Starting phenix.real_space_refine
on Wed Jul 23 09:56:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yl3_33902/07_2025/7yl3_33902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yl3_33902/07_2025/7yl3_33902.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yl3_33902/07_2025/7yl3_33902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yl3_33902/07_2025/7yl3_33902.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yl3_33902/07_2025/7yl3_33902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yl3_33902/07_2025/7yl3_33902.cif"
  }
  resolution = 3.2
  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=   0.003
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      12      5.16       5
     C    1800      2.51       5
     N     552      2.21       5
     O     594      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 2958
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "C"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "E"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 220
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "I"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "K"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 220
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "A"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "F"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 220
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "J"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "H"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 220
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "B"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "G"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 220
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "L"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 273
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "D"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 220
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
  Time building chain proxies: 2.71, per 1000 atoms: 0.92
  Number of scatterers: 2958
  At special positions: 0
  Unit cell: (132.08, 88.4, 42.64, 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      12     16.00
     O     594      8.00
     N     552      7.00
     C    1800      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS C   2 " - pdb=" SG  CYS C   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   2 " - pdb=" SG  CYS B   7 " distance=2.85
    Simple disulfide: pdb=" SG  CYS I   2 " - pdb=" SG  CYS I   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A   2 " - pdb=" SG  CYS A   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J   2 " - pdb=" SG  CYS J   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   2 " - pdb=" SG  CYS B   7 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L   2 " - pdb=" SG  CYS L   7 " 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: 0.83
  Conformation dependent library (CDL) restraints added in 369.5 milliseconds
  

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 43.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11
      removed outlier: 3.530A  pdb=" N   THR C   9 " --> pdb=" O   ALA A   8 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   ALA C   8 " --> pdb=" O   THR B   9 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   ARG B  11 " --> pdb=" O   ALA C   8 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   GLN C  10 " --> pdb=" O   ARG B  11 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 20
      removed outlier: 6.400A  pdb=" N   VAL C  17 " --> pdb=" O   HIS A  18 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   SER A  20 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   SER C  19 " --> pdb=" O   SER A  20 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.615A  pdb=" N   ILE C  26 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32
      removed outlier: 6.644A  pdb=" N   THR C  30 " --> pdb=" O   ASN B  31 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 22
      removed outlier: 7.041A  pdb=" N   GLN E  10 " --> pdb=" O   ARG G  11 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   ALA G  13 " --> pdb=" O   GLN E  10 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   LEU E  12 " --> pdb=" O   ALA G  13 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   PHE G  15 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ASN E  14 " --> pdb=" O   PHE G  15 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   VAL G  17 " --> pdb=" O   ASN E  14 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LEU E  16 " --> pdb=" O   VAL G  17 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   SER G  19 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 5.916A  pdb=" N   HIS E  18 " --> pdb=" O   SER G  19 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   ASN G  21 " --> pdb=" O   HIS E  18 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   SER E  20 " --> pdb=" O   ASN G  21 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 26 through 32
      removed outlier: 6.795A  pdb=" N   ILE E  26 " --> pdb=" O   LEU G  27 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   SER G  29 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   SER E  28 " --> pdb=" O   SER G  29 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'J' and resid 7 through 11
      removed outlier: 6.816A  pdb=" N   ALA I   8 " --> pdb=" O   THR L   9 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   ARG L  11 " --> pdb=" O   ALA I   8 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLN I  10 " --> pdb=" O   ARG L  11 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'J' and resid 17 through 20
      removed outlier: 6.404A  pdb=" N   VAL I  17 " --> pdb=" O   HIS J  18 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   SER J  20 " --> pdb=" O   VAL I  17 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   SER I  19 " --> pdb=" O   SER J  20 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'J' and resid 25 through 27
      removed outlier: 6.637A  pdb=" N   ILE I  26 " --> pdb=" O   LEU L  27 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'J' and resid 30 through 32
      removed outlier: 6.691A  pdb=" N   THR I  30 " --> pdb=" O   ASN L  31 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 10 through 22
      removed outlier: 3.587A  pdb=" N   ALA K  13 " --> pdb=" O   LEU H  12 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 26 through 32

    74 hydrogen bonds defined for protein.
