Starting phenix.real_space_refine
on Fri Aug 22 13:03:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yl3_33902/08_2025/7yl3_33902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yl3_33902/08_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_33902/08_2025/7yl3_33902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yl3_33902/08_2025/7yl3_33902.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yl3_33902/08_2025/7yl3_33902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yl3_33902/08_2025/7yl3_33902.cif"
  }
  resolution = 3.2
  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=   0.003
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.80, per 1000 atoms: 0.27
  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: 0.26
  Conformation dependent library (CDL) restraints added in 115.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.12
  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: 0.38

  Time building geometry restraints manager: 0.37 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: 0.00
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:             1.200
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.780
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.550
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.001   0.000   ARG K  11 
 PHE   0.011   0.002   PHE E  15 
 HIS   0.001   0.000   HIS L  18 

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

*********************** 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  : 0.129 
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: 0.0516
  time to fit residues: 3.0490
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  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.0170
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0050
   chunk 28 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    0.9636

-------------------------------------------------------------------------------
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 = 0.4249 r_free = 0.4249 target = 0.100789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.081667 restraints weight = 6347.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3822 rms_B_bonded: 3.22
r_work: 0.3753 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
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      :  0.003   0.019   3001  Z= 0.136
  Angle     :  0.486   6.860   4082  Z= 0.251
  Chirality :  0.042   0.130    492
  Planarity :  0.002   0.016    534
  Dihedral  :  5.841  21.599    480
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  8.02 %
    Favored  : 90.12 %
  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 aren not related in a simple way.
  whole: -4.13 (0.35), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  11 
 PHE   0.010   0.001   PHE K  15 
 HIS   0.003   0.001   HIS J  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 2994)
  covalent geometry    : angle       0.48430 ( 4068)
  SS BOND              : bond        0.00410 (    7)
  SS BOND              : angle       0.79694 (   14)
  hydrogen bonds       : bond        0.01971 (   74)
  hydrogen bonds       : angle       5.11579 (  222)

*********************** 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
  52 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.126 
Fit side-chains
REVERT: J   27 LEU cc_start: 0.8457 (mp) cc_final: 0.8134 (tt)
REVERT: G   34 SER cc_start: 0.8405 (t) cc_final: 0.8078 (p)
REVERT: D   11 ARG cc_start: 0.8477 (mtt180) cc_final: 0.6998 (pmt-80)
  outliers start: 6
  outliers final: 4
  residues processed: 52
  average time/residue: 0.0571
  time to fit residues: 3.7409
Evaluate side-chains
  43 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 21 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 5 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.4213 r_free = 0.4213 target = 0.098245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.079377 restraints weight = 6480.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 3.10
r_work: 0.3866 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3787 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   3001  Z= 0.182
  Angle     :  0.535   7.968   4082  Z= 0.262
  Chirality :  0.042   0.134    492
  Planarity :  0.002   0.016    534
  Dihedral  :  8.210  29.518    480
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 12.96 %
    Favored  : 83.95 %
  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 aren not related in a simple way.
  whole: -4.24 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  11 
 PHE   0.012   0.002   PHE E  15 
 HIS   0.006   0.002   HIS J  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 2994)
  covalent geometry    : angle       0.53498 ( 4068)
  SS BOND              : bond        0.00253 (    7)
  SS BOND              : angle       0.50249 (   14)
  hydrogen bonds       : bond        0.01803 (   74)
  hydrogen bonds       : angle       4.40404 (  222)

