Starting phenix.real_space_refine
on Sun Jul 27 22:43:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zxq_15014/07_2025/7zxq_15014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxq_15014/07_2025/7zxq_15014.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxq_15014/07_2025/7zxq_15014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxq_15014/07_2025/7zxq_15014.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxq_15014/07_2025/7zxq_15014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxq_15014/07_2025/7zxq_15014.cif"
  }
  resolution = 3.53
  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=   0.001
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      90      5.16       5
     C    6558      2.51       5
     N    1656      2.21       5
     O    1626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9930
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1655
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.56, per 1000 atoms: 0.46
  Number of scatterers: 9930
  At special positions: 0
  Unit cell: (100.062, 100.062, 92.214, 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      90     16.00
     O    1626      8.00
     N    1656      7.00
     C    6558      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  53 " - pdb=" SG  CYS E 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  53 " - pdb=" SG  CYS F 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  60 " - pdb=" SG  CYS E 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  60 " - pdb=" SG  CYS F 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  64 " - pdb=" SG  CYS D 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  64 " - pdb=" SG  CYS F 168 " 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: 2.61
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      73.8% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR A   7 " --> pdb=" O   TRP A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 42
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 107
      Proline residue:  A  87  - end of helix
    Processing helix  chain 'A' and resid 123 through 157
    Processing helix  chain 'A' and resid 183 through 220
    Processing helix  chain 'B' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR B   7 " --> pdb=" O   TRP B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 42
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 107
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 123 through 157
    Processing helix  chain 'B' and resid 183 through 220
    Processing helix  chain 'C' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR C   7 " --> pdb=" O   TRP C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 42
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 107
      Proline residue:  C  87  - end of helix
    Processing helix  chain 'C' and resid 123 through 157
    Processing helix  chain 'C' and resid 183 through 220
    Processing helix  chain 'D' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR D   7 " --> pdb=" O   TRP D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 42
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 107
      Proline residue:  D  87  - end of helix
    Processing helix  chain 'D' and resid 123 through 157
    Processing helix  chain 'D' and resid 183 through 220
    Processing helix  chain 'E' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR E   7 " --> pdb=" O   TRP E   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 42
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 107
      Proline residue:  E  87  - end of helix
    Processing helix  chain 'E' and resid 123 through 157
    Processing helix  chain 'E' and resid 183 through 220
    Processing helix  chain 'F' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR F   7 " --> pdb=" O   TRP F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 42
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 107
      Proline residue:  F  87  - end of helix
    Processing helix  chain 'F' and resid 123 through 157
    Processing helix  chain 'F' and resid 183 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53
      removed outlier: 4.123A  pdb=" N   ILE A  52 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE A 180 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE B  52 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE C  52 " --> pdb=" O   PHE C 180 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE C 180 " --> pdb=" O   ILE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE D  52 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE E  52 " --> pdb=" O   PHE E 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE E 180 " --> pdb=" O   ILE E  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE F  52 " --> pdb=" O   PHE F 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE F 180 " --> pdb=" O   ILE F  52 " (cutoff:3.500A)

    756 hydrogen bonds defined for protein.