    222 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: 0.68

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 521
        1.33 -     1.45: 871
        1.45 -     1.57: 1590
        1.57 -     1.69: 0
        1.69 -     1.81: 12
  Bond restraints: 2994
  Sorted by residual:
  bond pdb=" C   THR E  36 "
       pdb=" N   TYC E  37 "
    ideal  model  delta    sigma   weight residual
    1.329  1.204  0.125 1.40e-02 5.10e+03 7.95e+01
  bond pdb=" C   THR F  36 "
       pdb=" N   TYC F  37 "
    ideal  model  delta    sigma   weight residual
    1.329  1.205  0.124 1.40e-02 5.10e+03 7.91e+01
  bond pdb=" C   THR G  36 "
       pdb=" N   TYC G  37 "
    ideal  model  delta    sigma   weight residual
    1.329  1.205  0.124 1.40e-02 5.10e+03 7.91e+01
  bond pdb=" C   THR K  36 "
       pdb=" N   TYC K  37 "
    ideal  model  delta    sigma   weight residual
    1.329  1.207  0.122 1.40e-02 5.10e+03 7.63e+01
  bond pdb=" C   THR H  36 "
       pdb=" N   TYC H  37 "
    ideal  model  delta    sigma   weight residual
    1.329  1.207  0.122 1.40e-02 5.10e+03 7.55e+01
  ... (remaining 2989 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.93: 4021
        5.93 -    11.86: 11
       11.86 -    17.79: 12
       17.79 -    23.72: 18
       23.72 -    29.65: 6
  Bond angle restraints: 4068
  Sorted by residual:
  angle pdb=" C   THR E  36 "
        pdb=" N   TYC E  37 "
        pdb=" CA  TYC E  37 "
      ideal   model   delta    sigma   weight residual
     121.70  151.35  -29.65 1.80e+00 3.09e-01 2.71e+02
  angle pdb=" C   THR G  36 "
        pdb=" N   TYC G  37 "
        pdb=" CA  TYC G  37 "
      ideal   model   delta    sigma   weight residual
     121.70  151.34  -29.64 1.80e+00 3.09e-01 2.71e+02
  angle pdb=" C   THR F  36 "
        pdb=" N   TYC F  37 "
        pdb=" CA  TYC F  37 "
      ideal   model   delta    sigma   weight residual
     121.70  151.34  -29.64 1.80e+00 3.09e-01 2.71e+02
  angle pdb=" C   THR D  36 "
        pdb=" N   TYC D  37 "
        pdb=" CA  TYC D  37 "
      ideal   model   delta    sigma   weight residual
     121.70  150.02  -28.32 1.80e+00 3.09e-01 2.48e+02
  angle pdb=" C   THR K  36 "
        pdb=" N   TYC K  37 "
        pdb=" CA  TYC K  37 "
      ideal   model   delta    sigma   weight residual
     121.70  150.00  -28.30 1.80e+00 3.09e-01 2.47e+02
  ... (remaining 4063 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.18: 1560
       10.18 -    20.37: 154
       20.37 -    30.55: 47
       30.55 -    40.74: 24
       40.74 -    50.92: 12
  Dihedral angle restraints: 1797
    sinusoidal: 669
      harmonic: 1128
  Sorted by residual:
  dihedral pdb=" CB  CYS C   2 "
           pdb=" SG  CYS C   2 "
           pdb=" SG  CYS B   7 "
           pdb=" CB  CYS B   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   64.33   28.67     1      1.00e+01 1.00e-02 1.18e+01
  dihedral pdb=" CA  CYS I   2 "
           pdb=" CB  CYS I   2 "
           pdb=" SG  CYS I   2 "
           pdb=" SG  CYS I   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00 -123.92   50.92     1      2.00e+01 2.50e-03 8.87e+00
  dihedral pdb=" CA  CYS B   2 "
           pdb=" CB  CYS B   2 "
           pdb=" SG  CYS B   2 "
           pdb=" SG  CYS B   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00 -123.91   50.91     1      2.00e+01 2.50e-03 8.87e+00
  ... (remaining 1794 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 408
       0.058 -    0.117: 64
       0.117 -    0.175: 8
       0.175 -    0.233: 6
       0.233 -    0.292: 6
  Chirality restraints: 492
  Sorted by residual:
  chirality pdb=" CA  ASN A  14 "
            pdb=" N   ASN A  14 "
            pdb=" C   ASN A  14 "
            pdb=" CB  ASN A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  ASN C  14 "
            pdb=" N   ASN C  14 "
            pdb=" C   ASN C  14 "
            pdb=" CB  ASN C  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CA  ASN I  14 "
            pdb=" N   ASN I  14 "
            pdb=" C   ASN I  14 "
            pdb=" CB  ASN I  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.10e+00
  ... (remaining 489 not shown)

  Planarity restraints: 534
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR J  36 "    0.018 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   THR J  36 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR J  36 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TYC J  37 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I  36 "    0.018 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   THR I  36 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR I  36 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TYC I  37 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR L  36 "    0.018 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   THR L  36 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR L  36 "    0.017 2.00e-02 2.50e+03
        pdb=" N   TYC L  37 "    0.019 2.00e-02 2.50e+03
  ... (remaining 531 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.30: 8
        2.30 -     2.95: 1508
        2.95 -     3.60: 3838
        3.60 -     4.25: 6365
        4.25 -     4.90: 11193