*********************** 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
  56 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.146 
Fit side-chains
REVERT: J   27 LEU cc_start: 0.8539 (mp) cc_final: 0.8281 (tt)
REVERT: J   35 ASN cc_start: 0.8553 (m-40) cc_final: 0.8050 (m-40)
REVERT: G   34 SER cc_start: 0.8521 (t) cc_final: 0.8236 (p)
REVERT: D   35 ASN cc_start: 0.8522 (m110) cc_final: 0.8279 (m-40)
  outliers start: 10
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0436
  time to fit residues: 3.0699
Evaluate side-chains
  51 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    9 THR
Chi-restraints excluded: chain I residue   12 LEU
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 J residue    6 THR
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain G residue   29 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 11 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9990
   chunk 13 optimal weight:    8.9990
   chunk 29 optimal weight:    0.0870
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
C  14 ASN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4210 r_free = 0.4210 target = 0.098479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.079069 restraints weight = 6363.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 3.11
r_work: 0.3861 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3780 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.3829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.019   3001  Z= 0.195
  Angle     :  0.572   8.334   4082  Z= 0.270
  Chirality :  0.042   0.136    492
  Planarity :  0.002   0.014    534
  Dihedral  :  9.084  34.958    480
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.74 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG B  11 
 PHE   0.012   0.002   PHE E  15 
 HIS   0.006   0.002   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 2994)
  covalent geometry    : angle       0.57256 ( 4068)
  SS BOND              : bond        0.00226 (    7)
  SS BOND              : angle       0.46152 (   14)
  hydrogen bonds       : bond        0.01573 (   74)
  hydrogen bonds       : angle       4.11234 (  222)

*********************** 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
  52 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.073 
Fit side-chains
REVERT: C   14 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7830 (t0)
REVERT: J   27 LEU cc_start: 0.8656 (mp) cc_final: 0.8353 (tt)
REVERT: J   35 ASN cc_start: 0.8468 (m-40) cc_final: 0.8025 (m-40)
REVERT: G   34 SER cc_start: 0.8440 (t) cc_final: 0.8166 (p)
REVERT: D   35 ASN cc_start: 0.8497 (m110) cc_final: 0.8232 (m-40)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.0460
  time to fit residues: 2.9522
Evaluate side-chains
  47 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   14 ASN
Chi-restraints excluded: chain I residue   12 LEU
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 J residue    6 THR
Chi-restraints excluded: chain H residue   29 SER
Chi-restraints excluded: chain G residue   29 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 7 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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**
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.100468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.081016 restraints weight = 6198.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 3.12
r_work: 0.3979 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3890 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   3001  Z= 0.138
  Angle     :  0.532   7.833   4082  Z= 0.247
  Chirality :  0.042   0.132    492
  Planarity :  0.002   0.009    534
  Dihedral  :  7.348  27.952    480
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 16.98 %
    Favored  : 78.70 %
  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 aren not related in a simple way.
  whole: -4.36 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.31 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  11 
 PHE   0.011   0.001   PHE E  15 
 HIS   0.004   0.002   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 2994)
  covalent geometry    : angle       0.53247 ( 4068)
  SS BOND              : bond        0.00214 (    7)
  SS BOND              : angle       0.37474 (   14)
  hydrogen bonds       : bond        0.01320 (   74)
  hydrogen bonds       : angle       3.92694 (  222)

*********************** 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
  56 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   27 LEU cc_start: 0.8510 (mp) cc_final: 0.8250 (tt)
REVERT: J   35 ASN cc_start: 0.8163 (m-40) cc_final: 0.7807 (m-40)
REVERT: G   34 SER cc_start: 0.8463 (t) cc_final: 0.8207 (p)
REVERT: D   35 ASN cc_start: 0.8427 (m110) cc_final: 0.8134 (m-40)
  outliers start: 14
  outliers final: 13
  residues processed: 53
  average time/residue: 0.0415
  time to fit residues: 2.8239
Evaluate side-chains
  52 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain I residue   12 LEU
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 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 27 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
C  14 ASN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.097083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.077459 restraints weight = 6484.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 3.13
r_work: 0.3841 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.4214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   3001  Z= 0.279
  Angle     :  0.641   8.341   4082  Z= 0.307
  Chirality :  0.043   0.139    492
  Planarity :  0.003   0.017    534
  Dihedral  : 12.098  45.832    480
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 16.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.50 (0.33), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  11 
 PHE   0.014   0.002   PHE D  15 
 HIS   0.009   0.003   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 2994)
  covalent geometry    : angle       0.64132 ( 4068)
  SS BOND              : bond        0.00259 (    7)
  SS BOND              : angle       0.56456 (   14)
  hydrogen bonds       : bond        0.01619 (   74)
  hydrogen bonds       : angle       4.21045 (  222)

