Starting phenix.real_space_refine
on Thu Jun  5 11:39:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9opb_70687/06_2025/9opb_70687.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9opb_70687/06_2025/9opb_70687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9opb_70687/06_2025/9opb_70687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9opb_70687/06_2025/9opb_70687.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9opb_70687/06_2025/9opb_70687.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9opb_70687/06_2025/9opb_70687.cif"
  }
  resolution = 3.6
  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=   0.004 sd=   0.039
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       5      5.16       5
     C    3740      2.51       5
     N    1205      2.21       5
     O    1195      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6145
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "M"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
    Chain: "O"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "P"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
    Chain: "Q"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "T"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 603
          Classifications: {'peptide': 75}
          Link IDs: {'TRANS': 74}
          Chain breaks: 2
    Chain: "V"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 626
          Classifications: {'peptide': 81}
          Link IDs: {'TRANS': 80}
          Chain breaks: 1
  Time building chain proxies: 5.89, per 1000 atoms: 0.96
  Number of scatterers: 6145
  At special positions: 0
  Unit cell: (115.5, 114.4, 110, 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       5     16.00
     O    1195      8.00
     N    1205      7.00
     C    3740      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.60
  Conformation dependent library (CDL) restraints added in 727.9 milliseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1450

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      96.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'M' and resid 33 through 43
    Processing helix  chain 'M' and resid 53 through 62
      removed outlier: 3.687A  pdb=" N   ASP M  62 " --> pdb=" O   ARG M  58 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 104 through 154
    Processing helix  chain 'N' and resid 51 through 65
    Processing helix  chain 'N' and resid 106 through 169
      removed outlier: 3.750A  pdb=" N   ASN N 124 " --> pdb=" O   GLY N 120 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 34 through 44
      removed outlier: 4.524A  pdb=" N   MET O  44 " --> pdb=" O   LEU O  40 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 53 through 62
    Processing helix  chain 'O' and resid 104 through 154
    Processing helix  chain 'P' and resid 51 through 65
    Processing helix  chain 'P' and resid 106 through 169
    Processing helix  chain 'Q' and resid 34 through 44
    Processing helix  chain 'Q' and resid 53 through 62
    Processing helix  chain 'Q' and resid 104 through 154
    Processing helix  chain 'R' and resid 51 through 65
    Processing helix  chain 'R' and resid 106 through 169
      removed outlier: 3.868A  pdb=" N   ASN R 124 " --> pdb=" O   GLY R 120 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 34 through 43
    Processing helix  chain 'S' and resid 53 through 62
    Processing helix  chain 'S' and resid 104 through 154
      removed outlier: 3.578A  pdb=" N   THR S 154 " --> pdb=" O   LEU S 150 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 51 through 65
    Processing helix  chain 'T' and resid 106 through 169
    Processing helix  chain 'U' and resid 34 through 43
    Processing helix  chain 'U' and resid 53 through 62
    Processing helix  chain 'U' and resid 104 through 154
    Processing helix  chain 'V' and resid 51 through 65
    Processing helix  chain 'V' and resid 106 through 169

    648 hydrogen bonds defined for protein.
