Starting phenix.real_space_refine
on Wed Jul 23 17:56:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d4g_30573/07_2025/7d4g_30573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d4g_30573/07_2025/7d4g_30573.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d4g_30573/07_2025/7d4g_30573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d4g_30573/07_2025/7d4g_30573.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d4g_30573/07_2025/7d4g_30573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d4g_30573/07_2025/7d4g_30573.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2510      2.51       5
     N     648      2.21       5
     O     752      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3925
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 2206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2206
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 14, 'TRANS': 258}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "G"
      Number of atoms: 788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 788
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 6, 'TRANS': 102}
    Chain: "N"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 931
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 6, 'TRANS': 113}
  Time building chain proxies: 3.56, per 1000 atoms: 0.91
  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: 0.96
  Conformation dependent library (CDL) restraints added in 494.4 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: 0.51
  Creating SS restraints...
    Processing helix  chain 'B' and resid 156 through 158
      No H-bonds generated for 'chain 'B' and resid 156 through 158'
    Processing helix  chain 'G' and resid 80 through 84
      removed outlier: 4.334A  pdb=" N   GLU G  84 " --> pdb=" O   THR G  81 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 29 through 33
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31
      removed outlier: 4.087A  pdb=" N   SER B  31 " --> pdb=" O   SER B  60 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER B  60 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU B 191 " --> pdb=" O   LYS B 206 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS B 195 " --> pdb=" O   LYS B 202 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   PHE B 201 " --> pdb=" O   ASP B 228 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   ASP B 228 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ILE B 203 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER B 205 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU B 224 " --> pdb=" O   SER B 205 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55
      removed outlier: 3.918A  pdb=" N   THR B  51 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85
    Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 104
      removed outlier: 6.015A  pdb=" N   ILE B 101 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   ALA B 243 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   GLY B 103 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 120
      removed outlier: 3.813A  pdb=" N   VAL B 127 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   GLU B 132 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   CYS B 166 " --> pdb=" O   GLU B 132 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   GLN B 134 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 8.964A  pdb=" N   ASN B 164 " --> pdb=" O   GLN B 134 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 9 through 12
      removed outlier: 3.689A  pdb=" N   ASP G  86 " --> pdb=" O   GLN G  39 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL G  34 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   TYR G  50 " --> pdb=" O   VAL G  34 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   TRP G  36 " --> pdb=" O   LEU G  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 9 through 12
      removed outlier: 3.734A  pdb=" N   THR G  91 " --> pdb=" O   VAL G 100 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL G 100 " --> pdb=" O   THR G  91 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 20 through 23
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 4
      removed outlier: 3.836A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 22 through 23
      removed outlier: 3.602A  pdb=" N   ALA N  80 " --> pdb=" O   CYS N  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 46 through 49

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

  Time building geometry restraints manager: 1.15 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:             1.640
  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:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.950
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.860
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.84 (0.29), residues: 494
  helix: -4.21 (0.49), residues: 6
  sheet: -1.91 (0.36), residues: 126
  loop : -3.00 (0.26), residues: 362

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

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

*********************** 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  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   78 ARG cc_start: 0.6915 (mmt90) cc_final: 0.6522 (tmm-80)
REVERT: B   80 ASP cc_start: 0.7559 (t70) cc_final: 0.7359 (t0)
REVERT: N   39 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7178 (mtp180)
REVERT: N   55 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7106 (mt-10)
REVERT: N   82 MET cc_start: 0.7286 (ttp) cc_final: 0.7071 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1852
  time to fit residues: 32.7807
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  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    0.3980
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.5578

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

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

Total number of N/Q/H flips: 4

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

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4033  Z= 0.179
  Angle     :  0.840  11.545   5493  Z= 0.433
  Chirality :  0.048   0.229    603
  Planarity :  0.005   0.042    703
  Dihedral  :  7.412  45.207    541
  Min Nonbonded Distance : 2.517

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.31), residues: 494
  helix:  None (None), residues: 0
  sheet: -1.22 (0.37), residues: 143
  loop : -2.81 (0.27), residues: 351