*********************** 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
  52 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   14 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7900 (t0)
REVERT: A   11 ARG cc_start: 0.8082 (mtt180) cc_final: 0.6702 (pmt-80)
REVERT: J   27 LEU cc_start: 0.8695 (mp) cc_final: 0.8367 (tt)
REVERT: J   35 ASN cc_start: 0.8270 (m-40) cc_final: 0.7877 (m110)
REVERT: D   35 ASN cc_start: 0.8579 (m110) cc_final: 0.8266 (m-40)
  outliers start: 14
  outliers final: 12
  residues processed: 50
  average time/residue: 0.0443
  time to fit residues: 2.8597
Evaluate side-chains
  48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   14 ASN
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 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 1 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0270
   chunk 13 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.9640

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

Flipped N/Q/H residues before XYZ refinement:
C  10 GLN
A  10 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.099942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.080358 restraints weight = 6278.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 3.15
r_work: 0.3898 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3816 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3001  Z= 0.131
  Angle     :  0.576   8.327   4082  Z= 0.259
  Chirality :  0.042   0.129    492
  Planarity :  0.002   0.008    534
  Dihedral  :  8.552  34.731    480
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.59 %
    Favored  : 78.40 %
  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 aren not related in a simple way.
  whole: -4.50 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  11 
 PHE   0.010   0.001   PHE E  15 
 HIS   0.004   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 2994)
  covalent geometry    : angle       0.57632 ( 4068)
  SS BOND              : bond        0.00202 (    7)
  SS BOND              : angle       0.35990 (   14)
  hydrogen bonds       : bond        0.01280 (   74)
  hydrogen bonds       : angle       4.03052 (  222)

*********************** 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
  53 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   27 LEU cc_start: 0.8532 (mp) cc_final: 0.8297 (tt)
REVERT: J   35 ASN cc_start: 0.8164 (m-40) cc_final: 0.7812 (m110)
REVERT: D   35 ASN cc_start: 0.8393 (m110) cc_final: 0.7977 (m-40)
  outliers start: 13
  outliers final: 13
  residues processed: 52
  average time/residue: 0.0480
  time to fit residues: 3.2498
Evaluate side-chains
  51 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain I residue   12 LEU
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 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 25 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0980
   chunk 27 optimal weight:    7.9990
   chunk 19 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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**
** E  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 = 0.4263 r_free = 0.4263 target = 0.101449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.081679 restraints weight = 6376.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 3.19
r_work: 0.3921 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3837 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3001  Z= 0.115
  Angle     :  0.566   8.350   4082  Z= 0.249
  Chirality :  0.042   0.130    492
  Planarity :  0.002   0.007    534
  Dihedral  :  6.035  24.024    480
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.52 %
    Favored  : 77.78 %
  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 aren not related in a simple way.
  whole: -4.47 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  11 
 PHE   0.009   0.001   PHE E  15 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 2994)
  covalent geometry    : angle       0.56686 ( 4068)
  SS BOND              : bond        0.00170 (    7)
  SS BOND              : angle       0.33079 (   14)
  hydrogen bonds       : bond        0.01181 (   74)
  hydrogen bonds       : angle       3.90083 (  222)

*********************** 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
  54 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   27 LEU cc_start: 0.8646 (mp) cc_final: 0.8346 (tt)
REVERT: J   35 ASN cc_start: 0.8156 (m-40) cc_final: 0.7845 (m110)
REVERT: D   35 ASN cc_start: 0.8464 (m110) cc_final: 0.8072 (m-40)
  outliers start: 12
  outliers final: 12
  residues processed: 53
  average time/residue: 0.0460
  time to fit residues: 3.1853
Evaluate side-chains
  51 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain I residue    7 CYS
Chi-restraints excluded: chain I residue   12 LEU
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 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 24 optimal weight:    4.9990
   chunk 25 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0980
   chunk 8 optimal weight:    5.9990
   chunk 19 optimal weight:    0.3980
   chunk 10 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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**
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  10 GLN ** 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 = 0.4252 r_free = 0.4252 target = 0.101145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.081179 restraints weight = 6215.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 3.13
r_work: 0.3916 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3837 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3001  Z= 0.118
  Angle     :  0.572   8.411   4082  Z= 0.254
  Chirality :  0.042   0.129    492
  Planarity :  0.002   0.008    534
  Dihedral  :  5.849  24.301    480
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 18.83 %
    Favored  : 77.16 %
  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 aren not related in a simple way.
  whole: -4.43 (0.34), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.26), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  11 
 PHE   0.009   0.001   PHE E  15 
 HIS   0.004   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 2994)
  covalent geometry    : angle       0.57241 ( 4068)
  SS BOND              : bond        0.00174 (    7)
  SS BOND              : angle       0.33907 (   14)
  hydrogen bonds       : bond        0.01171 (   74)
  hydrogen bonds       : angle       3.81660 (  222)