    1944 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: 1.74

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2279
        1.34 -     1.46: 476
        1.46 -     1.57: 3395
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 6160
  Sorted by residual:
  bond pdb=" CB  GLU V 149 "
       pdb=" CG  GLU V 149 "
    ideal  model  delta    sigma   weight residual
    1.520  1.484  0.036 3.00e-02 1.11e+03 1.46e+00
  bond pdb=" CG  GLU V 149 "
       pdb=" CD  GLU V 149 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 1.01e+00
  bond pdb=" CB  GLU N 149 "
       pdb=" CG  GLU N 149 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.29e-01
  bond pdb=" N   GLU N 149 "
       pdb=" CA  GLU N 149 "
    ideal  model  delta    sigma   weight residual
    1.459  1.471 -0.012 1.25e-02 6.40e+03 9.07e-01
  bond pdb=" CB  ARG N 146 "
       pdb=" CG  ARG N 146 "
    ideal  model  delta    sigma   weight residual
    1.520  1.495  0.025 3.00e-02 1.11e+03 7.13e-01
  ... (remaining 6155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 8166
        1.48 -     2.96: 99
        2.96 -     4.44: 15
        4.44 -     5.92: 3
        5.92 -     7.39: 2
  Bond angle restraints: 8285
  Sorted by residual:
  angle pdb=" C   ARG V 148 "
        pdb=" N   GLU V 149 "
        pdb=" CA  GLU V 149 "
      ideal   model   delta    sigma   weight residual
     120.31  116.35    3.96 1.52e+00 4.33e-01 6.79e+00
  angle pdb=" CA  LEU V 143 "
        pdb=" CB  LEU V 143 "
        pdb=" CG  LEU V 143 "
      ideal   model   delta    sigma   weight residual
     116.30  123.69   -7.39 3.50e+00 8.16e-02 4.46e+00
  angle pdb=" CA  ASP R 147 "
        pdb=" CB  ASP R 147 "
        pdb=" CG  ASP R 147 "
      ideal   model   delta    sigma   weight residual
     112.60  114.67   -2.07 1.00e+00 1.00e+00 4.30e+00
  angle pdb=" C   ARG R 146 "
        pdb=" N   ASP R 147 "
        pdb=" CA  ASP R 147 "
      ideal   model   delta    sigma   weight residual
     120.68  117.19    3.49 1.70e+00 3.46e-01 4.23e+00
  angle pdb=" CA  LEU N 143 "
        pdb=" CB  LEU N 143 "
        pdb=" CG  LEU N 143 "
      ideal   model   delta    sigma   weight residual
     116.30  123.10   -6.80 3.50e+00 8.16e-02 3.77e+00
  ... (remaining 8280 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.39: 3314
       17.39 -    34.79: 370
       34.79 -    52.18: 60
       52.18 -    69.58: 14
       69.58 -    86.97: 17
  Dihedral angle restraints: 3775
    sinusoidal: 1550
      harmonic: 2225
  Sorted by residual:
  dihedral pdb=" CB  GLU N 130 "
           pdb=" CG  GLU N 130 "
           pdb=" CD  GLU N 130 "
           pdb=" OE1 GLU N 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.97  -86.97     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" CB  GLU N 145 "
           pdb=" CG  GLU N 145 "
           pdb=" CD  GLU N 145 "
           pdb=" OE1 GLU N 145 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.83  -85.83     1      3.00e+01 1.11e-03 9.89e+00
  dihedral pdb=" CB  GLU P 130 "
           pdb=" CG  GLU P 130 "
           pdb=" CD  GLU P 130 "
           pdb=" OE1 GLU P 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.74  -85.74     1      3.00e+01 1.11e-03 9.87e+00
  ... (remaining 3772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 707
       0.028 -    0.055: 170
       0.055 -    0.083: 85
       0.083 -    0.111: 9
       0.111 -    0.138: 4
  Chirality restraints: 975
  Sorted by residual:
  chirality pdb=" CA  ASP R 147 "
            pdb=" N   ASP R 147 "
            pdb=" C   ASP R 147 "
            pdb=" CB  ASP R 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CB  ILE N 114 "
            pdb=" CA  ILE N 114 "
            pdb=" CG1 ILE N 114 "
            pdb=" CG2 ILE N 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.12 2.00e-01 2.50e+01 3.66e-01
  chirality pdb=" CB  ILE S  53 "
            pdb=" CA  ILE S  53 "
            pdb=" CG1 ILE S  53 "
            pdb=" CG2 ILE S  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.53    0.12 2.00e-01 2.50e+01 3.48e-01
  ... (remaining 972 not shown)

  Planarity restraints: 1115
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU V 149 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.27e+00
        pdb=" CD  GLU V 149 "   -0.036 2.00e-02 2.50e+03
        pdb=" OE1 GLU V 149 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU V 149 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP R 147 "    0.006 2.00e-02 2.50e+03   1.10e-02 1.22e+00
        pdb=" C   ASP R 147 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ASP R 147 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ARG R 148 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG N 146 "    0.096 9.50e-02 1.11e+02   4.29e-02 1.14e+00
        pdb=" NE  ARG N 146 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  ARG N 146 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG N 146 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG N 146 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1112 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 2735
        2.97 -     3.45: 7429
        3.45 -     3.93: 9754
        3.93 -     4.42: 10281
        4.42 -     4.90: 15619
  Nonbonded interactions: 45818
  Sorted by model distance:
  nonbonded pdb=" O   GLU N 145 "
            pdb=" OE1 GLU N 149 "
     model   vdw
     2.483 3.040
  nonbonded pdb=" O   GLN R 144 "
            pdb=" OD1 ASP R 147 "
     model   vdw
     2.553 3.040
  nonbonded pdb=" O   LEU O 125 "
            pdb=" OG1 THR O 128 "
     model   vdw
     2.603 3.040
  nonbonded pdb=" O   GLU V 145 "
            pdb=" OE1 GLU V 149 "
     model   vdw
     2.608 3.040
  nonbonded pdb=" N   ALA N 105 "
            pdb=" N   PHE N 106 "
     model   vdw
     2.638 2.560
  ... (remaining 45813 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'M'
  selection = chain 'O'
  selection = chain 'Q'
  selection = chain 'S'
  selection = chain 'U'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'P'
  selection = chain 'R'
  selection = chain 'T'
  selection = chain 'V'
}

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:             27.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.920
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5750
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6160  Z= 0.118
  Angle     :  0.438   7.394   8285  Z= 0.237
  Chirality :  0.031   0.138    975
  Planarity :  0.003   0.043   1115
  Dihedral  : 15.828  86.969   2325
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.27 %
    Favored  : 98.57 %
  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:  6.54 (0.27), residues: 730
  helix:  4.18 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE U 126 
 TYR   0.013   0.001   TYR R  60 
 ARG   0.005   0.000   ARG V 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07029 (  648)
  hydrogen bonds       : angle       3.30874 ( 1944)
  covalent geometry    : bond        0.00209 ( 6160)
  covalent geometry    : angle       0.43793 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 312
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: N  122 ILE cc_start: 0.6290 (tt) cc_final: 0.5993 (tt)
REVERT: O  108 THR cc_start: 0.4925 (p) cc_final: 0.4590 (t)
REVERT: R  132 LEU cc_start: 0.8831 (mp) cc_final: 0.8606 (mm)
REVERT: S  143 LEU cc_start: 0.7576 (tt) cc_final: 0.6915 (mt)
REVERT: T   53 ILE cc_start: 0.7520 (mt) cc_final: 0.7319 (mt)
REVERT: U   60 TYR cc_start: 0.7131 (t80) cc_final: 0.6529 (t80)
REVERT: U  135 THR cc_start: 0.7829 (p) cc_final: 0.7599 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 312
  average time/residue: 0.3444
  time to fit residues: 123.8505
Evaluate side-chains
  142 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:   20.0000
   chunk 43 optimal weight:   40.0000
   chunk 68 optimal weight:    8.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
M 115 ASN
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 123 ASN
V 115 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.101944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.098132 restraints weight = 44569.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.098642 restraints weight = 32064.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.098996 restraints weight = 24472.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6163
moved from start:          0.5264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6160  Z= 0.147
  Angle     :  0.627  11.681   8285  Z= 0.318
  Chirality :  0.036   0.214    975
  Planarity :  0.004   0.071   1115
  Dihedral  :  3.098  10.990    880
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 17.30 %
    Favored  : 78.57 %
  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:  6.19 (0.26), residues: 730
  helix:  3.97 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.001   PHE N 106 
 TYR   0.019   0.002   TYR R  60 
 ARG   0.009   0.001   ARG O 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04756 (  648)
  hydrogen bonds       : angle       3.46373 ( 1944)
  covalent geometry    : bond        0.00303 ( 6160)
  covalent geometry    : angle       0.62696 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   55 ASP cc_start: 0.8006 (t0) cc_final: 0.7578 (p0)
REVERT: V   53 ILE cc_start: 0.8199 (tp) cc_final: 0.7647 (mm)
  outliers start: 26
  outliers final: 16
  residues processed: 168
  average time/residue: 0.2134
  time to fit residues: 44.5735
Evaluate side-chains
  147 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  128 THR
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue   52 ASP
Chi-restraints excluded: chain Q residue   57 VAL
Chi-restraints excluded: chain R residue  122 ILE
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   53 ILE
Chi-restraints excluded: chain S residue  126 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 70 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   chunk 37 optimal weight:   50.0000
   chunk 54 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 144 GLN
S 112 ASN
S 123 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.098331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.094642 restraints weight = 45109.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.095076 restraints weight = 31581.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.095436 restraints weight = 24297.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6342
moved from start:          0.6889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6160  Z= 0.149
  Angle     :  0.597   7.728   8285  Z= 0.309