    2268 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: 2.73

  Time building geometry restraints manager: 2.92 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2994
        1.35 -     1.47: 2716
        1.47 -     1.59: 4358
        1.59 -     1.71: 0
        1.71 -     1.83: 132
  Bond restraints: 10200
  Sorted by residual:
  bond pdb=" CG  PRO E  58 "
       pdb=" CD  PRO E  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.77e+00
  bond pdb=" CG  PRO B  58 "
       pdb=" CD  PRO B  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.75e+00
  bond pdb=" CG  PRO A  58 "
       pdb=" CD  PRO A  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  bond pdb=" CG  PRO D  58 "
       pdb=" CD  PRO D  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  bond pdb=" CG  PRO C  58 "
       pdb=" CD  PRO C  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  ... (remaining 10195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 13556
        1.88 -     3.75: 286
        3.75 -     5.63: 36
        5.63 -     7.51: 12
        7.51 -     9.38: 6
  Bond angle restraints: 13896
  Sorted by residual:
  angle pdb=" C   ASN B  14 "
        pdb=" CA  ASN B  14 "
        pdb=" CB  ASN B  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN E  14 "
        pdb=" CA  ASN E  14 "
        pdb=" CB  ASN E  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN D  14 "
        pdb=" CA  ASN D  14 "
        pdb=" CB  ASN D  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN A  14 "
        pdb=" CA  ASN A  14 "
        pdb=" CB  ASN A  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.75    6.59 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN F  14 "
        pdb=" CA  ASN F  14 "
        pdb=" CB  ASN F  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.75    6.59 1.40e+00 5.10e-01 2.21e+01
  ... (remaining 13891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.52: 5179
       13.52 -    27.03: 548
       27.03 -    40.55: 171
       40.55 -    54.07: 48
       54.07 -    67.58: 12
  Dihedral angle restraints: 5958
    sinusoidal: 2316
      harmonic: 3642
  Sorted by residual:
  dihedral pdb=" CB  CYS D  64 "
           pdb=" SG  CYS D  64 "
           pdb=" SG  CYS D 168 "
           pdb=" CB  CYS D 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.33  -50.33     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CB  CYS A  64 "
           pdb=" SG  CYS A  64 "
           pdb=" SG  CYS A 168 "
           pdb=" CB  CYS A 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.32  -50.32     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CB  CYS C  64 "
           pdb=" SG  CYS C  64 "
           pdb=" SG  CYS C 168 "
           pdb=" CB  CYS C 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.31  -50.31     1      1.00e+01 1.00e-02 3.47e+01
  ... (remaining 5955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1051
       0.033 -    0.066: 399
       0.066 -    0.099: 127
       0.099 -    0.133: 55
       0.133 -    0.166: 6
  Chirality restraints: 1638
  Sorted by residual:
  chirality pdb=" CA  ILE F  20 "
            pdb=" N   ILE F  20 "
            pdb=" C   ILE F  20 "
            pdb=" CB  ILE F  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CA  ILE C  20 "
            pdb=" N   ILE C  20 "
            pdb=" C   ILE C  20 "
            pdb=" CB  ILE C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CA  ILE A  20 "
            pdb=" N   ILE A  20 "
            pdb=" C   ILE A  20 "
            pdb=" CB  ILE A  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 1635 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  57 "   -0.050 5.00e-02 4.00e+02   7.56e-02 9.15e+00
        pdb=" N   PRO B  58 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B  58 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B  58 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  57 "    0.050 5.00e-02 4.00e+02   7.55e-02 9.12e+00
        pdb=" N   PRO A  58 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A  58 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A  58 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  57 "   -0.050 5.00e-02 4.00e+02   7.54e-02 9.10e+00
        pdb=" N   PRO C  58 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO C  58 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C  58 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 84
        2.60 -     3.18: 8797
        3.18 -     3.75: 16284
        3.75 -     4.33: 18793
        4.33 -     4.90: 33420
  Nonbonded interactions: 77378
  Sorted by model distance:
  nonbonded pdb=" O   ILE D  71 "
            pdb=" OH  TYR D 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE E  71 "
            pdb=" OH  TYR E 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE B  71 "
            pdb=" OH  TYR B 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE C  71 "
            pdb=" OH  TYR C 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE F  71 "
            pdb=" OH  TYR F 157 "
     model   vdw
     2.027 3.040
  ... (remaining 77373 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             43.170
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     22.720
  Find NCS groups from input model:        0.200