*********************** 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
  55 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   27 LEU cc_start: 0.8519 (mp) cc_final: 0.8274 (tt)
REVERT: J   35 ASN cc_start: 0.8158 (m-40) cc_final: 0.7835 (m110)
REVERT: B   11 ARG cc_start: 0.4669 (mmp-170) cc_final: 0.4339 (mmp-170)
REVERT: D   35 ASN cc_start: 0.8468 (m110) cc_final: 0.8112 (m-40)
  outliers start: 13
  outliers final: 11
  residues processed: 54
  average time/residue: 0.0280
  time to fit residues: 1.9974
Evaluate side-chains
  49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
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 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 15 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   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  10 GLN
C  14 ASN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  10 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.094836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.075494 restraints weight = 6671.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 3.11
r_work: 0.3799 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3719 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.036   3001  Z= 0.370
  Angle     :  0.735   8.912   4082  Z= 0.363
  Chirality :  0.045   0.150    492
  Planarity :  0.004   0.026    534
  Dihedral  : 14.300  50.797    480
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.78 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 18.21 %
    Favored  : 77.47 %
  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 aren not related in a simple way.
  whole: -4.72 (0.32), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.24), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG J  11 
 PHE   0.017   0.003   PHE D  15 
 HIS   0.013   0.005   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00752 ( 2994)
  covalent geometry    : angle       0.73472 ( 4068)
  SS BOND              : bond        0.00354 (    7)
  SS BOND              : angle       0.81872 (   14)
  hydrogen bonds       : bond        0.01905 (   74)
  hydrogen bonds       : angle       4.34343 (  222)

********************** 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
  52 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   14 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7908 (t0)
REVERT: A   11 ARG cc_start: 0.8014 (mtt180) cc_final: 0.6911 (pmt-80)
REVERT: A   34 SER cc_start: 0.8454 (p) cc_final: 0.7826 (m)
REVERT: J   27 LEU cc_start: 0.8797 (mp) cc_final: 0.8451 (tt)
REVERT: J   35 ASN cc_start: 0.8243 (m-40) cc_final: 0.7824 (m110)
REVERT: D   35 ASN cc_start: 0.8452 (m110) cc_final: 0.8080 (m-40)
  outliers start: 14
  outliers final: 12
  residues processed: 50
  average time/residue: 0.0476
  time to fit residues: 3.1049
Evaluate side-chains
  49 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   14 ASN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   chunk 15 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
C  14 ASN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  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 = 0.4177 r_free = 0.4177 target = 0.096707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.077124 restraints weight = 6479.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 3.10
r_work: 0.3833 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3753 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3001  Z= 0.258
  Angle     :  0.691  10.323   4082  Z= 0.325
  Chirality :  0.043   0.144    492
  Planarity :  0.003   0.019    534
  Dihedral  : 13.457  49.306    480
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.22 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.75 %
    Favored  : 76.54 %
  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 aren not related in a simple way.
  whole: -4.72 (0.32), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.25), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  11 
 PHE   0.013   0.002   PHE D  15 
 HIS   0.008   0.003   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 2994)
  covalent geometry    : angle       0.69127 ( 4068)
  SS BOND              : bond        0.00256 (    7)
  SS BOND              : angle       0.61702 (   14)
  hydrogen bonds       : bond        0.01651 (   74)
  hydrogen bonds       : angle       4.38088 (  222)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 973.88 seconds
wall clock time: 17 minutes 27.30 seconds (1047.30 seconds total)