  Nonbonded interactions: 22912
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C   6 "
            pdb=" N   THR B   6 "
     model   vdw
     1.654 3.120
  nonbonded pdb=" N   THR I   6 "
            pdb=" OG1 THR J   6 "
     model   vdw
     1.802 3.120
  nonbonded pdb=" CG2 THR B   6 "
            pdb=" NH1 ARG D  11 "
     model   vdw
     1.997 3.540
  nonbonded pdb=" CB  THR C   4 "
            pdb=" O   THR B   4 "
     model   vdw
     2.009 3.470
  nonbonded pdb=" O   THR I   4 "
            pdb=" CB  THR J   4 "
     model   vdw
     2.203 3.470
  ... (remaining 22907 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'K'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.080
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
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      :  0.017   0.820   3001  Z= 0.928
  Angle     :  2.137  29.653   4082  Z= 1.208
  Chirality :  0.061   0.292    492
  Planarity :  0.005   0.032    534
  Dihedral  : 10.324  42.455   1032
  Min Nonbonded Distance : 1.654

Molprobity Statistics.
  All-atom Clashscore : 22.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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: -4.03 (0.35), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS L  18 
 PHE   0.011   0.002   PHE E  15 
 ARG   0.001   0.000   ARG K  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19276 (   74)
  hydrogen bonds       : angle       8.87918 (  222)
  SS BOND              : bond        0.31010 (    7)
  SS BOND              : angle       3.13446 (   14)
  covalent geometry    : bond        0.00772 ( 2994)
  covalent geometry    : angle       2.13306 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.321 
Fit side-chains
REVERT: J   11 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6689 (pmt-80)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1190
  time to fit residues: 7.0594
Evaluate side-chains
  29 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0980
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.8188

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 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 = 0.4187 r_free = 0.4187 target = 0.097359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.078247 restraints weight = 6453.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 3.19
r_work: 0.3836 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3001  Z= 0.223
  Angle     :  0.550   7.278   4082  Z= 0.287
  Chirality :  0.044   0.146    492
  Planarity :  0.003   0.025    534
  Dihedral  :  9.064  33.437    480
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.57 %
    Favored  : 88.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.18 (0.35), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS J  18 
 PHE   0.014   0.002   PHE F  15 
 ARG   0.002   0.001   ARG L  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02256 (   74)
  hydrogen bonds       : angle       5.03247 (  222)
  SS BOND              : bond        0.00458 (    7)
  SS BOND              : angle       0.99913 (   14)
  covalent geometry    : bond        0.00441 ( 2994)
  covalent geometry    : angle       0.54767 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.316 
Fit side-chains
REVERT: C   15 PHE cc_start: 0.8552 (m-80) cc_final: 0.8317 (m-80)
REVERT: J   27 LEU cc_start: 0.8518 (mp) cc_final: 0.8211 (tt)
REVERT: J   35 ASN cc_start: 0.8414 (m-40) cc_final: 0.7669 (m110)
REVERT: H   35 ASN cc_start: 0.8593 (m110) cc_final: 0.8076 (m110)
REVERT: D   11 ARG cc_start: 0.8510 (mtt180) cc_final: 0.6907 (pmt-80)
REVERT: D   35 ASN cc_start: 0.8353 (m110) cc_final: 0.8139 (m-40)
  outliers start: 7
  outliers final: 5
  residues processed: 57
  average time/residue: 0.1227
  time to fit residues: 8.8483
Evaluate side-chains
  45 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 12 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0670
   chunk 10 optimal weight:    8.9990
   overall best weight:    1.7324

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 GLN
** H  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 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 = 0.4190 r_free = 0.4190 target = 0.097366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.078459 restraints weight = 6347.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 3.08
r_work: 0.3844 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3764 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3001  Z= 0.210
  Angle     :  0.598   8.768   4082  Z= 0.284
  Chirality :  0.042   0.138    492
  Planarity :  0.003   0.016    534
  Dihedral  :  9.525  38.427    480
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.58 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.31 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS J  18 
 PHE   0.009   0.002   PHE F  15 
 ARG   0.001   0.000   ARG L  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01922 (   74)
  hydrogen bonds       : angle       4.37740 (  222)
  SS BOND              : bond        0.00295 (    7)
  SS BOND              : angle       0.56527 (   14)
  covalent geometry    : bond        0.00412 ( 2994)
