Starting phenix.real_space_refine
on Fri May  9 23:06:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9eme_19818/05_2025/9eme_19818.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9eme_19818/05_2025/9eme_19818.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9eme_19818/05_2025/9eme_19818.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9eme_19818/05_2025/9eme_19818.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9eme_19818/05_2025/9eme_19818.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9eme_19818/05_2025/9eme_19818.cif"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2562      2.51       5
     N     714      2.21       5
     O     852      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-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4140
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 690
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 1, 'TRANS': 90}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.48, per 1000 atoms: 0.60
  Number of scatterers: 4140
  At special positions: 0
  Unit cell: (79.04, 92.56, 52, 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     852      8.00
     N     714      7.00
     C    2562      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  87 " distance=2.02
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  87 " distance=2.02

  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: 0.89
  Conformation dependent library (CDL) restraints added in 490.2 milliseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  984

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 32.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23
      removed outlier: 6.582A  pdb=" N   GLN A  16 " --> pdb=" O   THR B  17 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ARG B  19 " --> pdb=" O   GLN A  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL A  18 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   THR B  21 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE A  20 " --> pdb=" O   THR B  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN B  23 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   CYS A  22 " --> pdb=" O   GLN B  23 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLN B  16 " --> pdb=" O   THR C  17 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ARG C  19 " --> pdb=" O   GLN B  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL B  18 " --> pdb=" O   ARG C  19 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   THR C  21 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE B  20 " --> pdb=" O   THR C  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN C  23 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   CYS B  22 " --> pdb=" O   GLN C  23 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLN C  16 " --> pdb=" O   THR D  17 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ARG D  19 " --> pdb=" O   GLN C  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL C  18 " --> pdb=" O   ARG D  19 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   THR D  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE C  20 " --> pdb=" O   THR D  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN D  23 " --> pdb=" O   ILE C  20 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   CYS C  22 " --> pdb=" O   GLN D  23 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   GLN D  16 " --> pdb=" O   THR E  17 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ARG E  19 " --> pdb=" O   GLN D  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL D  18 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   THR E  21 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE D  20 " --> pdb=" O   THR E  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN E  23 " --> pdb=" O   ILE D  20 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   CYS D  22 " --> pdb=" O   GLN E  23 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   GLN E  16 " --> pdb=" O   THR F  17 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   ARG F  19 " --> pdb=" O   GLN E  16 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL E  18 " --> pdb=" O   ARG F  19 " (cutoff:3.500A)
      removed outlier: 7.323A  pdb=" N   THR F  21 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE E  20 " --> pdb=" O   THR F  21 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   GLN F  23 " --> pdb=" O   ILE E  20 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   CYS E  22 " --> pdb=" O   GLN F  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 30
    Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37
    Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 47
      removed outlier: 6.844A  pdb=" N   LEU A  45 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU B  45 " --> pdb=" O   VAL C  46 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU C  45 " --> pdb=" O   VAL D  46 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU D  45 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   LEU E  45 " --> pdb=" O   VAL F  46 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68
    Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 78
      removed outlier: 6.757A  pdb=" N   ALA B  77 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN A  78 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA C  77 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN B  78 " --> pdb=" O   ALA C  77 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA D  77 " --> pdb=" O   GLY C  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN C  78 " --> pdb=" O   ALA D  77 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA E  77 " --> pdb=" O   GLY D  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN D  78 " --> pdb=" O   ALA E  77 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   ALA F  77 " --> pdb=" O   GLY E  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   GLN E  78 " --> pdb=" O   ALA F  77 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83
      removed outlier: 8.450A  pdb=" N   ASP A  81 " --> pdb=" O   GLU B  82 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP B  81 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP C  81 " --> pdb=" O   GLU D  82 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP D  81 " --> pdb=" O   GLU E  82 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   ASP E  81 " --> pdb=" O   GLU F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 106

    80 hydrogen bonds defined for protein.
