Starting phenix.real_space_refine
on Tue Feb  3 15:02:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lbw_62957/02_2026/9lbw_62957.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lbw_62957/02_2026/9lbw_62957.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lbw_62957/02_2026/9lbw_62957.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lbw_62957/02_2026/9lbw_62957.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lbw_62957/02_2026/9lbw_62957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lbw_62957/02_2026/9lbw_62957.map"
  }
  resolution = 3.44
  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=   0.001 sd=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2626      2.51       5
     N     691      2.21       5
     O     755      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4092
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1119
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1119
          Classifications: {'peptide': 141}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 129}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 1151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1151
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 12, 'TRANS': 131}
    Chain: "H"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 970
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 852
          Classifications: {'peptide': 109}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100}
  Time building chain proxies: 1.15, per 1000 atoms: 0.28
  Number of scatterers: 4092
  At special positions: 0
  Unit cell: (112.112, 101.332, 66.836, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     755      8.00
     N     691      7.00
     C    2626      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  61 " - pdb=" SG  CYS B  61 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.15
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " 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: 0.32
  Conformation dependent library (CDL) restraints added in 157.8 milliseconds
  

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  960

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 5 sheets defined
      42.8% alpha, 20.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 12 through 17
      removed outlier: 3.583A  pdb=" N   SER A  17 " --> pdb=" O   VAL A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 43
      removed outlier: 3.751A  pdb=" N   SER A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ARG A  39 " --> pdb=" O   SER A  35 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   GLU A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   ALA A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 64
    Processing helix  chain 'A' and resid 64 through 76
      removed outlier: 3.613A  pdb=" N   THR A  70 " --> pdb=" O   MET A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 82
    Processing helix  chain 'A' and resid 91 through 111
      removed outlier: 3.869A  pdb=" N   LEU A  95 " --> pdb=" O   THR A  91 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LYS A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   PHE A  97 " --> pdb=" O   MET A  93 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   LEU A 100 " --> pdb=" O   LYS A  96 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TRP A 102 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 128
      removed outlier: 3.654A  pdb=" N   GLU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   VAL A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ARG A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR A 128 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 133
      removed outlier: 3.800A  pdb=" N   ARG A 133 " --> pdb=" O   PRO A 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 10
    Processing helix  chain 'B' and resid 12 through 18
    Processing helix  chain 'B' and resid 26 through 44
      removed outlier: 7.321A  pdb=" N   GLU B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ALA B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 75
    Processing helix  chain 'B' and resid 78 through 111
      removed outlier: 4.393A  pdb=" N   MET B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   GLY B  94 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS B  96 " --> pdb=" O   ASN B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 128
      removed outlier: 3.539A  pdb=" N   THR B 128 " --> pdb=" O   VAL B 124 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.780A  pdb=" N   TYR L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.935A  pdb=" N   LEU H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.719A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   THR H 121 " --> pdb=" O   GLY H  10 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY H  99 " --> pdb=" O   TYR H  33 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER H  50 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.729A  pdb=" N   ASP L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER L  68 " --> pdb=" O   ASP L  71 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.717A  pdb=" N   THR L 103 " --> pdb=" O   TYR L  87 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR L  87 " --> pdb=" O   THR L 103 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.717A  pdb=" N   THR L 103 " --> pdb=" O   TYR L  87 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR L  87 " --> pdb=" O   THR L 103 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN L  91 " --> pdb=" O   THR L  98 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)

    201 hydrogen bonds defined for protein.
    558 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: 0.57

