Starting phenix.real_space_refine
on Sat May 10 08:05:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cio_16683/05_2025/8cio_16683.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cio_16683/05_2025/8cio_16683.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cio_16683/05_2025/8cio_16683.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cio_16683/05_2025/8cio_16683.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cio_16683/05_2025/8cio_16683.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cio_16683/05_2025/8cio_16683.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3485      2.51       5
     N     965      2.21       5
     O    1185      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5655
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 159, 1131
          Classifications: {'peptide': 159}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 152}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.74, per 1000 atoms: 0.48
  Number of scatterers: 5655
  At special positions: 0
  Unit cell: (64.428, 64.428, 219.492, 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      20     16.00
     O    1185      8.00
     N     965      7.00
     C    3485      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  41 " - pdb=" SG  CYS A  85 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C  85 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B  85 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  41 " - pdb=" SG  CYS E  85 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  41 " - pdb=" SG  CYS D  85 " 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: 1.37
  Conformation dependent library (CDL) restraints added in 748.1 milliseconds
  

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1390

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 20 sheets defined
      0.0% alpha, 28.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 29
    Processing sheet with id=AA2, first strand: chain 'B' and resid 79 through 80
      removed outlier: 3.683A  pdb=" N   GLY B  76 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 79 through 80
      removed outlier: 3.683A  pdb=" N   GLY B  76 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
      removed outlier: 9.767A  pdb=" N   ASP B  71 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   GLY B  61 " --> pdb=" O   ASP B  71 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   GLN B  73 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   ASP B  59 " --> pdb=" O   GLN B  73 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   GLN A  34 " --> pdb=" O   PHE B  60 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   SER B  62 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   VAL A  36 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY B 170 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80
      removed outlier: 3.683A  pdb=" N   GLY A  76 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 79 through 80
      removed outlier: 3.683A  pdb=" N   GLY A  76 " --> pdb=" O   GLY A  79 " (cutoff:3.500A)
      removed outlier: 9.766A  pdb=" N   ASP A  71 " --> pdb=" O   GLY A  61 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   GLY A  61 " --> pdb=" O   ASP A  71 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   GLN A  73 " --> pdb=" O   ASP A  59 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   ASP A  59 " --> pdb=" O   GLN A  73 " (cutoff:3.500A)
      removed outlier: 7.120A  pdb=" N   VAL D  36 " --> pdb=" O   PHE A  60 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   SER A  62 " --> pdb=" O   VAL D  36 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 95
    Processing sheet with id=AA7, first strand: chain 'A' and resid 101 through 102
      removed outlier: 3.616A  pdb=" N   SER A 102 " --> pdb=" O   GLN A 105 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN A 105 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 29
    Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 80
      removed outlier: 3.684A  pdb=" N   GLY C  76 " --> pdb=" O   GLY C  79 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 79 through 80
      removed outlier: 3.684A  pdb=" N   GLY C  76 " --> pdb=" O   GLY C  79 " (cutoff:3.500A)
      removed outlier: 9.766A  pdb=" N   ASP C  71 " --> pdb=" O   GLY C  61 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   GLY C  61 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   GLN C  73 " --> pdb=" O   ASP C  59 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ASP C  59 " --> pdb=" O   GLN C  73 " (cutoff:3.500A)
      removed outlier: 8.698A  pdb=" N   GLN B  34 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   SER C  62 " --> pdb=" O   GLN B  34 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   VAL B  36 " --> pdb=" O   SER C  62 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY C 170 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 102
      removed outlier: 3.616A  pdb=" N   SER B 102 " --> pdb=" O   GLN B 105 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN B 105 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102
      removed outlier: 3.615A  pdb=" N   SER C 102 " --> pdb=" O   GLN C 105 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN C 105 " --> pdb=" O   SER C 102 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 79 through 80
      removed outlier: 3.683A  pdb=" N   GLY D  76 " --> pdb=" O   GLY D  79 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 79 through 80
      removed outlier: 3.683A  pdb=" N   GLY D  76 " --> pdb=" O   GLY D  79 " (cutoff:3.500A)
      removed outlier: 9.767A  pdb=" N   ASP D  71 " --> pdb=" O   GLY D  61 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   GLY D  61 " --> pdb=" O   ASP D  71 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   GLN D  73 " --> pdb=" O   ASP D  59 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ASP D  59 " --> pdb=" O   GLN D  73 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   VAL E  36 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   SER D  62 " --> pdb=" O   VAL E  36 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY D 170 " --> pdb=" O   ILE E  37 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 95
    Processing sheet with id=AB7, first strand: chain 'D' and resid 101 through 102
      removed outlier: 3.615A  pdb=" N   SER D 102 " --> pdb=" O   GLN D 105 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN D 105 " --> pdb=" O   SER D 102 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 57 through 58
      removed outlier: 3.684A  pdb=" N   GLY E  76 " --> pdb=" O   GLY E  79 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 57 through 58
    Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 95
    Processing sheet with id=AC2, first strand: chain 'E' and resid 101 through 102
      removed outlier: 3.616A  pdb=" N   SER E 102 " --> pdb=" O   GLN E 105 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN E 105 " --> pdb=" O   SER E 102 " (cutoff:3.500A)