    240 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 1.07 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 690
        1.30 -     1.43: 1224
        1.43 -     1.55: 2286
        1.55 -     1.68: 0
        1.68 -     1.81: 12
  Bond restraints: 4212
  Sorted by residual:
  bond pdb=" C   VAL A  46 "
       pdb=" O   VAL A  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.47e+01
  bond pdb=" C   VAL F  46 "
       pdb=" O   VAL F  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.46e+01
  bond pdb=" C   VAL E  46 "
       pdb=" O   VAL E  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.46e+01
  bond pdb=" C   VAL D  46 "
       pdb=" O   VAL D  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.45e+01
  bond pdb=" C   VAL B  46 "
       pdb=" O   VAL B  46 "
    ideal  model  delta    sigma   weight residual
    1.238  1.173  0.065 1.10e-02 8.26e+03 3.45e+01
  ... (remaining 4207 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 3919
        1.92 -     3.84: 1269
        3.84 -     5.76: 458
        5.76 -     7.68: 60
        7.68 -     9.61: 6
  Bond angle restraints: 5712
  Sorted by residual:
  angle pdb=" N   SER F  64 "
        pdb=" CA  SER F  64 "
        pdb=" C   SER F  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.58   -9.61 1.09e+00 8.42e-01 7.77e+01
  angle pdb=" N   SER C  64 "
        pdb=" CA  SER C  64 "
        pdb=" C   SER C  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.56   -9.59 1.09e+00 8.42e-01 7.75e+01
  angle pdb=" N   SER D  64 "
        pdb=" CA  SER D  64 "
        pdb=" C   SER D  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.54   -9.57 1.09e+00 8.42e-01 7.71e+01
  angle pdb=" N   SER E  64 "
        pdb=" CA  SER E  64 "
        pdb=" C   SER E  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.53   -9.56 1.09e+00 8.42e-01 7.70e+01
  angle pdb=" N   SER A  64 "
        pdb=" CA  SER A  64 "
        pdb=" C   SER A  64 "
      ideal   model   delta    sigma   weight residual
     110.97  120.53   -9.56 1.09e+00 8.42e-01 7.69e+01
  ... (remaining 5707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.03: 2160
       14.03 -    28.06: 156
       28.06 -    42.09: 84
       42.09 -    56.12: 24
       56.12 -    70.15: 6
  Dihedral angle restraints: 2430
    sinusoidal: 864
      harmonic: 1566
  Sorted by residual:
  dihedral pdb=" C   HIS E  95 "
           pdb=" N   HIS E  95 "
           pdb=" CA  HIS E  95 "
           pdb=" CB  HIS E  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.87    9.27     0      2.50e+00 1.60e-01 1.38e+01
  dihedral pdb=" C   HIS F  95 "
           pdb=" N   HIS F  95 "
           pdb=" CA  HIS F  95 "
           pdb=" CB  HIS F  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.86    9.26     0      2.50e+00 1.60e-01 1.37e+01
  dihedral pdb=" C   HIS C  95 "
           pdb=" N   HIS C  95 "
           pdb=" CA  HIS C  95 "
           pdb=" CB  HIS C  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.86    9.26     0      2.50e+00 1.60e-01 1.37e+01
  ... (remaining 2427 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 228
       0.062 -    0.124: 186
       0.124 -    0.186: 142
       0.186 -    0.248: 62
       0.248 -    0.310: 18
  Chirality restraints: 636
  Sorted by residual:
  chirality pdb=" CA  HIS B  95 "
            pdb=" N   HIS B  95 "
            pdb=" C   HIS B  95 "
            pdb=" CB  HIS B  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CA  HIS A  95 "
            pdb=" N   HIS A  95 "
            pdb=" C   HIS A  95 "
            pdb=" CB  HIS A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  HIS D  95 "
            pdb=" N   HIS D  95 "
            pdb=" C   HIS D  95 "
            pdb=" CB  HIS D  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.37e+00
  ... (remaining 633 not shown)

  Planarity restraints: 738
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY E 100 "    0.021 2.00e-02 2.50e+03   4.19e-02 1.76e+01
        pdb=" C   GLY E 100 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   GLY E 100 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLY E 101 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 100 "    0.021 2.00e-02 2.50e+03   4.18e-02 1.75e+01
        pdb=" C   GLY B 100 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   GLY B 100 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLY B 101 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 100 "    0.021 2.00e-02 2.50e+03   4.18e-02 1.75e+01
        pdb=" C   GLY C 100 "   -0.072 2.00e-02 2.50e+03
        pdb=" O   GLY C 100 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLY C 101 "    0.025 2.00e-02 2.50e+03
  ... (remaining 735 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 2442
        3.03 -     3.50: 3840
        3.50 -     3.96: 6802
        3.96 -     4.43: 7884
        4.43 -     4.90: 15157
  Nonbonded interactions: 36125
  Sorted by model distance:
  nonbonded pdb=" N   GLY B 100 "
            pdb=" O   GLY B 100 "
     model   vdw
     2.562 2.496
  nonbonded pdb=" N   GLY A 100 "
            pdb=" O   GLY A 100 "
     model   vdw
     2.562 2.496
  nonbonded pdb=" N   GLY C 100 "
            pdb=" O   GLY C 100 "
     model   vdw
     2.562 2.496
  nonbonded pdb=" N   GLY F 100 "
            pdb=" O   GLY F 100 "