  Chirality :  0.035   0.157    975
  Planarity :  0.004   0.070   1115
  Dihedral  :  3.155  12.117    880
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 21.75 %
    Favored  : 73.49 %
  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:  5.68 (0.26), residues: 730
  helix:  3.65 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE N 106 
 TYR   0.022   0.002   TYR R  60 
 ARG   0.006   0.001   ARG R 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05289 (  648)
  hydrogen bonds       : angle       3.57395 ( 1944)
  covalent geometry    : bond        0.00300 ( 6160)
  covalent geometry    : angle       0.59708 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 149
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  123 ASN cc_start: 0.7013 (m-40) cc_final: 0.6381 (m110)
REVERT: S  126 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6764 (t80)
REVERT: U   55 ASP cc_start: 0.7889 (t0) cc_final: 0.7627 (p0)
  outliers start: 30
  outliers final: 19
  residues processed: 169
  average time/residue: 0.2238
  time to fit residues: 47.3436
Evaluate side-chains
  150 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue   52 ASP
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   57 VAL
Chi-restraints excluded: chain S residue  124 ASN
Chi-restraints excluded: chain S residue  126 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 144 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.096262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.092681 restraints weight = 44123.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.093228 restraints weight = 31144.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.093588 restraints weight = 20672.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.7908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6160  Z= 0.157
  Angle     :  0.626   9.587   8285  Z= 0.323
  Chirality :  0.036   0.147    975
  Planarity :  0.004   0.066   1115
  Dihedral  :  3.188  13.772    880
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 16.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 21.90 %
    Favored  : 72.86 %
  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:  5.48 (0.26), residues: 730
  helix:  3.53 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.013   0.001   PHE N 106 
 TYR   0.020   0.002   TYR R  60 
 ARG   0.005   0.001   ARG V 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05606 (  648)
  hydrogen bonds       : angle       3.73537 ( 1944)
  covalent geometry    : bond        0.00316 ( 6160)
  covalent geometry    : angle       0.62620 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 151
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   55 ASP cc_start: 0.7115 (t0) cc_final: 0.6909 (t0)
REVERT: Q  143 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7069 (tt)
REVERT: U   55 ASP cc_start: 0.7777 (t0) cc_final: 0.7524 (p0)
  outliers start: 33
  outliers final: 19
  residues processed: 172
  average time/residue: 0.2252
  time to fit residues: 47.6415
Evaluate side-chains
  154 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain O residue  117 VAL
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   42 ILE
Chi-restraints excluded: chain Q residue  143 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   53 ILE
Chi-restraints excluded: chain T residue  119 GLU
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue   44 MET
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 32 optimal weight:   20.0000
   chunk 41 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 54 optimal weight:   30.0000
   chunk 40 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
M 136 ASN
** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 161 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 = 0.4233 r_free = 0.4233 target = 0.096331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.092615 restraints weight = 44516.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.093128 restraints weight = 30631.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.093479 restraints weight = 22877.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6406
moved from start:          0.8291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6160  Z= 0.147
  Angle     :  0.604   9.432   8285  Z= 0.309
  Chirality :  0.034   0.137    975
  Planarity :  0.004   0.053   1115
  Dihedral  :  3.121  11.508    880
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 24.44 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.71 (0.26), residues: 730
  helix:  3.67 (0.16), residues: 730
  sheet:  None (None), residues: 0
  loop :  None (None), residues: 0

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE N 106 
 TYR   0.016   0.002   TYR R  60 
 ARG   0.013   0.001   ARG R 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05429 (  648)
  hydrogen bonds       : angle       3.61968 ( 1944)
  covalent geometry    : bond        0.00286 ( 6160)
  covalent geometry    : angle       0.60368 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   55 ASP cc_start: 0.7232 (t0) cc_final: 0.7004 (t0)
REVERT: O  108 THR cc_start: 0.4508 (p) cc_final: 0.4157 (t)
REVERT: Q   53 ILE cc_start: 0.7318 (tp) cc_final: 0.7066 (mp)
  outliers start: 25
  outliers final: 19
  residues processed: 166