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04757 (  104)
  hydrogen bonds       : angle       8.49176 (  264)
  SS BOND              : bond        0.00234 (    4)
  SS BOND              : angle       2.33227 (    8)
  covalent geometry    : bond        0.00380 ( 4029)
  covalent geometry    : angle       0.83636 ( 5485)

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

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

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

  988 Ramachandran restraints generated.
    494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  168 PHE cc_start: 0.7480 (t80) cc_final: 0.7255 (t80)
REVERT: B  177 MET cc_start: 0.5888 (ppp) cc_final: 0.5321 (mtp)
REVERT: G   48 LEU cc_start: 0.8695 (mt) cc_final: 0.8356 (mp)
REVERT: G   74 LEU cc_start: 0.9007 (tp) cc_final: 0.8550 (tt)
REVERT: N   53 ASP cc_start: 0.7983 (t0) cc_final: 0.7757 (t0)
REVERT: N   55 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7274 (mt-10)
REVERT: N   60 MET cc_start: 0.5991 (mmp) cc_final: 0.5688 (mmm)
  outliers start: 16
  outliers final: 10
  residues processed: 105
  average time/residue: 0.2008
  time to fit residues: 25.6600
Evaluate side-chains
  86 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   35 SER
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue  101 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 4 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8562

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.210898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.146077 restraints weight = 4413.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.149810 restraints weight = 3416.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.153002 restraints weight = 2823.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.5785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4033  Z= 0.193
  Angle     :  0.799  14.768   5493  Z= 0.405
  Chirality :  0.047   0.194    603
  Planarity :  0.005   0.040    703
  Dihedral  :  6.821  41.612    541
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.51 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.59 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.34), residues: 494
  helix:  None (None), residues: 0
  sheet: -1.18 (0.35), residues: 194
  loop : -2.68 (0.32), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.004   TRP N 112 
 HIS   0.004   0.002   HIS B 207 
 PHE   0.024   0.003   PHE B 135 
 TYR   0.023   0.002   TYR B 248 
 ARG   0.009   0.001   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04383 (  104)
  hydrogen bonds       : angle       8.01153 (  264)
  SS BOND              : bond        0.00698 (    4)
  SS BOND              : angle       2.72377 (    8)
  covalent geometry    : bond        0.00432 ( 4029)
  covalent geometry    : angle       0.79240 ( 5485)

*********************** 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
  120 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 PHE cc_start: 0.7567 (m-10) cc_final: 0.7352 (m-10)
REVERT: B  116 SER cc_start: 0.7298 (m) cc_final: 0.6942 (p)
REVERT: B  177 MET cc_start: 0.6170 (ppp) cc_final: 0.5506 (mtp)
REVERT: B  215 ASP cc_start: 0.6248 (OUTLIER) cc_final: 0.5647 (p0)
REVERT: B  224 GLU cc_start: 0.7946 (pm20) cc_final: 0.7657 (pm20)
REVERT: G   48 LEU cc_start: 0.8847 (mt) cc_final: 0.8435 (mp)
REVERT: G   74 LEU cc_start: 0.8844 (tp) cc_final: 0.8298 (tp)
REVERT: N   39 ARG cc_start: 0.8542 (mtp180) cc_final: 0.7836 (mtp180)
REVERT: N   53 ASP cc_start: 0.8296 (t0) cc_final: 0.8051 (t0)
REVERT: N   55 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7274 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 113
  average time/residue: 0.2088
  time to fit residues: 29.1910
Evaluate side-chains
  98 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0050
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.5394

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.223256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.151825 restraints weight = 4618.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.151195 restraints weight = 3594.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.154026 restraints weight = 2883.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
moved from start:          0.6477