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   69.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
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      :  0.003   0.045  10218  Z= 0.151
  Angle     :  0.667   9.385  13932  Z= 0.365
  Chirality :  0.041   0.166   1638
  Planarity :  0.006   0.076   1662
  Dihedral  : 12.725  67.582   3540
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.45 (0.24), residues: 1212
  helix:  3.25 (0.16), residues: 852
  sheet: -0.01 (0.73), residues: 60
  loop : -3.28 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  44 
 HIS   0.003   0.001   HIS C  73 
 PHE   0.007   0.001   PHE B 190 
 TYR   0.011   0.001   TYR A 151 
 ARG   0.003   0.000   ARG E 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12449 (  756)
  hydrogen bonds       : angle       4.49650 ( 2268)
  SS BOND              : bond        0.00653 (   18)
  SS BOND              : angle       1.67906 (   36)
  covalent geometry    : bond        0.00328 (10200)
  covalent geometry    : angle       0.66236 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.152 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2846
  time to fit residues: 64.0510
Evaluate side-chains
  106 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.4980
   chunk 90 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 57 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   chunk 108 optimal weight:    2.9990
   overall best weight:    4.2988

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.066796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.051441 restraints weight = 47695.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.052841 restraints weight = 26318.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.053714 restraints weight = 18969.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10218  Z= 0.195
  Angle     :  0.609   7.644  13932  Z= 0.312
  Chirality :  0.042   0.172   1638
  Planarity :  0.004   0.040   1662
  Dihedral  :  4.009  23.791   1344
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  7.25 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.67 (0.24), residues: 1212
  helix:  3.18 (0.16), residues: 870
  sheet:  0.32 (0.78), residues: 60
  loop : -2.86 (0.30), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  77 
 HIS   0.003   0.001   HIS B 100 
 PHE   0.011   0.001   PHE C 180 
 TYR   0.013   0.002   TYR A 151 
 ARG   0.003   0.001   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  756)
  hydrogen bonds       : angle       3.90726 ( 2268)
  SS BOND              : bond        0.00638 (   18)
  SS BOND              : angle       1.70549 (   36)
  covalent geometry    : bond        0.00436 (10200)
  covalent geometry    : angle       0.60389 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.136 
Fit side-chains
REVERT: A   93 MET cc_start: 0.8886 (mtm) cc_final: 0.8667 (mtm)
REVERT: B   93 MET cc_start: 0.8834 (mtm) cc_final: 0.8353 (mtm)
REVERT: D   93 MET cc_start: 0.8871 (mtm) cc_final: 0.8653 (mtm)
  outliers start: 14
  outliers final: 4
  residues processed: 130
  average time/residue: 0.2324
  time to fit residues: 42.1303
Evaluate side-chains
  108 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain F residue   41 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 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 = 0.3639 r_free = 0.3639 target = 0.066966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.051371 restraints weight = 48257.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.052798 restraints weight = 26230.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.053568 restraints weight = 18765.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10218  Z= 0.151
  Angle     :  0.542   6.404  13932  Z= 0.280
  Chirality :  0.040   0.169   1638
  Planarity :  0.004   0.032   1662
  Dihedral  :  3.839  23.019   1344
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.33 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.90 (0.24), residues: 1212
  helix:  3.32 (0.16), residues: 864
  sheet:  0.34 (0.80), residues: 60
  loop : -2.50 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  77 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.010   0.001   PHE F  68 
 TYR   0.012   0.001   TYR F 171 
 ARG   0.003   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03757 (  756)
  hydrogen bonds       : angle       3.72393 ( 2268)
  SS BOND              : bond        0.00556 (   18)
  SS BOND              : angle       1.42533 (   36)
  covalent geometry    : bond        0.00339 (10200)
  covalent geometry    : angle       0.53756 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 1.126 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8345 (ttm)
REVERT: E  162 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8350 (ttm)
  outliers start: 26
  outliers final: 20
  residues processed: 128
  average time/residue: 0.2608
  time to fit residues: 46.8926
Evaluate side-chains
  125 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 115 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 80 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 77 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 49 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 98 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