  average time/residue: 0.2232
  time to fit residues: 45.7371
Evaluate side-chains
  161 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  150 LEU
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain Q residue  143 LEU
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  125 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 48 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 35 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 28 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 112 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.093704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.090244 restraints weight = 44858.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.090758 restraints weight = 30560.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.091099 restraints weight = 22445.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
moved from start:          0.9161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6160  Z= 0.174
  Angle     :  0.686   9.517   8285  Z= 0.353
  Chirality :  0.037   0.134    975
  Planarity :  0.005   0.078   1115
  Dihedral  :  3.368  15.658    880
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 23.02 %
    Favored  : 70.79 %
  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:  4.80 (0.26), residues: 730
  helix:  3.14 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop : -1.91 (0.99), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.010   0.001   PHE U 126 
 TYR   0.021   0.002   TYR R  60 
 ARG   0.012   0.001   ARG R 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06187 (  648)
  hydrogen bonds       : angle       3.98997 ( 1944)
  covalent geometry    : bond        0.00351 ( 6160)
  covalent geometry    : angle       0.68562 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 144
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   55 ASP cc_start: 0.7640 (t0) cc_final: 0.7357 (t0)
REVERT: O  108 THR cc_start: 0.5215 (p) cc_final: 0.4850 (t)
REVERT: O  121 TYR cc_start: 0.5977 (t80) cc_final: 0.5755 (t80)
REVERT: Q   53 ILE cc_start: 0.7660 (tp) cc_final: 0.7330 (mp)
REVERT: T   54 ASN cc_start: 0.7568 (m110) cc_final: 0.6952 (t0)
REVERT: V  148 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6895 (tpp80)
  outliers start: 39
  outliers final: 23
  residues processed: 168
  average time/residue: 0.2300
  time to fit residues: 47.6820
Evaluate side-chains
  158 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain M residue  117 VAL
Chi-restraints excluded: chain N residue   62 ASP
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  123 ASN
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  106 PHE
Chi-restraints excluded: chain T residue  119 GLU
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  108 THR
Chi-restraints excluded: chain V residue  125 LEU
Chi-restraints excluded: chain V residue  136 ASN
Chi-restraints excluded: chain V residue  148 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 57 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 10 optimal weight:   20.0000
   chunk 62 optimal weight:   20.0000
   chunk 29 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  54 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.093074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.089465 restraints weight = 44410.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.089971 restraints weight = 31014.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.090349 restraints weight = 23384.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.9533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6160  Z= 0.167
  Angle     :  0.649   9.153   8285  Z= 0.338
  Chirality :  0.037   0.252    975
  Planarity :  0.004   0.051   1115
  Dihedral  :  3.287  14.284    880
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 24.76 %
    Favored  : 69.84 %
  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:  4.89 (0.26), residues: 730
  helix:  3.19 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop : -0.82 (1.15), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE U 126 
 TYR   0.018   0.002   TYR R  60 
 ARG   0.011   0.001   ARG R 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06145 (  648)
  hydrogen bonds       : angle       3.92349 ( 1944)
  covalent geometry    : bond        0.00339 ( 6160)
  covalent geometry    : angle       0.64931 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O  108 THR cc_start: 0.5282 (p) cc_final: 0.4897 (t)
REVERT: O  121 TYR cc_start: 0.5772 (t80) cc_final: 0.5554 (t80)
REVERT: Q   53 ILE cc_start: 0.7405 (tp) cc_final: 0.7152 (mm)
REVERT: R   53 ILE cc_start: 0.6965 (mt) cc_final: 0.5869 (mt)
REVERT: T   54 ASN cc_start: 0.7334 (m110) cc_final: 0.6941 (t0)
REVERT: V  148 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6828 (tpp80)
  outliers start: 34
  outliers final: 23
  residues processed: 164
  average time/residue: 0.2245
  time to fit residues: 45.8851
Evaluate side-chains
  161 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue   62 ASP
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  123 ASN
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain O residue  117 VAL
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  106 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  108 THR