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= 0.155
  Angle     :  0.773  13.010   5493  Z= 0.382
  Chirality :  0.046   0.203    603
  Planarity :  0.006   0.077    703
  Dihedral  :  6.415  33.480    541
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.32 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 17.59 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.34), residues: 494
  helix:  None (None), residues: 0
  sheet: -1.03 (0.39), residues: 160
  loop : -2.59 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.004   TRP N 112 
 HIS   0.003   0.001   HIS B  66 
 PHE   0.020   0.002   PHE B 135 
 TYR   0.024   0.002   TYR G  37 
 ARG   0.007   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  104)
  hydrogen bonds       : angle       7.96780 (  264)
  SS BOND              : bond        0.00339 (    4)
  SS BOND              : angle       2.79343 (    8)
  covalent geometry    : bond        0.00354 ( 4029)
  covalent geometry    : angle       0.76567 ( 5485)

*********************** 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
  117 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   18 LEU cc_start: 0.8119 (pt) cc_final: 0.7805 (pt)
REVERT: B   79 PHE cc_start: 0.6616 (m-80) cc_final: 0.5818 (m-80)
REVERT: B  116 SER cc_start: 0.7267 (m) cc_final: 0.6709 (p)
REVERT: B  177 MET cc_start: 0.6079 (ppp) cc_final: 0.5448 (mtp)
REVERT: B  224 GLU cc_start: 0.8101 (pm20) cc_final: 0.7723 (pm20)
REVERT: G   48 LEU cc_start: 0.8779 (mt) cc_final: 0.8379 (mp)
REVERT: G   74 LEU cc_start: 0.8929 (tp) cc_final: 0.8557 (tp)
REVERT: G  106 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7936 (mmtm)
REVERT: N   39 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8097 (mtp180)
REVERT: N   53 ASP cc_start: 0.8354 (t0) cc_final: 0.8115 (t0)
REVERT: N   55 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7350 (mt-10)
REVERT: N   71 MET cc_start: 0.9129 (ppp) cc_final: 0.8874 (ppp)
  outliers start: 23
  outliers final: 17
  residues processed: 110
  average time/residue: 0.1668
  time to fit residues: 22.4969
Evaluate side-chains
  104 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   69 HIS
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain N residue  107 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0470
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0370
   chunk 35 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.4356

-------------------------------------------------------------------------------
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
B 239 GLN
G  32 ASN
N   7 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.224020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.144268 restraints weight = 4907.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.150228 restraints weight = 3429.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.153979 restraints weight = 2654.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.6983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4033  Z= 0.144
  Angle     :  0.760   9.345   5493  Z= 0.380
  Chirality :  0.046   0.190    603
  Planarity :  0.005   0.041    703
  Dihedral  :  6.031  29.161    541
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.32 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 18.06 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.34), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.96 (0.38), residues: 163
  loop : -2.49 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP N 112 
 HIS   0.002   0.001   HIS B 245 
 PHE   0.017   0.002   PHE B 133 
 TYR   0.016   0.002   TYR B 248 
 ARG   0.006   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  104)
  hydrogen bonds       : angle       7.56358 (  264)
  SS BOND              : bond        0.00579 (    4)
  SS BOND              : angle       2.45638 (    8)
  covalent geometry    : bond        0.00321 ( 4029)
  covalent geometry    : angle       0.75491 ( 5485)

*********************** 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
  124 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 PHE cc_start: 0.6534 (m-80) cc_final: 0.6258 (m-80)
REVERT: B  177 MET cc_start: 0.6041 (ppp) cc_final: 0.5487 (mtp)
REVERT: G   36 TRP cc_start: 0.8129 (m100) cc_final: 0.7796 (m100)
REVERT: G   48 LEU cc_start: 0.8838 (mt) cc_final: 0.8427 (mp)
REVERT: G   54 LYS cc_start: 0.7643 (mmtp) cc_final: 0.7436 (mmtp)
REVERT: G   74 LEU cc_start: 0.8879 (tp) cc_final: 0.8526 (tp)
REVERT: G  106 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7925 (mmtm)
REVERT: N   39 ARG cc_start: 0.8889 (mtp180) cc_final: 0.8238 (mtp180)
REVERT: N   53 ASP cc_start: 0.8287 (t0) cc_final: 0.7946 (t0)
REVERT: N   55 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7392 (mt-10)
REVERT: N   82 MET cc_start: 0.8590 (tmm) cc_final: 0.7849 (tmm)
REVERT: N   83 GLU cc_start: 0.8106 (tp30) cc_final: 0.7870 (tp30)
REVERT: N   96 TYR cc_start: 0.8731 (m-80) cc_final: 0.8151 (m-10)
REVERT: N  112 TRP cc_start: 0.6200 (p90) cc_final: 0.5812 (p90)
  outliers start: 27
  outliers final: 21
  residues processed: 113
  average time/residue: 0.2279
  time to fit residues: 31.6943
Evaluate side-chains
  101 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue   96 LEU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain N residue  107 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0270
   chunk 4 optimal weight:    0.4980
   chunk 0 optimal weight:    7.9990
   chunk 22 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0980
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    0.3638