  covalent geometry    : angle       0.59802 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.345 
Fit side-chains
REVERT: J   27 LEU cc_start: 0.8564 (mp) cc_final: 0.8291 (tt)
REVERT: J   35 ASN cc_start: 0.8536 (m-40) cc_final: 0.7852 (m110)
REVERT: H   15 PHE cc_start: 0.7899 (m-80) cc_final: 0.7611 (m-80)
REVERT: H   35 ASN cc_start: 0.8709 (m110) cc_final: 0.8230 (m110)
REVERT: D   35 ASN cc_start: 0.8523 (m110) cc_final: 0.8302 (m-40)
  outliers start: 11
  outliers final: 10
  residues processed: 52
  average time/residue: 0.1100
  time to fit residues: 7.4613
Evaluate side-chains
  48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
C  10 GLN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.100035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.080576 restraints weight = 6348.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 3.15
r_work: 0.3879 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3797 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   3001  Z= 0.145
  Angle     :  0.543   7.459   4082  Z= 0.252
  Chirality :  0.042   0.131    492
  Planarity :  0.002   0.009    534
  Dihedral  :  7.496  28.351    480
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 14.51 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A  18 
 PHE   0.008   0.001   PHE F  15 
 ARG   0.001   0.000   ARG L  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01401 (   74)
  hydrogen bonds       : angle       4.00020 (  222)
  SS BOND              : bond        0.00214 (    7)
  SS BOND              : angle       0.41642 (   14)
  covalent geometry    : bond        0.00279 ( 2994)
  covalent geometry    : angle       0.54355 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   27 LEU cc_start: 0.8558 (mp) cc_final: 0.8295 (tt)
REVERT: J   35 ASN cc_start: 0.8440 (m-40) cc_final: 0.8013 (m-40)
REVERT: D   35 ASN cc_start: 0.8564 (m110) cc_final: 0.8280 (m-40)
  outliers start: 13
  outliers final: 12
  residues processed: 53
  average time/residue: 0.1040
  time to fit residues: 7.2056
Evaluate side-chains
  49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain A residue    7 CYS
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 5 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 4 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
C  10 GLN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  35 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 = 0.4209 r_free = 0.4209 target = 0.098672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.079110 restraints weight = 6358.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 3.13
r_work: 0.3858 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3775 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   3001  Z= 0.206
  Angle     :  0.577   8.004   4082  Z= 0.272
  Chirality :  0.042   0.135    492
  Planarity :  0.002   0.021    534
  Dihedral  :  9.459  36.232    480
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 14.51 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.42 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A  18 
 PHE   0.010   0.002   PHE D  15 
 ARG   0.002   0.000   ARG B  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01519 (   74)
  hydrogen bonds       : angle       3.99396 (  222)
  SS BOND              : bond        0.00252 (    7)
  SS BOND              : angle       0.45936 (   14)
  covalent geometry    : bond        0.00405 ( 2994)
  covalent geometry    : angle       0.57693 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 37
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   27 LEU cc_start: 0.8640 (mp) cc_final: 0.8340 (tt)
REVERT: J   35 ASN cc_start: 0.8246 (m-40) cc_final: 0.7823 (m-40)
REVERT: D   35 ASN cc_start: 0.8509 (m110) cc_final: 0.8159 (m-40)
  outliers start: 16
  outliers final: 14
  residues processed: 50
  average time/residue: 0.1036
  time to fit residues: 6.7866
Evaluate side-chains
  48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 34
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain A residue    7 CYS
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue    7 CYS
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:   20.0000
   chunk 28 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 GLN
** G  35 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 = 0.4138 r_free = 0.4138 target = 0.094695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.075506 restraints weight = 6796.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 3.17
r_work: 0.3785 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.4437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035   3001  Z= 0.370
  Angle     :  0.719   8.755   4082  Z= 0.356
  Chirality :  0.045   0.144    492
  Planarity :  0.004   0.028    534
  Dihedral  : 15.623  59.150    480
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 15.74 %
    Favored  : 79.63 %
  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: -4.70 (0.32), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.24), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.004   HIS A  18 
 PHE   0.018   0.003   PHE D  15 
 ARG   0.002   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01825 (   74)
