Starting phenix.real_space_refine
on Tue Mar  3 13:53:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cio_16683/03_2026/8cio_16683.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cio_16683/03_2026/8cio_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cio_16683/03_2026/8cio_16683.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cio_16683/03_2026/8cio_16683.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cio_16683/03_2026/8cio_16683.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cio_16683/03_2026/8cio_16683.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 0.91, per 1000 atoms: 0.16
  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 B  41 " - pdb=" SG  CYS B  85 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C  85 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  41 " - pdb=" SG  CYS D  85 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  41 " - pdb=" SG  CYS E  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: 0.40
  Conformation dependent library (CDL) restraints added in 331.6 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: 0.18
  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: 0.61

  Time building geometry restraints manager: 0.56 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.790
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.070
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.260
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG B 128 
 TYR   0.006   0.001   TYR B 120 
 PHE   0.004   0.001   PHE C  60 
 TRP   0.003   0.001   TRP D  55 
 HIS   0.002   0.001   HIS D 100 

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

*********************** 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  : 0.223 
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: 0.0400
  time to fit residues: 7.1907
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  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3164 r_free = 0.3164 target = 0.088464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.075545 restraints weight = 12036.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.078270 restraints weight = 6539.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.080139 restraints weight = 4284.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.081417 restraints weight = 3122.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.082374 restraints weight = 2454.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5745  Z= 0.133
  Angle     :  0.573   8.786   7900  Z= 0.296
  Chirality :  0.049   0.145   1005
  Planarity :  0.003   0.027   1015
  Dihedral  :  4.037  17.082    835
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.45 %
    Favored  : 89.55 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.30), residues: 785
  helix:  None (None), residues: 0
  sheet:  1.32 (0.46), residues: 135
  loop : -1.81 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 156 
 TYR   0.020   0.001   TYR D 107 
 PHE   0.009   0.002   PHE C  60 
 TRP   0.003   0.001   TRP D 182 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5740)
  covalent geometry    : angle       0.57176 ( 7890)
  SS BOND              : bond        0.00070 (    5)
  SS BOND              : angle       1.03266 (   10)
  hydrogen bonds       : bond        0.03907 (  126)
  hydrogen bonds       : angle       5.01298 (  264)

*********************** 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
  97 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.220 
Fit side-chains
REVERT: D  108 MET cc_start: 0.7942 (mtt) cc_final: 0.7716 (mtp)
  outliers start: 10
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0434
  time to fit residues: 6.3505
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  : 0.137 
-------------------------------------------------------------------------------
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 25 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0060
   chunk 42 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.089937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.077139 restraints weight = 11777.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.079866 restraints weight = 6371.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.081733 restraints weight = 4162.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.083037 restraints weight = 3031.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.083941 restraints weight = 2366.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5745  Z= 0.121
  Angle     :  0.590  14.065   7900  Z= 0.288
  Chirality :  0.048   0.138   1005
  Planarity :  0.003   0.027   1015
  Dihedral  :  3.978  17.780    835
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.17 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.30), residues: 785
  helix:  None (None), residues: 0
  sheet:  1.37 (0.46), residues: 135
  loop : -1.83 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 128 
 TYR   0.007   0.001   TYR D 107 
 PHE   0.006   0.001   PHE C  60 
 TRP   0.003   0.000   TRP D  55 
 HIS   0.002   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5740)
  covalent geometry    : angle       0.58940 ( 7890)
  SS BOND              : bond        0.00082 (    5)
  SS BOND              : angle       1.03056 (   10)
  hydrogen bonds       : bond        0.03053 (  126)
  hydrogen bonds       : angle       4.40156 (  264)

*********************** 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
  107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B   84 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8332 (tm-30)
  outliers start: 20
  outliers final: 12
  residues processed: 102
  average time/residue: 0.0433
  time to fit residues: 6.8984
Evaluate side-chains
  85 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain C residue   96 ASN
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
Chi-restraints excluded: chain E residue  177 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0470
   chunk 73 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.8086