Chi-restraints excluded: chain V residue  125 LEU
Chi-restraints excluded: chain V residue  136 ASN
Chi-restraints excluded: chain V residue  148 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 71 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:   20.0000
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.094706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.091210 restraints weight = 44592.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.091712 restraints weight = 30059.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.092070 restraints weight = 22244.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.9637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6160  Z= 0.154
  Angle     :  0.653   9.710   8285  Z= 0.335
  Chirality :  0.035   0.133    975
  Planarity :  0.004   0.059   1115
  Dihedral  :  3.138  12.123    880
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 16.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 27.30 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.23 (0.26), residues: 730
  helix:  3.40 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop : -1.32 (0.78), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE N 106 
 TYR   0.015   0.002   TYR R  60 
 ARG   0.012   0.001   ARG N 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05855 (  648)
  hydrogen bonds       : angle       3.67326 ( 1944)
  covalent geometry    : bond        0.00302 ( 6160)
  covalent geometry    : angle       0.65309 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   53 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6307 (mp)
REVERT: O  108 THR cc_start: 0.5320 (p) cc_final: 0.5004 (t)
REVERT: O  121 TYR cc_start: 0.5677 (t80) cc_final: 0.5416 (t80)
REVERT: Q   53 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7172 (mm)
REVERT: T   54 ASN cc_start: 0.7170 (m110) cc_final: 0.6911 (t0)
REVERT: V  148 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6989 (tpp80)
  outliers start: 25
  outliers final: 17
  residues processed: 167
  average time/residue: 0.2395
  time to fit residues: 49.3075
Evaluate side-chains
  152 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue   62 ASP
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   52 ASP
Chi-restraints excluded: chain Q residue   53 ILE
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   60 TYR
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain U residue   44 MET
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  108 THR
Chi-restraints excluded: chain V residue  148 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 50 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 34 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 123 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 = 0.4192 r_free = 0.4192 target = 0.093699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.090233 restraints weight = 45583.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.090734 restraints weight = 36002.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.091015 restraints weight = 23610.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.9977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6160  Z= 0.168
  Angle     :  0.689   9.857   8285  Z= 0.358
  Chirality :  0.039   0.271    975
  Planarity :  0.005   0.064   1115
  Dihedral  :  3.288  14.318    880
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 19.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 27.14 %
    Favored  : 68.57 %
  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:  4.85 (0.26), residues: 730
  helix:  3.15 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop :  1.41 (2.11), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.008   0.001   PHE N 106 
 TYR   0.018   0.002   TYR R  60 
 ARG   0.010   0.001   ARG R 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06151 (  648)
  hydrogen bonds       : angle       3.89708 ( 1944)
  covalent geometry    : bond        0.00337 ( 6160)
  covalent geometry    : angle       0.68939 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M   53 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6488 (mp)
REVERT: O  108 THR cc_start: 0.5578 (p) cc_final: 0.5224 (t)
REVERT: O  121 TYR cc_start: 0.5745 (t80) cc_final: 0.5472 (t80)
REVERT: Q   53 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7275 (mp)
REVERT: S  125 LEU cc_start: 0.7512 (pp) cc_final: 0.7281 (pp)
REVERT: T   54 ASN cc_start: 0.7162 (m110) cc_final: 0.6863 (t0)
REVERT: V  148 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6491 (tpp80)
  outliers start: 27
  outliers final: 22
  residues processed: 158
  average time/residue: 0.2306
  time to fit residues: 45.9321
Evaluate side-chains
  154 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue   62 ASP
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain O residue   53 ILE
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain Q residue   37 LEU
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   52 ASP
Chi-restraints excluded: chain Q residue   53 ILE
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   60 TYR
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  106 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue   44 MET