E  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.064639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.049196 restraints weight = 48492.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.050479 restraints weight = 26877.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.051393 restraints weight = 19298.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  10218  Z= 0.218
  Angle     :  0.613   7.573  13932  Z= 0.319
  Chirality :  0.042   0.174   1638
  Planarity :  0.004   0.031   1662
  Dihedral  :  4.037  23.012   1344
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 11.05 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.56 (0.24), residues: 1212
  helix:  3.09 (0.16), residues: 864
  sheet: -0.33 (0.83), residues: 60
  loop : -2.58 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F  44 
 HIS   0.003   0.001   HIS E  73 
 PHE   0.013   0.002   PHE F  68 
 TYR   0.016   0.002   TYR A 151 
 ARG   0.003   0.000   ARG D 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04261 (  756)
  hydrogen bonds       : angle       3.85266 ( 2268)
  SS BOND              : bond        0.00687 (   18)
  SS BOND              : angle       1.73803 (   36)
  covalent geometry    : bond        0.00481 (10200)
  covalent geometry    : angle       0.60754 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 1.148 
Fit side-chains
REVERT: A  105 MET cc_start: 0.1024 (OUTLIER) cc_final: 0.0824 (mtt)
REVERT: B  162 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8429 (ttm)
REVERT: D  105 MET cc_start: 0.1027 (OUTLIER) cc_final: 0.0824 (mtt)
REVERT: E  162 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8414 (ttm)
  outliers start: 30
  outliers final: 22
  residues processed: 123
  average time/residue: 0.2491
  time to fit residues: 42.4729
Evaluate side-chains
  118 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   89 LEU
Chi-restraints excluded: chain D residue  105 MET
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 101 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
B  80 GLN
C  80 GLN
D  80 GLN
F  80 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.067394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.052259 restraints weight = 48051.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.053674 restraints weight = 25687.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.054567 restraints weight = 18281.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10218  Z= 0.102
  Angle     :  0.500   7.313  13932  Z= 0.256
  Chirality :  0.038   0.158   1638
  Planarity :  0.003   0.025   1662
  Dihedral  :  3.614  19.021   1344
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.95 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.10 (0.24), residues: 1212
  helix:  3.56 (0.16), residues: 864
  sheet: -0.21 (0.80), residues: 60
  loop : -2.60 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP D   3 
 HIS   0.002   0.001   HIS D  94 
 PHE   0.007   0.001   PHE C  31 
 TYR   0.006   0.001   TYR F 160 
 ARG   0.003   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03201 (  756)
  hydrogen bonds       : angle       3.47474 ( 2268)
  SS BOND              : bond        0.00555 (   18)
  SS BOND              : angle       1.20890 (   36)
  covalent geometry    : bond        0.00219 (10200)
  covalent geometry    : angle       0.49668 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 1.069 
Fit side-chains
REVERT: C  171 TYR cc_start: 0.9001 (t80) cc_final: 0.8757 (t80)
REVERT: F  171 TYR cc_start: 0.8999 (t80) cc_final: 0.8759 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 135
  average time/residue: 0.2190
  time to fit residues: 41.6944
Evaluate side-chains
  114 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 115 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 64 optimal weight:    3.9990
   chunk 41 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 74 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9980
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
B 205 ASN
** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 205 ASN
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.066238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.050918 restraints weight = 48718.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.052273 restraints weight = 26463.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.053144 restraints weight = 18949.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10218  Z= 0.134
  Angle     :  0.529   7.828  13932  Z= 0.268
  Chirality :  0.039   0.161   1638
  Planarity :  0.003   0.024   1662
  Dihedral  :  3.606  19.490   1344
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.86 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.07 (0.24), residues: 1212
  helix:  3.48 (0.16), residues: 870
  sheet: -0.29 (0.79), residues: 60
  loop : -2.52 (0.31), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  77 
 HIS   0.002   0.001   HIS A  73 
 PHE   0.009   0.001   PHE A  68 
 TYR   0.019   0.001   TYR B 171 
 ARG   0.003   0.000   ARG F 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03387 (  756)
  hydrogen bonds       : angle       3.46031 ( 2268)
  SS BOND              : bond        0.00571 (   18)
  SS BOND              : angle       1.31950 (   36)