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
** B  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 ASN
C 150 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.085950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.073536 restraints weight = 11868.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.076093 restraints weight = 6453.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.077871 restraints weight = 4246.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.079104 restraints weight = 3113.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.079994 restraints weight = 2445.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076   5745  Z= 0.281
  Angle     :  0.733  14.049   7900  Z= 0.370
  Chirality :  0.052   0.147   1005
  Planarity :  0.004   0.029   1015
  Dihedral  :  5.252  30.811    835
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 13.25 %
    Favored  : 86.11 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.35 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.80 (0.44), residues: 135
  loop : -1.98 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 128 
 TYR   0.013   0.002   TYR D 123 
 PHE   0.014   0.002   PHE C  60 
 TRP   0.006   0.001   TRP D  55 
 HIS   0.005   0.002   HIS C  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00686 ( 5740)
  covalent geometry    : angle       0.73005 ( 7890)
  SS BOND              : bond        0.00429 (    5)
  SS BOND              : angle       2.11790 (   10)
  hydrogen bonds       : bond        0.03929 (  126)
  hydrogen bonds       : angle       4.37720 (  264)

*********************** 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
  100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  108 MET cc_start: 0.8223 (mtt) cc_final: 0.8000 (mtp)
REVERT: A  166 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8174 (p)
  outliers start: 27
  outliers final: 18
  residues processed: 96
  average time/residue: 0.0414
  time to fit residues: 6.2911
Evaluate side-chains
  84 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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  149 VAL
Chi-restraints excluded: chain C residue   42 THR
Chi-restraints excluded: chain C residue   96 ASN
Chi-restraints excluded: chain C residue  150 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:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 63 optimal weight:    0.3980
   chunk 74 optimal weight:    0.0010
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 73 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
B  96 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 150 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.086797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.073873 restraints weight = 12174.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.076658 restraints weight = 6477.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.078553 restraints weight = 4191.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.079864 restraints weight = 3029.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.080781 restraints weight = 2358.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2612

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= 0.116
  Angle     :  0.636  16.600   7900  Z= 0.307
  Chirality :  0.049   0.141   1005
  Planarity :  0.003   0.028   1015
  Dihedral  :  4.400  26.702    835
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  9.04 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.95 (0.44), residues: 135
  loop : -1.91 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 128 
 TYR   0.006   0.001   TYR D 172 
 PHE   0.007   0.001   PHE C  60 
 TRP   0.006   0.001   TRP A 182 
 HIS   0.003   0.001   HIS E 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5740)
  covalent geometry    : angle       0.63533 ( 7890)
  SS BOND              : bond        0.00161 (    5)
  SS BOND              : angle       1.03228 (   10)
  hydrogen bonds       : bond        0.02624 (  126)
  hydrogen bonds       : angle       3.97629 (  264)

*********************** 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
  98 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8222 (p)
  outliers start: 24
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0424
  time to fit residues: 6.2875
Evaluate side-chains
  81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
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  149 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   58 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  139 ASP
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 60 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0670
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 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 = 0.3185 r_free = 0.3185 target = 0.089866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.077687 restraints weight = 11694.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.080238 restraints weight = 6559.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.082029 restraints weight = 4366.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.083266 restraints weight = 3207.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.084173 restraints weight = 2520.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5745  Z= 0.118
  Angle     :  0.642  16.106   7900  Z= 0.308
  Chirality :  0.049   0.140   1005
  Planarity :  0.003   0.026   1015
  Dihedral  :  4.094  23.830    835
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 11.21 %
    Favored  : 88.15 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.25 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  1.06 (0.45), residues: 135
  loop : -1.90 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 128 
 TYR   0.009   0.001   TYR B 172 
 PHE   0.006   0.001   PHE C  60 
 TRP   0.005   0.001   TRP D 182 
 HIS   0.001   0.001   HIS E 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5740)
  covalent geometry    : angle       0.63547 ( 7890)
  SS BOND              : bond        0.00876 (    5)
  SS BOND              : angle       2.65111 (   10)
  hydrogen bonds       : bond        0.02460 (  126)
  hydrogen bonds       : angle       3.89061 (  264)