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.229705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.149080 restraints weight = 4809.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.155007 restraints weight = 3322.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.159508 restraints weight = 2564.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.7362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4033  Z= 0.137
  Angle     :  0.745   9.232   5493  Z= 0.374
  Chirality :  0.045   0.142    603
  Planarity :  0.005   0.044    703
  Dihedral  :  5.802  26.339    541
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.12 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 21.30 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.74 (0.39), residues: 167
  loop : -2.30 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP N 112 
 HIS   0.002   0.001   HIS B 245 
 PHE   0.013   0.002   PHE B 135 
 TYR   0.020   0.002   TYR G  37 
 ARG   0.006   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03489 (  104)
  hydrogen bonds       : angle       7.29739 (  264)
  SS BOND              : bond        0.00217 (    4)
  SS BOND              : angle       1.82815 (    8)
  covalent geometry    : bond        0.00309 ( 4029)
  covalent geometry    : angle       0.74234 ( 5485)

*********************** 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
  105 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 PHE cc_start: 0.6675 (m-80) cc_final: 0.6468 (m-80)
REVERT: B  177 MET cc_start: 0.6034 (ppp) cc_final: 0.5683 (mtt)
REVERT: B  224 GLU cc_start: 0.8067 (pm20) cc_final: 0.7659 (pm20)
REVERT: G   48 LEU cc_start: 0.8846 (mt) cc_final: 0.8417 (mp)
REVERT: G   74 LEU cc_start: 0.8883 (tp) cc_final: 0.8644 (tp)
REVERT: N   39 ARG cc_start: 0.8905 (mtp180) cc_final: 0.8273 (mtp180)
REVERT: N   53 ASP cc_start: 0.8232 (t0) cc_final: 0.7960 (t0)
REVERT: N   55 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7357 (mt-10)
REVERT: N   83 GLU cc_start: 0.8194 (tp30) cc_final: 0.7992 (tp30)
REVERT: N   96 TYR cc_start: 0.8709 (m-80) cc_final: 0.8189 (m-10)
REVERT: N  112 TRP cc_start: 0.6020 (p90) cc_final: 0.5584 (p90)
  outliers start: 21
  outliers final: 19
  residues processed: 98
  average time/residue: 0.1696
  time to fit residues: 21.3890
Evaluate side-chains
  98 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
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  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   17 LYS
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   84 LEU
Chi-restraints excluded: chain N residue  101 THR
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 18 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 7 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  69 HIS
G  32 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.187221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.121722 restraints weight = 4354.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.125849 restraints weight = 2980.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.129090 restraints weight = 2300.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.7720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4033  Z= 0.178
  Angle     :  0.756   9.555   5493  Z= 0.380
  Chirality :  0.045   0.148    603
  Planarity :  0.005   0.041    703
  Dihedral  :  5.793  26.072    541
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.53 %
    Favored  : 89.27 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 21.06 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.37), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.54 (0.41), residues: 159
  loop : -2.21 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP G  36 
 HIS   0.004   0.002   HIS B 207 
 PHE   0.026   0.002   PHE B  58 
 TYR   0.021   0.002   TYR B 248 
 ARG   0.005   0.001   ARG G  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03502 (  104)
  hydrogen bonds       : angle       7.23977 (  264)
  SS BOND              : bond        0.00603 (    4)
  SS BOND              : angle       1.75578 (    8)
  covalent geometry    : bond        0.00415 ( 4029)
  covalent geometry    : angle       0.75395 ( 5485)