  hydrogen bonds       : angle       4.47248 (  222)
  SS BOND              : bond        0.00327 (    7)
  SS BOND              : angle       0.78489 (   14)
  covalent geometry    : bond        0.00748 ( 2994)
  covalent geometry    : angle       0.71855 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ARG cc_start: 0.8030 (mtt180) cc_final: 0.6675 (pmt-80)
REVERT: J   11 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7119 (pmt-80)
REVERT: J   27 LEU cc_start: 0.8780 (mp) cc_final: 0.8433 (tt)
REVERT: J   35 ASN cc_start: 0.8276 (m-40) cc_final: 0.7860 (m110)
  outliers start: 15
  outliers final: 14
  residues processed: 53
  average time/residue: 0.1205
  time to fit residues: 8.0966
Evaluate side-chains
  53 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain A residue    7 CYS
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue    7 CYS
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 3 optimal weight:    0.2980
   chunk 14 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
C  10 GLN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.099263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.079560 restraints weight = 6463.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 3.18
r_work: 0.3873 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.4399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   3001  Z= 0.171
  Angle     :  0.580   8.359   4082  Z= 0.272
  Chirality :  0.043   0.135    492
  Planarity :  0.002   0.014    534
  Dihedral  : 11.940  52.763    480
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 15.43 %
    Favored  : 79.63 %
  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: -4.64 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.53 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A  18 
 PHE   0.010   0.001   PHE D  15 
 ARG   0.001   0.000   ARG A  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01414 (   74)
  hydrogen bonds       : angle       4.17760 (  222)
  SS BOND              : bond        0.00223 (    7)
  SS BOND              : angle       0.45334 (   14)
  covalent geometry    : bond        0.00331 ( 2994)
  covalent geometry    : angle       0.58043 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8147 (t0)
REVERT: J   27 LEU cc_start: 0.8462 (mp) cc_final: 0.8228 (tt)
REVERT: J   35 ASN cc_start: 0.8043 (m-40) cc_final: 0.7680 (m110)
REVERT: D   35 ASN cc_start: 0.8533 (m110) cc_final: 0.8124 (m-40)
  outliers start: 16
  outliers final: 14
  residues processed: 57
  average time/residue: 0.1035
  time to fit residues: 7.8939
Evaluate side-chains
  54 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain A residue    7 CYS
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue    7 CYS
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain L residue    7 CYS
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 7 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:   20.0000
   chunk 22 optimal weight:    0.7980
   chunk 15 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
C  10 GLN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.096750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.076710 restraints weight = 6594.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 3.16
r_work: 0.3793 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   3001  Z= 0.293
  Angle     :  0.699   9.948   4082  Z= 0.330
  Chirality :  0.043   0.138    492
  Planarity :  0.003   0.026    534
  Dihedral  : 14.222  57.416    480
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 15.74 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.75 (0.32), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.24), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.004   HIS A  18 
 PHE   0.015   0.002   PHE D  15 
 ARG   0.002   0.000   ARG A  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01660 (   74)
  hydrogen bonds       : angle       4.41635 (  222)
  SS BOND              : bond        0.00276 (    7)
  SS BOND              : angle       0.61929 (   14)
  covalent geometry    : bond        0.00588 ( 2994)
  covalent geometry    : angle       0.69952 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 ARG cc_start: 0.7898 (mtt180) cc_final: 0.6662 (pmt-80)
REVERT: J   27 LEU cc_start: 0.8745 (mp) cc_final: 0.8378 (tt)
REVERT: J   35 ASN cc_start: 0.8015 (m-40) cc_final: 0.7529 (m110)
REVERT: D   35 ASN cc_start: 0.8396 (m110) cc_final: 0.7999 (m-40)
  outliers start: 16
  outliers final: 16
  residues processed: 56
  average time/residue: 0.1050
  time to fit residues: 7.5854
Evaluate side-chains
  58 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain A residue    7 CYS
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue    7 CYS
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain L residue    7 CYS
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.098305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.078071 restraints weight = 6446.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 3.18
r_work: 0.3822 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.4556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3001  Z= 0.227