*********************** 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
  92 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  108 MET cc_start: 0.8084 (mtt) cc_final: 0.7881 (mtp)
REVERT: A  166 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8270 (p)
  outliers start: 20
  outliers final: 17
  residues processed: 87
  average time/residue: 0.0445
  time to fit residues: 6.0997
Evaluate side-chains
  86 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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  147 THR
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 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   58 LEU
Chi-restraints excluded: chain D residue   96 ASN
Chi-restraints excluded: chain D residue  139 ASP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0870
   chunk 65 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.1362

-------------------------------------------------------------------------------
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 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.086014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.073237 restraints weight = 12056.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.075929 restraints weight = 6446.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.077790 restraints weight = 4198.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.079083 restraints weight = 3051.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.080029 restraints weight = 2381.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5745  Z= 0.188
  Angle     :  0.699  16.001   7900  Z= 0.339
  Chirality :  0.050   0.142   1005
  Planarity :  0.004   0.029   1015
  Dihedral  :  4.574  28.604    835
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 11.08 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.05 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.85 (0.44), residues: 135
  loop : -1.96 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 128 
 TYR   0.010   0.002   TYR D 107 
 PHE   0.008   0.002   PHE C  60 
 TRP   0.005   0.001   TRP D 182 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 5740)
  covalent geometry    : angle       0.69450 ( 7890)
  SS BOND              : bond        0.00909 (    5)
  SS BOND              : angle       2.24017 (   10)
  hydrogen bonds       : bond        0.02938 (  126)
  hydrogen bonds       : angle       3.95040 (  264)

*********************** 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
  88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A  108 MET cc_start: 0.8256 (mtt) cc_final: 0.8040 (mtp)
REVERT: A  166 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8239 (p)
REVERT: C   96 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8000 (p0)
  outliers start: 22
  outliers final: 18
  residues processed: 84
  average time/residue: 0.0440
  time to fit residues: 5.8580
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  : 0.149 
-------------------------------------------------------------------------------
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   42 THR
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   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 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  100 HIS
Chi-restraints excluded: chain E residue  131 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0270
   overall best weight:    0.7838

-------------------------------------------------------------------------------
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**
D 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.089497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.076966 restraints weight = 11626.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.079673 restraints weight = 6192.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.081523 restraints weight = 4009.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.082826 restraints weight = 2901.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.083730 restraints weight = 2246.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5745  Z= 0.146
  Angle     :  0.675  15.728   7900  Z= 0.324
  Chirality :  0.050   0.141   1005
  Planarity :  0.003   0.027   1015
  Dihedral  :  4.419  27.773    835
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 10.45 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.68 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.87 (0.45), residues: 135
  loop : -1.94 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 128 
 TYR   0.009   0.001   TYR D 107 
 PHE   0.005   0.001   PHE C  60 
 TRP   0.006   0.001   TRP A 182 
 HIS   0.002   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5740)
  covalent geometry    : angle       0.67125 ( 7890)
  SS BOND              : bond        0.00854 (    5)
  SS BOND              : angle       2.13817 (   10)
  hydrogen bonds       : bond        0.02613 (  126)
  hydrogen bonds       : angle       3.88453 (  264)

