angle       0.78571 ( 5485)
  SS BOND              : bond        0.00614 (    4)
  SS BOND              : angle       1.85405 (    8)
  hydrogen bonds       : bond        0.03578 (  104)
  hydrogen bonds       : angle       6.88609 (  264)

********************** 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
  108 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.7005 (mm110) cc_final: 0.5830 (pt0)
REVERT: B   83 VAL cc_start: 0.8916 (t) cc_final: 0.8530 (m)
REVERT: B  116 SER cc_start: 0.7724 (m) cc_final: 0.7464 (p)
REVERT: B  215 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.5643 (p0)
REVERT: B  224 GLU cc_start: 0.8177 (pm20) cc_final: 0.7635 (pm20)
REVERT: G   46 LYS cc_start: 0.8252 (tttt) cc_final: 0.7856 (ttpp)
REVERT: G   48 LEU cc_start: 0.8697 (mt) cc_final: 0.8482 (mp)
REVERT: G   55 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7497 (ttm-80)
REVERT: N   28 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7358 (m-80)
REVERT: N   37 TRP cc_start: 0.8535 (m100) cc_final: 0.8036 (m100)
REVERT: N   53 ASP cc_start: 0.8307 (t0) cc_final: 0.8025 (t0)
REVERT: N   55 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7989 (mt-10)
  outliers start: 21
  outliers final: 16
  residues processed: 100
  average time/residue: 0.0511
  time to fit residues: 6.7291
Evaluate side-chains
  105 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
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  111 ASP
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  124 THR
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 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   28 TYR
Chi-restraints excluded: chain N residue   69 VAL
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 31 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 33 optimal weight:    9.9990
   chunk 32 optimal weight:    0.2980
   chunk 12 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0970
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0770
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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 = 0.4510 r_free = 0.4510 target = 0.203671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.135205 restraints weight = 4542.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.139166 restraints weight = 3417.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.142028 restraints weight = 2794.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.144221 restraints weight = 2421.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.145332 restraints weight = 2172.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.9025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4033  Z= 0.140
  Angle     :  0.759   9.109   5493  Z= 0.377
  Chirality :  0.046   0.183    603
  Planarity :  0.005   0.051    703
  Dihedral  :  6.028  27.496    541
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.75 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.46 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.27 (0.37), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.65 (0.39), residues: 177
  loop : -2.13 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  55 
 TYR   0.014   0.002   TYR G  37 
 PHE   0.029   0.003   PHE B  58 
 TRP   0.036   0.003   TRP G  36 
 HIS   0.002   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4029)
  covalent geometry    : angle       0.75747 ( 5485)
  SS BOND              : bond        0.00592 (    4)
  SS BOND              : angle       1.59004 (    8)
  hydrogen bonds       : bond        0.03410 (  104)
  hydrogen bonds       : angle       6.81583 (  264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 999.91 seconds
wall clock time: 17 minutes 53.33 seconds (1073.33 seconds total)