*********************** 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
  115 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 88
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   79 PHE cc_start: 0.6821 (m-80) cc_final: 0.6621 (m-80)
REVERT: B  133 PHE cc_start: 0.5562 (m-80) cc_final: 0.5086 (m-80)
REVERT: B  177 MET cc_start: 0.6162 (ppp) cc_final: 0.5657 (mtt)
REVERT: B  224 GLU cc_start: 0.8192 (pm20) cc_final: 0.7664 (pm20)
REVERT: G   36 TRP cc_start: 0.8169 (m100) cc_final: 0.7503 (m100)
REVERT: G   48 LEU cc_start: 0.8884 (mt) cc_final: 0.8457 (mp)
REVERT: G   55 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7532 (ttm-80)
REVERT: G   74 LEU cc_start: 0.8861 (tp) cc_final: 0.8548 (tp)
REVERT: N   39 ARG cc_start: 0.8936 (mtp180) cc_final: 0.8217 (mtp180)
REVERT: N   53 ASP cc_start: 0.8334 (t0) cc_final: 0.8051 (t0)
REVERT: N   55 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7558 (mt-10)
REVERT: N   83 GLU cc_start: 0.8128 (tp30) cc_final: 0.7842 (tp30)
REVERT: N   96 TYR cc_start: 0.8704 (m-80) cc_final: 0.8259 (m-10)
REVERT: N  112 TRP cc_start: 0.6005 (p90) cc_final: 0.5580 (p90)
  outliers start: 27
  outliers final: 26
  residues processed: 103
  average time/residue: 0.2608
  time to fit residues: 33.4817
Evaluate side-chains
  110 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.850 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   17 LYS
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   49 ILE
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue    2 VAL
Chi-restraints excluded: chain N residue   84 LEU
Chi-restraints excluded: chain N residue   99 THR
Chi-restraints excluded: chain N residue  101 THR
Chi-restraints excluded: chain N residue  103 PHE
Chi-restraints excluded: chain N residue  107 TYR
Chi-restraints excluded: chain N residue  109 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.8786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.185036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.120184 restraints weight = 4327.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.124446 restraints weight = 2949.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.127585 restraints weight = 2266.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.8106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4033  Z= 0.177
  Angle     :  0.760  10.027   5493  Z= 0.380
  Chirality :  0.045   0.153    603
  Planarity :  0.005   0.041    703
  Dihedral  :  5.850  26.125    541
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.54 %
    Favored  : 88.26 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 21.53 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.37), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.42 (0.40), residues: 166
  loop : -2.17 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP G  36 
 HIS   0.004   0.001   HIS B 207 
 PHE   0.027   0.002   PHE B  58 
 TYR   0.018   0.002   TYR B 248 
 ARG   0.003   0.001   ARG B 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  104)
  hydrogen bonds       : angle       7.07774 (  264)
  SS BOND              : bond        0.00333 (    4)
  SS BOND              : angle       1.71253 (    8)
  covalent geometry    : bond        0.00409 ( 4029)
  covalent geometry    : angle       0.75782 ( 5485)