*********************** 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
  93 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8291 (p)
REVERT: C   59 ASP cc_start: 0.8349 (t0) cc_final: 0.8095 (t0)
REVERT: C   96 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7966 (p0)
  outliers start: 23
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0440
  time to fit residues: 6.0796
Evaluate side-chains
  84 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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  147 THR
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   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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3151 r_free = 0.3151 target = 0.087786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.075044 restraints weight = 11822.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.077757 restraints weight = 6309.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.079642 restraints weight = 4105.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.080953 restraints weight = 2978.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.081901 restraints weight = 2314.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5745  Z= 0.147
  Angle     :  0.676  15.750   7900  Z= 0.326
  Chirality :  0.049   0.141   1005
  Planarity :  0.003   0.028   1015
  Dihedral  :  4.402  27.492    835
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 10.32 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.87 (0.45), residues: 135
  loop : -1.97 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 128 
 TYR   0.009   0.001   TYR D 107 
 PHE   0.005   0.001   PHE C  60 
 TRP   0.004   0.001   TRP D 182 
 HIS   0.002   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5740)
  covalent geometry    : angle       0.67260 ( 7890)
  SS BOND              : bond        0.00798 (    5)
  SS BOND              : angle       2.07859 (   10)
  hydrogen bonds       : bond        0.02643 (  126)
  hydrogen bonds       : angle       3.92574 (  264)

*********************** 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: 21
    poor density    : 68
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8300 (p)
REVERT: C   96 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.7980 (p0)
  outliers start: 21
  outliers final: 17
  residues processed: 85
  average time/residue: 0.0414
  time to fit residues: 5.4920
Evaluate side-chains
  86 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
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  147 THR
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   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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.088280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.075460 restraints weight = 11950.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.078195 restraints weight = 6385.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.080093 restraints weight = 4153.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.081399 restraints weight = 3010.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.082302 restraints weight = 2346.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5745  Z= 0.125
  Angle     :  0.662  15.490   7900  Z= 0.317
  Chirality :  0.049   0.140   1005
  Planarity :  0.003   0.027   1015
  Dihedral  :  4.197  25.237    835
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  :  9.94 %
    Favored  : 89.43 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.79 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.91 (0.45), residues: 135
  loop : -1.95 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 128 
 TYR   0.008   0.001   TYR B 172 
 PHE   0.004   0.001   PHE C  60 
 TRP   0.004   0.001   TRP A 182 
 HIS   0.002   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5740)
  covalent geometry    : angle       0.65911 ( 7890)
  SS BOND              : bond        0.00729 (    5)
  SS BOND              : angle       1.87339 (   10)
  hydrogen bonds       : bond        0.02447 (  126)
  hydrogen bonds       : angle       3.91343 (  264)

********************** 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
  86 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  166 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8343 (p)
REVERT: C   96 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7909 (p0)
REVERT: D  117 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8740 (p)
  outliers start: 18
  outliers final: 14
  residues processed: 84
  average time/residue: 0.0448
  time to fit residues: 5.8500
Evaluate side-chains
  82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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  147 THR
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   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 D residue  145 THR
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 45 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 60 optimal weight:    0.2980
   chunk 44 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.087975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.075268 restraints weight = 11725.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.077954 restraints weight = 6303.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.079836 restraints weight = 4120.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.081129 restraints weight = 2993.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.082061 restraints weight = 2338.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5745  Z= 0.134
  Angle     :  0.666  14.931   7900  Z= 0.320
  Chirality :  0.049   0.140   1005
  Planarity :  0.003   0.028   1015
  Dihedral  :  4.199  24.867    835
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 10.32 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.48 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.29), residues: 785
  helix:  None (None), residues: 0
  sheet:  0.91 (0.45), residues: 135
  loop : -1.97 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 128 
 TYR   0.009   0.001   TYR D 107 
 PHE   0.004   0.001   PHE C  60 
 TRP   0.005   0.001   TRP A 182 
 HIS   0.002   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5740)
  covalent geometry    : angle       0.66282 ( 7890)
  SS BOND              : bond        0.00693 (    5)
  SS BOND              : angle       1.81106 (   10)
  hydrogen bonds       : bond        0.02564 (  126)
  hydrogen bonds       : angle       3.99701 (  264)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1004.38 seconds
wall clock time: 18 minutes 2.44 seconds (1082.44 seconds total)