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  108 THR
Chi-restraints excluded: chain V residue  148 ARG
Chi-restraints excluded: chain V residue  154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 31 optimal weight:    8.9990
   chunk 71 optimal weight:   20.0000
   chunk 42 optimal weight:   20.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 123 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 = 0.4188 r_free = 0.4188 target = 0.093448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.090055 restraints weight = 45728.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.090592 restraints weight = 32263.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.090932 restraints weight = 21485.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
moved from start:          1.0197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6160  Z= 0.168
  Angle     :  0.711  10.160   8285  Z= 0.368
  Chirality :  0.038   0.241    975
  Planarity :  0.005   0.061   1115
  Dihedral  :  3.315  14.423    880
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 18.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 27.46 %
    Favored  : 68.25 %
  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:  4.73 (0.27), residues: 730
  helix:  3.08 (0.16), residues: 725
  sheet:  None (None), residues: 0
  loop :  0.75 (1.74), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHE N 106 
 TYR   0.018   0.002   TYR R  60 
 ARG   0.010   0.001   ARG Q 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06205 (  648)
  hydrogen bonds       : angle       3.92810 ( 1944)
  covalent geometry    : bond        0.00339 ( 6160)
  covalent geometry    : angle       0.71128 ( 8285)

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: M   53 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6498 (mp)
REVERT: O  108 THR cc_start: 0.5500 (p) cc_final: 0.5156 (t)
REVERT: O  121 TYR cc_start: 0.5789 (t80) cc_final: 0.5522 (t80)
REVERT: Q   53 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7452 (mp)
REVERT: S  125 LEU cc_start: 0.7454 (pp) cc_final: 0.7235 (pp)
REVERT: T   54 ASN cc_start: 0.7094 (m110) cc_final: 0.6826 (t0)
REVERT: V  148 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7013 (tpp80)
  outliers start: 27
  outliers final: 21
  residues processed: 153
  average time/residue: 0.2401
  time to fit residues: 45.7711
Evaluate side-chains
  152 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   53 ILE
Chi-restraints excluded: chain N residue   62 ASP
Chi-restraints excluded: chain N residue  108 THR
Chi-restraints excluded: chain N residue  136 ASN
Chi-restraints excluded: chain N residue  154 THR
Chi-restraints excluded: chain O residue   61 LEU
Chi-restraints excluded: chain P residue  136 ASN
Chi-restraints excluded: chain Q residue   40 LEU
Chi-restraints excluded: chain Q residue   52 ASP
Chi-restraints excluded: chain Q residue   53 ILE
Chi-restraints excluded: chain Q residue  118 LEU
Chi-restraints excluded: chain R residue   50 VAL
Chi-restraints excluded: chain R residue  136 ASN
Chi-restraints excluded: chain R residue  149 GLU
Chi-restraints excluded: chain S residue   42 ILE
Chi-restraints excluded: chain S residue   60 TYR
Chi-restraints excluded: chain T residue   62 ASP
Chi-restraints excluded: chain T residue  106 PHE
Chi-restraints excluded: chain T residue  136 ASN
Chi-restraints excluded: chain U residue   44 MET
Chi-restraints excluded: chain U residue  118 LEU
Chi-restraints excluded: chain V residue  108 THR
Chi-restraints excluded: chain V residue  148 ARG
Chi-restraints excluded: chain V residue  154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 37 optimal weight:   40.0000
   chunk 24 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** N 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 123 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 = 0.4188 r_free = 0.4188 target = 0.093349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.089717 restraints weight = 45562.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.090268 restraints weight = 30893.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.090588 restraints weight = 22395.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6537
moved from start:          1.0310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6160  Z= 0.167
  Angle     :  0.710   9.909   8285  Z= 0.369
  Chirality :  0.038   0.221    975
  Planarity :  0.004   0.057   1115
  Dihedral  :  3.304  14.441    880
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 18.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 27.78 %
    Favored  : 68.10 %
  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:  4.78 (0.27), residues: 730
  helix:  3.12 (0.17), residues: 725
  sheet:  None (None), residues: 0
  loop :  0.11 (1.86), residues: 5

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHE N 106 
 TYR   0.019   0.002   TYR R  60 
 ARG   0.010   0.001   ARG R 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06173 (  648)
  hydrogen bonds       : angle       3.90845 ( 1944)
  covalent geometry    : bond        0.00340 ( 6160)
  covalent geometry    : angle       0.70982 ( 8285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2812.04 seconds
wall clock time: 50 minutes 44.24 seconds (3044.24 seconds total)