  covalent geometry    : bond        0.00299 (10200)
  covalent geometry    : angle       0.52575 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 1.119 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8359 (ttm)
REVERT: C  171 TYR cc_start: 0.9059 (t80) cc_final: 0.8713 (t80)
REVERT: E  162 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8377 (ttm)
REVERT: F  171 TYR cc_start: 0.9065 (t80) cc_final: 0.8717 (t80)
  outliers start: 30
  outliers final: 20
  residues processed: 124
  average time/residue: 0.1907
  time to fit residues: 35.5324
Evaluate side-chains
  114 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 111 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 19 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** F 205 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 = 0.3616 r_free = 0.3616 target = 0.065651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.050480 restraints weight = 49522.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.051823 restraints weight = 27140.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.052619 restraints weight = 19494.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10218  Z= 0.138
  Angle     :  0.532   7.916  13932  Z= 0.272
  Chirality :  0.039   0.159   1638
  Planarity :  0.003   0.024   1662
  Dihedral  :  3.666  20.933   1344
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.21 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.02 (0.24), residues: 1212
  helix:  3.44 (0.16), residues: 876
  sheet: -0.36 (0.79), residues: 60
  loop : -2.66 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  44 
 HIS   0.003   0.001   HIS C  73 
 PHE   0.009   0.001   PHE F  68 
 TYR   0.010   0.001   TYR E 151 
 ARG   0.002   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03460 (  756)
  hydrogen bonds       : angle       3.44446 ( 2268)
  SS BOND              : bond        0.00689 (   18)
  SS BOND              : angle       1.28839 (   36)
  covalent geometry    : bond        0.00306 (10200)
  covalent geometry    : angle       0.52865 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 1.061 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8363 (ttm)
REVERT: C  171 TYR cc_start: 0.9048 (t80) cc_final: 0.8725 (t80)
REVERT: E  162 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8380 (ttm)
REVERT: F  171 TYR cc_start: 0.9050 (t80) cc_final: 0.8733 (t80)
  outliers start: 29
  outliers final: 24
  residues processed: 125
  average time/residue: 0.1686
  time to fit residues: 32.1163
Evaluate side-chains
  125 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 94 optimal weight:    8.9990
   chunk 96 optimal weight:    7.9990
   chunk 115 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C  14 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 = 0.3611 r_free = 0.3611 target = 0.065436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.050304 restraints weight = 49527.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.051633 restraints weight = 27103.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.052357 restraints weight = 19484.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.4367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10218  Z= 0.140
  Angle     :  0.538   8.013  13932  Z= 0.274
  Chirality :  0.039   0.162   1638
  Planarity :  0.003   0.029   1662
  Dihedral  :  3.631  20.015   1344
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.21 %
    Favored  : 81.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.05 (0.24), residues: 1212
  helix:  3.47 (0.16), residues: 876
  sheet: -0.52 (0.78), residues: 60
  loop : -2.65 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 132 
 HIS   0.002   0.001   HIS B  73 
 PHE   0.009   0.001   PHE D  68 
 TYR   0.030   0.001   TYR A 171 
 ARG   0.002   0.000   ARG B  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03404 (  756)
  hydrogen bonds       : angle       3.43698 ( 2268)
  SS BOND              : bond        0.00580 (   18)
  SS BOND              : angle       1.43885 (   36)
  covalent geometry    : bond        0.00312 (10200)
  covalent geometry    : angle       0.53402 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 1.238 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8390 (ttm)
REVERT: C  171 TYR cc_start: 0.9052 (t80) cc_final: 0.8747 (t80)
REVERT: E  162 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8366 (ttm)
REVERT: F  171 TYR cc_start: 0.9060 (t80) cc_final: 0.8751 (t80)
  outliers start: 26
  outliers final: 22
  residues processed: 122
  average time/residue: 0.1749
  time to fit residues: 33.0265
Evaluate side-chains
  119 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 116 optimal weight:    0.0670
   chunk 102 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0170
   chunk 32 optimal weight:    0.9990
   chunk 118 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0270
   chunk 7 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.8218

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 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 = 0.3670 r_free = 0.3670 target = 0.067379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.052501 restraints weight = 49109.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.053862 restraints weight = 26315.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.054700 restraints weight = 18803.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.4447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10218  Z= 0.097