    132 hydrogen bonds defined for protein.
    264 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 1.61 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: 1905
        1.34 -     1.46: 1123
        1.46 -     1.57: 2682
        1.57 -     1.69: 0
        1.69 -     1.80: 30
  Bond restraints: 5740
  Sorted by residual:
  bond pdb=" CA  THR E  77 "
       pdb=" CB  THR E  77 "
    ideal  model  delta    sigma   weight residual
    1.530  1.546 -0.015 1.69e-02 3.50e+03 8.22e-01
  bond pdb=" CA  THR C  77 "
       pdb=" CB  THR C  77 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.85e-01
  bond pdb=" CA  THR B  77 "
       pdb=" CB  THR B  77 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.56e-01
  bond pdb=" CA  THR A  77 "
       pdb=" CB  THR A  77 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 7.49e-01
  bond pdb=" CB  ASP C 125 "
       pdb=" CG  ASP C 125 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.43e-01
  ... (remaining 5735 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 7712
        1.40 -     2.80: 135
        2.80 -     4.20: 33
        4.20 -     5.59: 5
        5.59 -     6.99: 5
  Bond angle restraints: 7890
  Sorted by residual:
  angle pdb=" CA  THR D  77 "
        pdb=" CB  THR D  77 "
        pdb=" CG2 THR D  77 "
      ideal   model   delta    sigma   weight residual
     110.50  114.10   -3.60 1.70e+00 3.46e-01 4.48e+00
  angle pdb=" CA  THR A  77 "
        pdb=" CB  THR A  77 "
        pdb=" CG2 THR A  77 "
      ideal   model   delta    sigma   weight residual
     110.50  114.07   -3.57 1.70e+00 3.46e-01 4.41e+00
  angle pdb=" CA  THR B  77 "
        pdb=" CB  THR B  77 "
        pdb=" CG2 THR B  77 "
      ideal   model   delta    sigma   weight residual
     110.50  114.06   -3.56 1.70e+00 3.46e-01 4.40e+00
  angle pdb=" CA  THR C  77 "
        pdb=" CB  THR C  77 "
        pdb=" CG2 THR C  77 "
      ideal   model   delta    sigma   weight residual
     110.50  114.06   -3.56 1.70e+00 3.46e-01 4.39e+00
  angle pdb=" CA  THR E  77 "
        pdb=" CB  THR E  77 "
        pdb=" CG2 THR E  77 "
      ideal   model   delta    sigma   weight residual
     110.50  114.06   -3.56 1.70e+00 3.46e-01 4.39e+00
  ... (remaining 7885 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.25: 2845
       10.25 -    20.51: 305
       20.51 -    30.76: 125
       30.76 -    41.02: 45
       41.02 -    51.27: 15
  Dihedral angle restraints: 3335
    sinusoidal: 1130
      harmonic: 2205
  Sorted by residual:
  dihedral pdb=" CA  GLN B 133 "
           pdb=" CB  GLN B 133 "
           pdb=" CG  GLN B 133 "
           pdb=" CD  GLN B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  133.78   46.22     3      1.50e+01 4.44e-03 8.30e+00
  dihedral pdb=" CA  GLN C 133 "
           pdb=" CB  GLN C 133 "
           pdb=" CG  GLN C 133 "
           pdb=" CD  GLN C 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  133.79   46.21     3      1.50e+01 4.44e-03 8.30e+00
  dihedral pdb=" CA  GLN A 133 "
           pdb=" CB  GLN A 133 "
           pdb=" CG  GLN A 133 "
           pdb=" CD  GLN A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  133.80   46.20     3      1.50e+01 4.44e-03 8.30e+00
  ... (remaining 3332 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 630
       0.032 -    0.063: 204
       0.063 -    0.095: 72
       0.095 -    0.127: 84
       0.127 -    0.159: 15
  Chirality restraints: 1005
  Sorted by residual:
  chirality pdb=" CB  THR D  77 "
            pdb=" CA  THR D  77 "
            pdb=" OG1 THR D  77 "
            pdb=" CG2 THR D  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.29e-01
  chirality pdb=" CB  THR A  77 "
            pdb=" CA  THR A  77 "
            pdb=" OG1 THR A  77 "
            pdb=" CG2 THR A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" CB  THR B  77 "
            pdb=" CA  THR B  77 "
            pdb=" OG1 THR B  77 "
            pdb=" CG2 THR B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 1002 not shown)