     model   vdw
     2.562 2.496
  nonbonded pdb=" N   GLY E 100 "
            pdb=" O   GLY E 100 "
     model   vdw
     2.562 2.496
  ... (remaining 36120 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             7.140
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     12.190
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5839
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      :  0.015   0.065   4218  Z= 1.114
  Angle     :  2.114   9.606   5724  Z= 1.589
  Chirality :  0.121   0.310    636
  Planarity :  0.012   0.042    738
  Dihedral  : 14.206  70.153   1428
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.40 (0.21), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.35 (0.16), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.005   TRP C  34 
 HIS   0.007   0.003   HIS B  95 
 PHE   0.006   0.002   PHE C  61 
 TYR   0.014   0.002   TYR B  30 
 ARG   0.007   0.002   ARG E  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17634 (   80)
  hydrogen bonds       : angle       8.45019 (  240)
  SS BOND              : bond        0.01219 (    6)
  SS BOND              : angle       1.00173 (   12)
  covalent geometry    : bond        0.01474 ( 4212)
  covalent geometry    : angle       2.11604 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.586 
Fit side-chains
REVERT: A   23 GLN cc_start: 0.7914 (tt0) cc_final: 0.6979 (tm-30)
REVERT: A   89 SER cc_start: 0.6068 (t) cc_final: 0.5827 (t)
REVERT: B   23 GLN cc_start: 0.6604 (tt0) cc_final: 0.5670 (tm-30)
REVERT: C   19 ARG cc_start: 0.5982 (ttm170) cc_final: 0.5702 (ttm170)
REVERT: C   23 GLN cc_start: 0.6797 (tt0) cc_final: 0.5708 (tm-30)
REVERT: C   27 LEU cc_start: 0.6638 (tt) cc_final: 0.6275 (mp)
REVERT: D   23 GLN cc_start: 0.7023 (tt0) cc_final: 0.5726 (tm-30)
REVERT: D   33 SER cc_start: 0.7831 (p) cc_final: 0.7617 (p)
REVERT: D   38 LYS cc_start: 0.7392 (mttt) cc_final: 0.7167 (mtpp)
REVERT: D   78 GLN cc_start: 0.7055 (mt0) cc_final: 0.6721 (mt0)
REVERT: F   23 GLN cc_start: 0.6897 (tt0) cc_final: 0.6431 (tm-30)
REVERT: F   78 GLN cc_start: 0.7283 (mt0) cc_final: 0.6979 (mt0)
REVERT: F   80 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6218 (tt0)
REVERT: F   90 ARG cc_start: 0.6815 (ttt180) cc_final: 0.6035 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 1.0345
  time to fit residues: 128.8662
Evaluate side-chains
  61 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  68 ASN
A  78 GLN
B  52 ASN
B  68 ASN
B  78 GLN
C  68 ASN
C  78 GLN
D  68 ASN
E  16 GLN
E  68 ASN
** E  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  65 ASN
F  68 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.119720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.108983 restraints weight = 5626.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 2.00
r_work: 0.3791 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4218  Z= 0.123
  Angle     :  0.555   6.719   5724  Z= 0.311
  Chirality :  0.043   0.119    636
  Planarity :  0.002   0.034    738
  Dihedral  :  4.997  18.169    600
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 15.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.47 (0.27), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.20), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  34 
 HIS   0.002   0.001   HIS E  95 
 PHE   0.002   0.001   PHE A  99 
 TYR   0.011   0.002   TYR A  31 
 ARG   0.003   0.000   ARG E  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03178 (   80)
  hydrogen bonds       : angle       5.04607 (  240)
  SS BOND              : bond        0.00303 (    6)
  SS BOND              : angle       0.38616 (   12)
  covalent geometry    : bond        0.00268 ( 4212)
  covalent geometry    : angle       0.55547 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8539 (mttt)
REVERT: D   23 GLN cc_start: 0.7999 (tt0) cc_final: 0.7542 (tm-30)
REVERT: E   90 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7321 (ttm-80)
REVERT: F   19 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7697 (ttp-110)
REVERT: F   80 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7876 (tt0)
REVERT: F   90 ARG cc_start: 0.8107 (ttt180) cc_final: 0.6963 (tpm170)
  outliers start: 15
  outliers final: 9
  residues processed: 65
  average time/residue: 1.2063
  time to fit residues: 81.6082
Evaluate side-chains
  55 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain F residue   22 CYS
Chi-restraints excluded: chain F residue   49 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
B  68 ASN
D  68 ASN
** D  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  78 GLN
F  68 ASN
F  78 GLN
F  88 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.118849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.108190 restraints weight = 5560.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 1.99
r_work: 0.3789 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3689 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4218  Z= 0.129
  Angle     :  0.522   6.261   5724  Z= 0.292
  Chirality :  0.043   0.115    636
  Planarity :  0.002   0.022    738
  Dihedral  :  4.746  17.685    600
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.89 %
    Favored  : 81.31 %
  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: -3.13 (0.29), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D  34 