*********************** 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
  118 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.6621 (mm-40) cc_final: 0.5909 (pt0)
REVERT: B   79 PHE cc_start: 0.6922 (m-80) cc_final: 0.6720 (m-80)
REVERT: B  116 SER cc_start: 0.7198 (m) cc_final: 0.6492 (p)
REVERT: B  131 CYS cc_start: 0.4472 (OUTLIER) cc_final: 0.3177 (p)
REVERT: B  177 MET cc_start: 0.6213 (ppp) cc_final: 0.5735 (mtt)
REVERT: B  221 SER cc_start: 0.7423 (m) cc_final: 0.7189 (m)
REVERT: B  224 GLU cc_start: 0.8205 (pm20) cc_final: 0.7662 (pm20)
REVERT: G   36 TRP cc_start: 0.8160 (m100) cc_final: 0.7603 (m100)
REVERT: G   37 TYR cc_start: 0.7993 (m-10) cc_final: 0.7556 (m-80)
REVERT: G   48 LEU cc_start: 0.8871 (mt) cc_final: 0.8475 (mp)
REVERT: G   55 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7602 (ttt-90)
REVERT: G   74 LEU cc_start: 0.8885 (tp) cc_final: 0.8571 (tp)
REVERT: N   39 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8196 (mtp180)
REVERT: N   53 ASP cc_start: 0.8369 (t0) cc_final: 0.8043 (t0)
REVERT: N   55 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7704 (mt-10)
REVERT: N   83 GLU cc_start: 0.8171 (tp30) cc_final: 0.7876 (tp30)
  outliers start: 26
  outliers final: 20
  residues processed: 109
  average time/residue: 0.1470
  time to fit residues: 20.2539
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  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
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   84 LEU
Chi-restraints excluded: chain N residue   99 THR
Chi-restraints excluded: chain N residue  107 TYR
Chi-restraints excluded: chain N residue  109 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4465 r_free = 0.4465 target = 0.211672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.127321 restraints weight = 4571.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.131179 restraints weight = 3468.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.133512 restraints weight = 2830.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.8372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4033  Z= 0.165
  Angle     :  0.784  14.037   5493  Z= 0.387
  Chirality :  0.046   0.219    603
  Planarity :  0.005   0.074    703
  Dihedral  :  5.908  25.942    541
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.35 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 24.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.37), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.40 (0.38), residues: 182
  loop : -2.23 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.003   TRP N 112 
 HIS   0.003   0.001   HIS B 207 
 PHE   0.030   0.003   PHE B  58 
 TYR   0.016   0.002   TYR B 248 
 ARG   0.009   0.001   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03501 (  104)
  hydrogen bonds       : angle       6.99184 (  264)
  SS BOND              : bond        0.00584 (    4)
  SS BOND              : angle       1.29923 (    8)
  covalent geometry    : bond        0.00384 ( 4029)
  covalent geometry    : angle       0.78269 ( 5485)

*********************** 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
  114 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.6625 (mm-40) cc_final: 0.5799 (pt0)
REVERT: B   79 PHE cc_start: 0.6837 (m-80) cc_final: 0.6358 (m-80)
REVERT: B  116 SER cc_start: 0.7623 (m) cc_final: 0.7048 (p)
REVERT: B  131 CYS cc_start: 0.4353 (OUTLIER) cc_final: 0.3788 (p)
REVERT: B  177 MET cc_start: 0.6137 (ppp) cc_final: 0.5821 (mtt)
REVERT: B  224 GLU cc_start: 0.8208 (pm20) cc_final: 0.7708 (pm20)
REVERT: G   36 TRP cc_start: 0.8187 (m100) cc_final: 0.7634 (m100)
REVERT: G   48 LEU cc_start: 0.8756 (mt) cc_final: 0.8389 (mp)
REVERT: G   74 LEU cc_start: 0.8937 (tp) cc_final: 0.8624 (tp)
REVERT: N   39 ARG cc_start: 0.8917 (mtp180) cc_final: 0.8235 (mtp180)
REVERT: N   53 ASP cc_start: 0.8324 (t0) cc_final: 0.7994 (t0)
REVERT: N   55 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7898 (mt-10)
REVERT: N   83 GLU cc_start: 0.8167 (tp30) cc_final: 0.7865 (tp30)
  outliers start: 21
  outliers final: 16
  residues processed: 108
  average time/residue: 0.1423
  time to fit residues: 19.7168
Evaluate side-chains
  101 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue   84 LEU
Chi-restraints excluded: chain N residue  107 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 8 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** G  32 ASN ** 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 = 0.4435 r_free = 0.4435 target = 0.207155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.123101 restraints weight = 4576.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.126868 restraints weight = 3503.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.129611 restraints weight = 2867.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.8750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4033  Z= 0.191
  Angle     :  0.812  13.123   5493  Z= 0.404
  Chirality :  0.046   0.166    603
  Planarity :  0.005   0.061    703
  Dihedral  :  6.065  26.634    541
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.96 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 24.54 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.32 (0.40), residues: 173
  loop : -2.35 (0.32), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.003   TRP N 112 
 HIS   0.004   0.001   HIS B  49 
 PHE   0.029   0.003   PHE N 109 
 TYR   0.018   0.002   TYR B 248 
 ARG   0.008   0.001   ARG G  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03638 (  104)
  hydrogen bonds       : angle       7.02433 (  264)
  SS BOND              : bond        0.00498 (    4)
  SS BOND              : angle       1.27130 (    8)
  covalent geometry    : bond        0.00442 ( 4029)
  covalent geometry    : angle       0.81091 ( 5485)