  Planarity restraints: 1015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 151 "    0.017 5.00e-02 4.00e+02   2.58e-02 1.06e+00
        pdb=" N   PRO B 152 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO B 152 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 152 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 151 "   -0.017 5.00e-02 4.00e+02   2.56e-02 1.05e+00
        pdb=" N   PRO E 152 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO E 152 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO E 152 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 151 "    0.017 5.00e-02 4.00e+02   2.56e-02 1.05e+00
        pdb=" N   PRO C 152 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO C 152 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C 152 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1012 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.91: 2489
        2.91 -     3.41: 5100
        3.41 -     3.91: 8534
        3.91 -     4.40: 9411
        4.40 -     4.90: 16364
  Nonbonded interactions: 41898
  Sorted by model distance:
  nonbonded pdb=" O   SER E 144 "
            pdb=" OG1 THR E 145 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" O   SER C 144 "
            pdb=" OG1 THR C 145 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" O   SER D 144 "
            pdb=" OG1 THR D 145 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" O   SER B 144 "
            pdb=" OG1 THR B 145 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" O   SER A 144 "
            pdb=" OG1 THR A 145 "
     model   vdw
     2.419 3.040
  ... (remaining 41893 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.060
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
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   0.023   5745  Z= 0.115
  Angle     :  0.548   6.992   7900  Z= 0.284
  Chirality :  0.048   0.159   1005
  Planarity :  0.003   0.026   1015
  Dihedral  : 11.522  51.274   1930
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.60 (0.30), residues: 785
  helix:  None (None), residues: 0
  sheet:  1.41 (0.47), residues: 135
  loop : -1.80 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  55 
 HIS   0.002   0.001   HIS D 100 
 PHE   0.004   0.001   PHE C  60 
 TYR   0.006   0.001   TYR B 120 
 ARG   0.002   0.000   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25275 (  126)
  hydrogen bonds       : angle       7.76365 (  264)
  SS BOND              : bond        0.00183 (    5)
  SS BOND              : angle       1.04394 (   10)
  covalent geometry    : bond        0.00230 ( 5740)
  covalent geometry    : angle       0.54696 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A  165 PRO cc_start: 0.7375 (Cg_exo) cc_final: 0.7134 (Cg_endo)
REVERT: B   84 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8501 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1102
  time to fit residues: 18.9033
Evaluate side-chains
  78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.7120