 HIS   0.003   0.001   HIS E  95 
 PHE   0.003   0.001   PHE A  99 
 TYR   0.016   0.002   TYR F  86 
 ARG   0.003   0.000   ARG E  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03065 (   80)
  hydrogen bonds       : angle       4.67361 (  240)
  SS BOND              : bond        0.00320 (    6)
  SS BOND              : angle       0.43087 (   12)
  covalent geometry    : bond        0.00281 ( 4212)
  covalent geometry    : angle       0.52194 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8492 (mttt)
REVERT: A   90 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7509 (ttp80)
REVERT: E   90 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7103 (ttm170)
REVERT: F   19 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7650 (ttp-110)
REVERT: F   80 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7874 (tt0)
REVERT: F   90 ARG cc_start: 0.7901 (ttt180) cc_final: 0.6839 (tpm170)
  outliers start: 8
  outliers final: 5
  residues processed: 50
  average time/residue: 1.2788
  time to fit residues: 66.3308
Evaluate side-chains
  48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LYS
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain E residue  107 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 3 optimal weight:    0.2980
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
D  68 ASN
** D  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.120205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.109435 restraints weight = 5671.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 2.02
r_work: 0.3810 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3710 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4218  Z= 0.114
  Angle     :  0.488   5.137   5724  Z= 0.273
  Chirality :  0.043   0.113    636
  Planarity :  0.002   0.009    738
  Dihedral  :  4.509  17.362    600
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.67 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.29), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP D  34 
 HIS   0.003   0.001   HIS D  95 
 PHE   0.002   0.001   PHE A  99 
 TYR   0.016   0.001   TYR B  86 
 ARG   0.002   0.000   ARG E  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02642 (   80)
  hydrogen bonds       : angle       4.50646 (  240)
  SS BOND              : bond        0.00244 (    6)
  SS BOND              : angle       0.31180 (   12)
  covalent geometry    : bond        0.00243 ( 4212)
  covalent geometry    : angle       0.48788 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8097 (mm-30)
REVERT: A   90 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7433 (ttp80)
REVERT: F   80 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7857 (tt0)
REVERT: F   90 ARG cc_start: 0.7902 (ttt180) cc_final: 0.6580 (tpm170)
  outliers start: 12
  outliers final: 9
  residues processed: 55
  average time/residue: 1.1809
  time to fit residues: 67.4944
Evaluate side-chains
  53 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   62 SER
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain D residue   22 CYS
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain F residue   22 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 48 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    3.6588

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

Flipped N/Q/H residues before XYZ refinement:
B  51 ASN
B  78 GLN
D  51 ASN
D  68 ASN
D  78 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.107616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.097307 restraints weight = 6304.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.02
r_work: 0.3646 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
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      :  0.010   0.048   4218  Z= 0.457
  Angle     :  0.740   6.069   5724  Z= 0.413
  Chirality :  0.049   0.114    636
  Planarity :  0.004   0.034    738
  Dihedral  :  5.848  19.490    600
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 22.52 %
    Favored  : 76.13 %
  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: -3.12 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP D  34 
 HIS   0.013   0.004   HIS D  95 
 PHE   0.014   0.003   PHE B  99 
 TYR   0.026   0.004   TYR A  30 
 ARG   0.004   0.001   ARG F  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (   80)
  hydrogen bonds       : angle       4.66016 (  240)
  SS BOND              : bond        0.00867 (    6)
  SS BOND              : angle       0.70700 (   12)
  covalent geometry    : bond        0.00992 ( 4212)
  covalent geometry    : angle       0.73996 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.508 
Fit side-chains
REVERT: C   82 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7800 (mt-10)
REVERT: F   80 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7830 (tt0)
REVERT: F   90 ARG cc_start: 0.8026 (ttt180) cc_final: 0.6600 (tpm170)
  outliers start: 6
  outliers final: 1
  residues processed: 42
  average time/residue: 1.3646
  time to fit residues: 59.5064
Evaluate side-chains
  38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.115726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.105149 restraints weight = 5778.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 1.99