  Angle     :  0.655  10.127   4082  Z= 0.304
  Chirality :  0.043   0.135    492
  Planarity :  0.003   0.019    534
  Dihedral  : 13.366  58.056    480
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 15.43 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.74 (0.32), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS A  18 
 PHE   0.011   0.002   PHE D  15 
 ARG   0.002   0.000   ARG I  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01504 (   74)
  hydrogen bonds       : angle       4.31905 (  222)
  SS BOND              : bond        0.00254 (    7)
  SS BOND              : angle       0.53817 (   14)
  covalent geometry    : bond        0.00447 ( 2994)
  covalent geometry    : angle       0.65559 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   11 ARG cc_start: 0.7751 (mtt180) cc_final: 0.6693 (pmt-80)
REVERT: J   27 LEU cc_start: 0.8637 (mp) cc_final: 0.8335 (tt)
REVERT: J   35 ASN cc_start: 0.7961 (m-40) cc_final: 0.7431 (m110)
REVERT: D   35 ASN cc_start: 0.8334 (m110) cc_final: 0.8011 (m-40)
  outliers start: 17
  outliers final: 15
  residues processed: 55
  average time/residue: 0.1000
  time to fit residues: 7.2812
Evaluate side-chains
  55 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain A residue    7 CYS
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue    7 CYS
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    0.3980
   chunk 29 optimal weight:    0.5980
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 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 = 0.4174 r_free = 0.4174 target = 0.097674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.078358 restraints weight = 6400.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 3.12
r_work: 0.3825 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3749 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7393
moved from start:          0.4595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   3001  Z= 0.236
  Angle     :  0.677  10.281   4082  Z= 0.311
  Chirality :  0.043   0.135    492
  Planarity :  0.003   0.022    534
  Dihedral  : 13.174  58.371    480
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 15.74 %
    Favored  : 79.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.78 (0.32), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.63 (0.24), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS A  18 
 PHE   0.015   0.002   PHE F  15 
 ARG   0.002   0.000   ARG A  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01512 (   74)
  hydrogen bonds       : angle       4.38500 (  222)
  SS BOND              : bond        0.00241 (    7)
  SS BOND              : angle       0.64176 (   14)
  covalent geometry    : bond        0.00468 ( 2994)
  covalent geometry    : angle       0.67674 ( 4068)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   11 ARG cc_start: 0.7863 (mtt180) cc_final: 0.6981 (pmt-80)
REVERT: J   27 LEU cc_start: 0.8690 (mp) cc_final: 0.8378 (tt)
REVERT: J   35 ASN cc_start: 0.8180 (m-40) cc_final: 0.7712 (m110)
REVERT: D   35 ASN cc_start: 0.8389 (m110) cc_final: 0.8101 (m-40)
  outliers start: 16
  outliers final: 15
  residues processed: 54
  average time/residue: 0.1072
  time to fit residues: 7.8138
Evaluate side-chains
  56 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain A residue    7 CYS
Chi-restraints excluded: chain A residue   14 ASN
Chi-restraints excluded: chain F residue   29 SER
Chi-restraints excluded: chain J residue    6 THR
Chi-restraints excluded: chain J residue    7 CYS
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain G residue   29 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain D residue   29 SER
Chi-restraints excluded: chain D residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 2 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.095682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.077902 restraints weight = 6621.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 3.02
r_work: 0.3607 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3528 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.4871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.040   3001  Z= 0.449
  Angle     :  0.830  10.416   4082  Z= 0.414
  Chirality :  0.048   0.148    492
  Planarity :  0.005   0.036    534
  Dihedral  : 17.203  59.349    480
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.89 %
    Favored  : 86.11 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 15.43 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.00 (0.31), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.80 (0.23), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   0.005   HIS A  18 
 PHE   0.020   0.003   PHE F  15 
 ARG   0.004   0.001   ARG I  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01952 (   74)
  hydrogen bonds       : angle       4.95938 (  222)
  SS BOND              : bond        0.00329 (    7)
  SS BOND              : angle       1.02616 (   14)
  covalent geometry    : bond        0.00908 ( 2994)
  covalent geometry    : angle       0.82899 ( 4068)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2053.29 seconds
wall clock time: 35 minutes 56.32 seconds (2156.32 seconds total)