-------------------------------------------------------------------------------
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 = 0.3200 r_free = 0.3200 target = 0.090600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.078338 restraints weight = 11719.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.080884 restraints weight = 6640.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.082639 restraints weight = 4441.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5745  Z= 0.142
  Angle     :  0.583   8.907   7900  Z= 0.301
  Chirality :  0.049   0.146   1005
  Planarity :  0.003   0.028   1015
  Dihedral  :  4.099  17.141    835
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.57 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 11.11 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.63 (0.30), residues: 785
  helix:  None (None), residues: 0
  sheet:  1.33 (0.46), residues: 135
  loop : -1.81 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D 182 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.009   0.002   PHE C  60 
 TYR   0.020   0.001   TYR D 107 
 ARG   0.002   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03856 (  126)
  hydrogen bonds       : angle       4.96623 (  264)
  SS BOND              : bond        0.00293 (    5)
  SS BOND              : angle       1.26362 (   10)
  covalent geometry    : bond        0.00336 ( 5740)
  covalent geometry    : angle       0.58114 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.591 
Fit side-chains
REVERT: D  108 MET cc_start: 0.7942 (mtt) cc_final: 0.7721 (mtp)
  outliers start: 10
  outliers final: 8
  residues processed: 94
  average time/residue: 0.1079
  time to fit residues: 15.4062
Evaluate side-chains
  82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 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 = 0.3170 r_free = 0.3170 target = 0.088786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.075922 restraints weight = 11891.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.078640 restraints weight = 6412.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.080511 restraints weight = 4191.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5745  Z= 0.142
  Angle     :  0.605  13.760   7900  Z= 0.298
  Chirality :  0.049   0.140   1005
  Planarity :  0.003   0.028   1015
  Dihedral  :  4.172  20.215    835
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 13.02 %
    Favored  : 83.49 %
  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: -1.69 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  1.28 (0.45), residues: 135
  loop : -1.85 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D  55 
 HIS   0.002   0.001   HIS D  63 
 PHE   0.008   0.001   PHE C  60 
 TYR   0.007   0.001   TYR D 120 
 ARG   0.001   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03252 (  126)
  hydrogen bonds       : angle       4.38021 (  264)
  SS BOND              : bond        0.00272 (    5)
  SS BOND              : angle       1.16003 (   10)
  covalent geometry    : bond        0.00339 ( 5740)
  covalent geometry    : angle       0.60357 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.566 
Fit side-chains
REVERT: B   84 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8353 (tp40)
  outliers start: 22
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0999
  time to fit residues: 14.9500
Evaluate side-chains
  89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain E residue   30 GLN
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 GLN
C 150 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.089608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.077357 restraints weight = 11913.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.079891 restraints weight = 6661.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.081635 restraints weight = 4432.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5745  Z= 0.167
  Angle     :  0.640  14.663   7900  Z= 0.312
  Chirality :  0.049   0.141   1005
  Planarity :  0.004   0.028   1015
  Dihedral  :  4.418  24.206    835
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 10.32 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 15.08 %
    Favored  : 80.63 %
  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: -1.74 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  1.13 (0.45), residues: 135
  loop : -1.85 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  55 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.008   0.001   PHE C  60 
 TYR   0.010   0.001   TYR A 172 
 ARG   0.002   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03084 (  126)
  hydrogen bonds       : angle       4.15456 (  264)
  SS BOND              : bond        0.00349 (    5)
  SS BOND              : angle       1.39645 (   10)
  covalent geometry    : bond        0.00405 ( 5740)
  covalent geometry    : angle       0.63835 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8274 (p)
  outliers start: 27
  outliers final: 18
  residues processed: 99
  average time/residue: 0.1007
  time to fit residues: 15.2413
Evaluate side-chains
  90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   73 GLN
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain E residue   30 GLN
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 70 optimal weight:    0.0670
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
B  96 ASN
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.091053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.078442 restraints weight = 11594.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.081149 restraints weight = 6262.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.083009 restraints weight = 4094.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5745  Z= 0.126
  Angle     :  0.628  16.572   7900  Z= 0.302
  Chirality :  0.049   0.139   1005
  Planarity :  0.003   0.027   1015
  Dihedral  :  4.235  23.925    835
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  9.55 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 17.14 %
    Favored  : 78.73 %
  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: -1.72 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  1.18 (0.45), residues: 135
  loop : -1.85 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D 182 
 HIS   0.002   0.001   HIS D  63 
 PHE   0.007   0.001   PHE C  60 
 TYR   0.007   0.001   TYR B 172 
 ARG   0.002   0.000   ARG D 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02699 (  126)
  hydrogen bonds       : angle       4.01071 (  264)
  SS BOND              : bond        0.00328 (    5)
  SS BOND              : angle       1.22501 (   10)
  covalent geometry    : bond        0.00299 ( 5740)
  covalent geometry    : angle       0.62708 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.611 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8273 (p)
REVERT: C   59 ASP cc_start: 0.8276 (t0) cc_final: 0.8038 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 93
  average time/residue: 0.1013
  time to fit residues: 14.3504
Evaluate side-chains
  85 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   73 GLN
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue   58 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain E residue   30 GLN
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 ASN
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 150 ASN
E 150 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.084800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.072412 restraints weight = 11908.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.074942 restraints weight = 6488.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.076708 restraints weight = 4273.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057   5745  Z= 0.303
  Angle     :  0.750  15.777   7900  Z= 0.380
  Chirality :  0.053   0.149   1005
  Planarity :  0.004   0.030   1015
  Dihedral  :  5.467  39.034    835
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 14.39 %
    Favored  : 84.97 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 17.30 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.64 (0.44), residues: 135
  loop : -2.04 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 182 
 HIS   0.005   0.002   HIS C  63 
 PHE   0.011   0.002   PHE C  60 
 TYR   0.013   0.002   TYR D 123 
 ARG   0.003   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03830 (  126)
  hydrogen bonds       : angle       4.35496 (  264)
  SS BOND              : bond        0.00236 (    5)
  SS BOND              : angle       2.27661 (   10)
  covalent geometry    : bond        0.00741 ( 5740)
  covalent geometry    : angle       0.74594 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 71
  time to evaluate  : 0.562 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8230 (p)
REVERT: C   59 ASP cc_start: 0.8308 (t0) cc_final: 0.8066 (t0)
REVERT: C   96 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8024 (p0)
REVERT: E   68 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8624 (m110)
  outliers start: 27
  outliers final: 19
  residues processed: 95
  average time/residue: 0.0974
  time to fit residues: 14.1266
Evaluate side-chains
  86 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 64
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  113 THR
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain D residue  145 THR
Chi-restraints excluded: chain D residue  150 ASN
Chi-restraints excluded: chain E residue   30 GLN
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   68 ASN
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0970
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 41 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 150 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.089553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.077470 restraints weight = 11734.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.080001 restraints weight = 6569.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.081735 restraints weight = 4372.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5745  Z= 0.132
  Angle     :  0.647  15.725   7900  Z= 0.317
  Chirality :  0.050   0.143   1005
  Planarity :  0.003   0.029   1015
  Dihedral  :  4.586  30.108    835
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  9.94 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.68 %
    Favored  : 76.98 %
  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: -1.99 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.77 (0.44), residues: 135
  loop : -2.00 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 182 
 HIS   0.003   0.001   HIS E 100 
 PHE   0.006   0.001   PHE C  60 
 TYR   0.009   0.001   TYR D 107 
 ARG   0.001   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02663 (  126)
  hydrogen bonds       : angle       3.99014 (  264)
  SS BOND              : bond        0.00254 (    5)
  SS BOND              : angle       1.18929 (   10)
  covalent geometry    : bond        0.00309 ( 5740)
  covalent geometry    : angle       0.64561 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8217 (p)
REVERT: C   59 ASP cc_start: 0.8363 (t0) cc_final: 0.8152 (t0)
REVERT: C   96 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7882 (p0)
  outliers start: 21
  outliers final: 13
  residues processed: 92
  average time/residue: 0.1019
  time to fit residues: 14.3515
Evaluate side-chains
  81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0170
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0270
   overall best weight:    1.2082