********************** 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
  109 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: B   23 GLN cc_start: 0.6964 (mm-40) cc_final: 0.5900 (pt0)
REVERT: B   79 PHE cc_start: 0.6870 (m-80) cc_final: 0.6357 (m-80)
REVERT: B  116 SER cc_start: 0.7682 (m) cc_final: 0.7121 (p)
REVERT: B  131 CYS cc_start: 0.4525 (OUTLIER) cc_final: 0.3973 (p)
REVERT: B  224 GLU cc_start: 0.8243 (pm20) cc_final: 0.7622 (pm20)
REVERT: G   36 TRP cc_start: 0.8161 (m100) cc_final: 0.7681 (m100)
REVERT: G   37 TYR cc_start: 0.7863 (m-10) cc_final: 0.7545 (m-80)
REVERT: G   48 LEU cc_start: 0.8847 (mt) cc_final: 0.8490 (mp)
REVERT: G   74 LEU cc_start: 0.9000 (tp) cc_final: 0.8676 (tp)
REVERT: N    7 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6572 (mt0)
REVERT: N   39 ARG cc_start: 0.8926 (mtp180) cc_final: 0.8312 (mtp180)
REVERT: N   53 ASP cc_start: 0.8422 (t0) cc_final: 0.8101 (t0)
REVERT: N   55 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7970 (mt-10)
REVERT: N   71 MET cc_start: 0.8440 (ppp) cc_final: 0.8033 (ppp)
  outliers start: 20
  outliers final: 17
  residues processed: 103
  average time/residue: 0.1393
  time to fit residues: 18.9855
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  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue  108 THR
Chi-restraints excluded: chain B residue  120 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  131 CYS
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  215 ASP
Chi-restraints excluded: chain B residue  239 GLN
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   73 THR
Chi-restraints excluded: chain G residue   93 ASP
Chi-restraints excluded: chain G residue  105 THR
Chi-restraints excluded: chain N residue    7 GLN
Chi-restraints excluded: chain N residue   84 LEU
Chi-restraints excluded: chain N residue  107 TYR
Chi-restraints excluded: chain N residue  109 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** G  32 ASN ** 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 = 0.4447 r_free = 0.4447 target = 0.191168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.126388 restraints weight = 4230.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.130055 restraints weight = 3171.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.132776 restraints weight = 2558.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.8965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4033  Z= 0.188
  Angle     :  0.811  14.024   5493  Z= 0.402
  Chirality :  0.046   0.158    603
  Planarity :  0.005   0.043    703
  Dihedral  :  6.058  26.295    541
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.75 %
    Favored  : 87.04 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.24 (0.36), residues: 494
  helix:  None (None), residues: 0
  sheet: -0.40 (0.39), residues: 178
  loop : -2.28 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP N 112 
 HIS   0.004   0.001   HIS B  49 
 PHE   0.029   0.003   PHE N 109 
 TYR   0.017   0.002   TYR B 248 
 ARG   0.006   0.001   ARG G  55 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03580 (  104)
  hydrogen bonds       : angle       6.97664 (  264)
  SS BOND              : bond        0.00493 (    4)
  SS BOND              : angle       1.16218 (    8)
  covalent geometry    : bond        0.00436 ( 4029)
  covalent geometry    : angle       0.81017 ( 5485)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2275.62 seconds
wall clock time: 41 minutes 13.51 seconds (2473.51 seconds total)