r_work: 0.3755 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3655 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4218  Z= 0.138
  Angle     :  0.519   6.251   5724  Z= 0.286
  Chirality :  0.043   0.113    636
  Planarity :  0.002   0.023    738
  Dihedral  :  4.837  17.723    600
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 22.52 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  34 
 HIS   0.003   0.001   HIS D  95 
 PHE   0.004   0.001   PHE E  61 
 TYR   0.016   0.001   TYR C  35 
 ARG   0.003   0.000   ARG E  28 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02858 (   80)
  hydrogen bonds       : angle       4.47695 (  240)
  SS BOND              : bond        0.00260 (    6)
  SS BOND              : angle       0.41946 (   12)
  covalent geometry    : bond        0.00295 ( 4212)
  covalent geometry    : angle       0.51924 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7478 (ttp80)
REVERT: C   82 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7784 (mt-10)
REVERT: D   90 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8166 (ttp80)
REVERT: E   90 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7406 (ptm160)
REVERT: F   80 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7980 (tt0)
REVERT: F   90 ARG cc_start: 0.7913 (ttt180) cc_final: 0.6508 (tpm170)
  outliers start: 5
  outliers final: 4
  residues processed: 44
  average time/residue: 1.2364
  time to fit residues: 56.5416
Evaluate side-chains
  45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain D residue   90 ARG
Chi-restraints excluded: chain E residue   22 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    1.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.113719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.102981 restraints weight = 5887.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 2.08
r_work: 0.3727 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3626 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4218  Z= 0.190
  Angle     :  0.553   6.855   5724  Z= 0.304
  Chirality :  0.043   0.112    636
  Planarity :  0.002   0.022    738
  Dihedral  :  4.968  17.740    600
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 23.87 %
    Favored  : 75.00 %
  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: -3.08 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.34 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D  34 
 HIS   0.005   0.002   HIS D  95 
 PHE   0.005   0.001   PHE B  99 
 TYR   0.016   0.002   TYR C  35 
 ARG   0.002   0.000   ARG B  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03180 (   80)
  hydrogen bonds       : angle       4.42355 (  240)
  SS BOND              : bond        0.00367 (    6)
  SS BOND              : angle       0.46547 (   12)
  covalent geometry    : bond        0.00411 ( 4212)
  covalent geometry    : angle       0.55342 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7686 (mt-10)
REVERT: D   38 LYS cc_start: 0.8789 (mttt) cc_final: 0.8466 (mptt)
REVERT: F   80 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7823 (tt0)
REVERT: F   90 ARG cc_start: 0.7885 (ttt180) cc_final: 0.6284 (tpm170)
  outliers start: 5
  outliers final: 3
  residues processed: 43
  average time/residue: 1.2643
  time to fit residues: 56.4656
Evaluate side-chains
  42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain E residue   22 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
C  51 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.115244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.104604 restraints weight = 5791.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 2.05
r_work: 0.3756 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.3730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4218  Z= 0.153
  Angle     :  0.530   7.064   5724  Z= 0.290
  Chirality :  0.043   0.112    636
  Planarity :  0.002   0.027    738
  Dihedral  :  4.747  17.457    600
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 24.10 %
    Favored  : 74.55 %
  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: -3.04 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  34 
 HIS   0.004   0.001   HIS A  95 
 PHE   0.003   0.001   PHE E  61 
 TYR   0.017   0.002   TYR B  86 
 ARG   0.004   0.000   ARG C  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02938 (   80)
  hydrogen bonds       : angle       4.37281 (  240)
  SS BOND              : bond        0.00292 (    6)
  SS BOND              : angle       0.45563 (   12)
  covalent geometry    : bond        0.00328 ( 4212)
  covalent geometry    : angle       0.53025 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7699 (mt-10)
REVERT: D   38 LYS cc_start: 0.8805 (mttt) cc_final: 0.8486 (mptt)
REVERT: D   90 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7974 (ptt90)
REVERT: E   90 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7156 (ptm160)
REVERT: F   80 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7830 (tt0)
REVERT: F   90 ARG cc_start: 0.7860 (ttt180) cc_final: 0.6488 (ttm170)
  outliers start: 6
  outliers final: 5
  residues processed: 46
  average time/residue: 1.1389
  time to fit residues: 54.6336
Evaluate side-chains
  45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain B residue   38 LYS