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

Flipped N/Q/H residues before XYZ refinement:
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.087975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.075982 restraints weight = 11696.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.078484 restraints weight = 6532.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.080228 restraints weight = 4341.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5745  Z= 0.198
  Angle     :  0.717  15.726   7900  Z= 0.351
  Chirality :  0.051   0.146   1005
  Planarity :  0.004   0.029   1015
  Dihedral  :  4.776  31.251    835
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 12.74 %
    Favored  : 86.62 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 19.52 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.63 (0.44), residues: 135
  loop : -2.07 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 182 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.007   0.002   PHE C  60 
 TYR   0.010   0.002   TYR D 107 
 ARG   0.002   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03041 (  126)
  hydrogen bonds       : angle       4.07966 (  264)
  SS BOND              : bond        0.01252 (    5)
  SS BOND              : angle       3.03325 (   10)
  covalent geometry    : bond        0.00481 ( 5740)
  covalent geometry    : angle       0.70958 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.610 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8248 (p)
REVERT: C   59 ASP cc_start: 0.8322 (t0) cc_final: 0.8077 (t0)
REVERT: C   96 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8090 (p0)
  outliers start: 24
  outliers final: 18
  residues processed: 88
  average time/residue: 0.1036
  time to fit residues: 13.9276
Evaluate side-chains
  85 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue   41 CYS
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 66 optimal weight:    0.0270
   chunk 71 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.087176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.074426 restraints weight = 11758.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.077149 restraints weight = 6327.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.079029 restraints weight = 4123.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5745  Z= 0.127
  Angle     :  0.673  15.661   7900  Z= 0.322
  Chirality :  0.050   0.141   1005
  Planarity :  0.003   0.028   1015
  Dihedral  :  4.314  27.248    835
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  9.94 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.79 %
    Favored  : 76.19 %
  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: -1.98 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.82 (0.45), residues: 135
  loop : -2.00 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 182 
 HIS   0.002   0.001   HIS E 100 
 PHE   0.004   0.001   PHE C  60 
 TYR   0.008   0.001   TYR D 107 
 ARG   0.001   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02455 (  126)
  hydrogen bonds       : angle       3.92415 (  264)
  SS BOND              : bond        0.00986 (    5)
  SS BOND              : angle       2.48770 (   10)
  covalent geometry    : bond        0.00298 ( 5740)
  covalent geometry    : angle       0.66754 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8266 (p)
REVERT: C   96 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7924 (p0)
  outliers start: 19
  outliers final: 14
  residues processed: 87
  average time/residue: 0.1069
  time to fit residues: 14.0882
Evaluate side-chains
  85 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue   41 CYS
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 71 optimal weight:    0.4980
   chunk 63 optimal weight:    0.3980
   chunk 74 optimal weight:    0.0030
   chunk 44 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 26 optimal weight:    8.9990
   overall best weight:    0.4990