  Angle     :  0.517   8.526  13932  Z= 0.260
  Chirality :  0.038   0.152   1638
  Planarity :  0.003   0.031   1662
  Dihedral  :  3.457  18.411   1344
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.12 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.22 (0.24), residues: 1212
  helix:  3.56 (0.16), residues: 882
  sheet: -0.69 (0.78), residues: 60
  loop : -2.50 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP D   3 
 HIS   0.001   0.000   HIS E 100 
 PHE   0.006   0.001   PHE B 149 
 TYR   0.006   0.001   TYR D   7 
 ARG   0.003   0.000   ARG A  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02897 (  756)
  hydrogen bonds       : angle       3.28473 ( 2268)
  SS BOND              : bond        0.00522 (   18)
  SS BOND              : angle       1.11695 (   36)
  covalent geometry    : bond        0.00205 (10200)
  covalent geometry    : angle       0.51500 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 1.062 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8364 (ttm)
REVERT: E  162 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8311 (ttm)
  outliers start: 26
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1790
  time to fit residues: 32.5070
Evaluate side-chains
  110 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 103 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0020
   chunk 2 optimal weight:    4.9990
   chunk 75 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9990
   chunk 40 optimal weight:    7.9990
   chunk 106 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 70 optimal weight:    8.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 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 = 0.3692 r_free = 0.3692 target = 0.068146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.053370 restraints weight = 48968.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.054667 restraints weight = 27007.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.055260 restraints weight = 19623.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10218  Z= 0.097
  Angle     :  0.522   8.875  13932  Z= 0.260
  Chirality :  0.038   0.151   1638
  Planarity :  0.003   0.029   1662
  Dihedral  :  3.311  16.737   1344
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.30 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.18 (0.24), residues: 1212
  helix:  3.58 (0.15), residues: 882
  sheet: -0.76 (0.77), residues: 60
  loop : -2.71 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP C   3 
 HIS   0.001   0.000   HIS D 100 
 PHE   0.006   0.001   PHE E 149 
 TYR   0.037   0.001   TYR D 171 
 ARG   0.003   0.000   ARG D  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02684 (  756)
  hydrogen bonds       : angle       3.18807 ( 2268)
  SS BOND              : bond        0.00470 (   18)
  SS BOND              : angle       1.09954 (   36)
  covalent geometry    : bond        0.00208 (10200)
  covalent geometry    : angle       0.51987 (13896)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.522 
Fit side-chains
REVERT: C  105 MET cc_start: 0.1765 (mtt) cc_final: 0.1486 (mtp)
REVERT: F  105 MET cc_start: 0.1748 (mtt) cc_final: 0.1477 (mtp)
  outliers start: 20
  outliers final: 20
  residues processed: 113
  average time/residue: 0.2439
  time to fit residues: 40.6423
Evaluate side-chains
  109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 74 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 76 optimal weight:   20.0000
   chunk 21 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   overall best weight:    3.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 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 = 0.3606 r_free = 0.3606 target = 0.065146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.049685 restraints weight = 49744.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.051014 restraints weight = 27193.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.051770 restraints weight = 19641.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10218  Z= 0.155
  Angle     :  0.561   7.709  13932  Z= 0.287
  Chirality :  0.040   0.162   1638
  Planarity :  0.004   0.029   1662
  Dihedral  :  3.570  19.536   1344
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.12 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.03 (0.24), residues: 1212
  helix:  3.44 (0.16), residues: 882
  sheet: -0.73 (0.77), residues: 60
  loop : -2.67 (0.31), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 132 
 HIS   0.003   0.001   HIS F  73 
 PHE   0.011   0.001   PHE F  68 
 TYR   0.012   0.001   TYR D 151 
 ARG   0.002   0.000   ARG B 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03458 (  756)
  hydrogen bonds       : angle       3.37248 ( 2268)
  SS BOND              : bond        0.00556 (   18)
  SS BOND              : angle       1.30266 (   36)
  covalent geometry    : bond        0.00344 (10200)
  covalent geometry    : angle       0.55829 (13896)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2964.30 seconds
wall clock time: 53 minutes 34.18 seconds (3214.18 seconds total)