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain F residue   22 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 32 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.116104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.105419 restraints weight = 5879.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 2.07
r_work: 0.3768 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3667 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4218  Z= 0.135
  Angle     :  0.520   7.180   5724  Z= 0.284
  Chirality :  0.043   0.113    636
  Planarity :  0.002   0.018    738
  Dihedral  :  4.622  17.288    600
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 25.00 %
    Favored  : 73.87 %
  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: -3.00 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  34 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.003   0.001   PHE E  61 
 TYR   0.017   0.002   TYR B  86 
 ARG   0.003   0.000   ARG C  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02794 (   80)
  hydrogen bonds       : angle       4.33530 (  240)
  SS BOND              : bond        0.00268 (    6)
  SS BOND              : angle       0.44945 (   12)
  covalent geometry    : bond        0.00289 ( 4212)
  covalent geometry    : angle       0.52034 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   82 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7755 (mt-10)
REVERT: D   90 ARG cc_start: 0.8222 (ttp80) cc_final: 0.8020 (ptt90)
REVERT: E   90 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7185 (ptm160)
REVERT: F   80 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7835 (tt0)
REVERT: F   90 ARG cc_start: 0.7861 (ttt180) cc_final: 0.6492 (ttm170)
  outliers start: 5
  outliers final: 4
  residues processed: 44
  average time/residue: 1.3366
  time to fit residues: 61.3122
Evaluate side-chains
  44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain F residue   22 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.116479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.105984 restraints weight = 5872.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 1.99
r_work: 0.3776 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3676 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
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   0.022   4218  Z= 0.133
  Angle     :  0.524   7.077   5724  Z= 0.285
  Chirality :  0.043   0.111    636
  Planarity :  0.002   0.017    738
  Dihedral  :  4.593  17.213    600
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 24.77 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.21), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  34 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.003   0.001   PHE E  61 
 TYR   0.015   0.001   TYR C  35 
 ARG   0.003   0.000   ARG C  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02795 (   80)
  hydrogen bonds       : angle       4.31846 (  240)
  SS BOND              : bond        0.00263 (    6)
  SS BOND              : angle       0.42641 (   12)
  covalent geometry    : bond        0.00286 ( 4212)
  covalent geometry    : angle       0.52376 ( 5712)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7190 (ttm110)
REVERT: C   82 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7766 (mt-10)
REVERT: D   38 LYS cc_start: 0.8827 (mttp) cc_final: 0.8405 (mptt)
REVERT: E   90 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7258 (ptm160)
REVERT: F   80 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7922 (tt0)
REVERT: F   90 ARG cc_start: 0.7949 (ttt180) cc_final: 0.6606 (ttm170)
  outliers start: 5
  outliers final: 5
  residues processed: 45
  average time/residue: 1.1756
  time to fit residues: 55.0566
Evaluate side-chains
  46 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 ARG
Chi-restraints excluded: chain B residue   22 CYS
Chi-restraints excluded: chain C residue   22 CYS
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain F residue   22 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.115082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.104383 restraints weight = 5812.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 2.04
r_work: 0.3752 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3651 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4218  Z= 0.156
  Angle     :  0.536   6.981   5724  Z= 0.292
  Chirality :  0.043   0.111    636
  Planarity :  0.002   0.019    738
  Dihedral  :  4.706  17.388    600
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 24.55 %
    Favored  : 74.32 %
  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: -2.93 (0.28), residues: 528
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D  34 
 HIS   0.004   0.001   HIS A  95 
 PHE   0.004   0.001   PHE B  99 
 TYR   0.015   0.002   TYR C  35 
 ARG   0.004   0.000   ARG C  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02927 (   80)
  hydrogen bonds       : angle       4.29800 (  240)
  SS BOND              : bond        0.00310 (    6)
  SS BOND              : angle       0.46670 (   12)
  covalent geometry    : bond        0.00336 ( 4212)
  covalent geometry    : angle       0.53609 ( 5712)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2901.52 seconds
wall clock time: 51 minutes 19.55 seconds (3079.55 seconds total)