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

Flipped N/Q/H residues before XYZ refinement:
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 150 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 = 0.3160 r_free = 0.3160 target = 0.088581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.075791 restraints weight = 11813.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.078529 restraints weight = 6313.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.080417 restraints weight = 4102.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5745  Z= 0.118
  Angle     :  0.659  15.264   7900  Z= 0.314
  Chirality :  0.049   0.139   1005
  Planarity :  0.003   0.027   1015
  Dihedral  :  4.124  24.186    835
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 10.83 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.32 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.92 (0.45), residues: 135
  loop : -1.99 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 182 
 HIS   0.002   0.001   HIS D  63 
 PHE   0.004   0.001   PHE C  60 
 TYR   0.011   0.001   TYR B 172 
 ARG   0.001   0.000   ARG D 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02367 (  126)
  hydrogen bonds       : angle       3.92928 (  264)
  SS BOND              : bond        0.00781 (    5)
  SS BOND              : angle       2.20084 (   10)
  covalent geometry    : bond        0.00278 ( 5740)
  covalent geometry    : angle       0.65440 ( 7890)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 70
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  110 ASN cc_start: 0.8584 (t0) cc_final: 0.8382 (t0)
REVERT: A  166 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8332 (p)
REVERT: C   96 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7947 (p0)
  outliers start: 18
  outliers final: 15
  residues processed: 87
  average time/residue: 0.1030
  time to fit residues: 13.6537
Evaluate side-chains
  85 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue  166 THR
Chi-restraints excluded: chain B residue   41 CYS
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  147 THR
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  166 THR
Chi-restraints excluded: chain C residue  177 LEU
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue   41 CYS
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  139 ASP
Chi-restraints excluded: chain E residue   36 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  100 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0470
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.6086

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

Flipped N/Q/H residues before XYZ refinement:
A  63 HIS
** A  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 GLN
C 150 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.087148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.075090 restraints weight = 11919.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.077612 restraints weight = 6635.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.079333 restraints weight = 4399.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   5745  Z= 0.250
  Angle     :  0.743  14.999   7900  Z= 0.367
  Chirality :  0.052   0.153   1005
  Planarity :  0.004   0.029   1015
  Dihedral  :  5.000  32.686    835
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 13.50 %
    Favored  : 85.86 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.00 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.61 (0.45), residues: 135
  loop : -2.11 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 182 
 HIS   0.004   0.002   HIS D  63 
 PHE   0.006   0.002   PHE C  60 
 TYR   0.012   0.002   TYR B 172 
 ARG   0.002   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03297 (  126)
  hydrogen bonds       : angle       4.23066 (  264)
  SS BOND              : bond        0.00830 (    5)
  SS BOND              : angle       2.54144 (   10)
  covalent geometry    : bond        0.00610 ( 5740)
  covalent geometry    : angle       0.73797 ( 7890)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1899.61 seconds
wall clock time: 34 minutes 4.13 seconds (2044.13 seconds total)