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 744
        1.32 -     1.45: 1201
        1.45 -     1.58: 2232
        1.58 -     1.71: 0
        1.71 -     1.83: 30
  Bond restraints: 4207
  Sorted by residual:
  bond pdb=" CA  SER A  44 "
       pdb=" C   SER A  44 "
    ideal  model  delta    sigma   weight residual
    1.524  1.477  0.047 1.26e-02 6.30e+03 1.41e+01
  bond pdb=" C   SER A  44 "
       pdb=" O   SER A  44 "
    ideal  model  delta    sigma   weight residual
    1.238  1.198  0.040 1.28e-02 6.10e+03 9.87e+00
  bond pdb=" CA  SER A  44 "
       pdb=" CB  SER A  44 "
    ideal  model  delta    sigma   weight residual
    1.530  1.480  0.050 1.58e-02 4.01e+03 9.86e+00
  bond pdb=" C   PRO A  45 "
       pdb=" O   PRO A  45 "
    ideal  model  delta    sigma   weight residual
    1.235  1.210  0.025 1.30e-02 5.92e+03 3.78e+00
  bond pdb=" CA  PRO A  45 "
       pdb=" CB  PRO A  45 "
    ideal  model  delta    sigma   weight residual
    1.533  1.507  0.026 1.42e-02 4.96e+03 3.43e+00
  ... (remaining 4202 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 5599
        1.84 -     3.69: 119
        3.69 -     5.53: 13
        5.53 -     7.38: 4
        7.38 -     9.22: 2
  Bond angle restraints: 5737
  Sorted by residual:
  angle pdb=" N   GLU A  46 "
        pdb=" CA  GLU A  46 "
        pdb=" C   GLU A  46 "
      ideal   model   delta    sigma   weight residual
     108.52  117.74   -9.22 1.63e+00 3.76e-01 3.20e+01
  angle pdb=" C   PRO A  45 "
        pdb=" CA  PRO A  45 "
        pdb=" CB  PRO A  45 "
      ideal   model   delta    sigma   weight residual
     111.56  118.43   -6.87 1.65e+00 3.67e-01 1.73e+01
  angle pdb=" N   PRO L  95 "
        pdb=" CA  PRO L  95 "
        pdb=" C   PRO L  95 "
      ideal   model   delta    sigma   weight residual
     110.70  114.62   -3.92 1.22e+00 6.72e-01 1.03e+01
  angle pdb=" CA  PRO L  96 "
        pdb=" C   PRO L  96 "
        pdb=" O   PRO L  96 "
      ideal   model   delta    sigma   weight residual
     123.07  118.85    4.22 1.38e+00 5.25e-01 9.37e+00
  angle pdb=" N   SER A  44 "
        pdb=" CA  SER A  44 "
        pdb=" C   SER A  44 "
      ideal   model   delta    sigma   weight residual
     109.81  115.65   -5.84 2.21e+00 2.05e-01 6.99e+00
  ... (remaining 5732 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 2169
       17.51 -    35.02: 246
       35.02 -    52.52: 50
       52.52 -    70.03: 6
       70.03 -    87.54: 2
  Dihedral angle restraints: 2473
    sinusoidal: 971
      harmonic: 1502
  Sorted by residual:
  dihedral pdb=" CA  TYR H 107 "
           pdb=" C   TYR H 107 "
           pdb=" N   VAL H 108 "
           pdb=" CA  VAL H 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.80   17.20     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CB  GLU B  77 "
           pdb=" CG  GLU B  77 "
           pdb=" CD  GLU B  77 "
           pdb=" OE1 GLU B  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.54   87.54     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU A  77 "
           pdb=" CG  GLU A  77 "
           pdb=" CD  GLU A  77 "
           pdb=" OE1 GLU A  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.42   87.42     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 2470 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 558
       0.068 -    0.136: 66
       0.136 -    0.204: 3
       0.204 -    0.271: 0
       0.271 -    0.339: 1
  Chirality restraints: 628
  Sorted by residual:
  chirality pdb=" CA  PRO A  45 "
            pdb=" N   PRO A  45 "
            pdb=" C   PRO A  45 "
            pdb=" CB  PRO A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.38    0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" CA  SER A  44 "
            pdb=" N   SER A  44 "
            pdb=" C   SER A  44 "
            pdb=" CB  SER A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ASN B  75 "
            pdb=" N   ASN B  75 "
            pdb=" C   ASN B  75 "
            pdb=" CB  ASN B  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.94e-01
  ... (remaining 625 not shown)

  Planarity restraints: 736
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  42 "    0.021 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   LEU A  42 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   LEU A  42 "    0.026 2.00e-02 2.50e+03
        pdb=" N   GLU A  43 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H  40 "    0.045 5.00e-02 4.00e+02   6.73e-02 7.24e+00
        pdb=" N   PRO H  41 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  44 "    0.028 5.00e-02 4.00e+02   4.25e-02 2.89e+00
        pdb=" N   PRO B  45 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B  45 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  45 "    0.024 5.00e-02 4.00e+02
  ... (remaining 733 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 102
        2.70 -     3.25: 3809
        3.25 -     3.80: 5967
        3.80 -     4.35: 7404
        4.35 -     4.90: 13306
  Nonbonded interactions: 30588
  Sorted by model distance:
  nonbonded pdb=" N   GLU A  40 "
            pdb=" OE1 GLU A  40 "
     model   vdw
     2.149 3.120
  nonbonded pdb=" OE1 GLU A   8 "
            pdb=" NH1 ARG B  56 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OE2 GLU A  77 "
            pdb=" NH2 ARG L  27 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   GLU A  40 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" NH1 ARG A  56 "
            pdb=" OE1 GLU B   8 "
     model   vdw
     2.292 3.120
  ... (remaining 30583 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' and (resid 1 through 45 or (resid 46 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 47 through 132 or (resid 133 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 134 through 141))
}

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:             0.570
  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:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.330
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
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      :  0.006   0.118   4210  Z= 0.294
  Angle     :  0.735  21.810   5743  Z= 0.399
  Chirality :  0.046   0.339    628
  Planarity :  0.005   0.067    736
  Dihedral  : 15.029  87.541   1504
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.81 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.38), residues: 511
  helix:  0.50 (0.37), residues: 197
  sheet: -0.25 (0.54), residues: 100
  loop :  0.72 (0.46), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  55 
 TYR   0.009   0.001   TYR A  88 
 PHE   0.014   0.002   PHE A 110 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 4207)
  covalent geometry    : angle       0.67310 ( 5737)
  SS BOND              : bond        0.06836 (    3)
  SS BOND              : angle       9.18571 (    6)
  hydrogen bonds       : bond        0.21194 (  198)
  hydrogen bonds       : angle       7.67862 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.150 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0918
  time to fit residues: 5.7134
Evaluate side-chains
  48 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0170
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.136061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.100027 restraints weight = 5023.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.77
r_work: 0.2848 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.0970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4210  Z= 0.136
  Angle     :  0.560   8.223   5743  Z= 0.295
  Chirality :  0.039   0.127    628
  Planarity :  0.005   0.042    736
  Dihedral  :  4.255  16.910    576
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 22.90 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.39), residues: 511
  helix:  0.89 (0.37), residues: 202
  sheet:  0.33 (0.49), residues: 119
  loop :  1.11 (0.50), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  56 
 TYR   0.008   0.001   TYR A 118 
 PHE   0.010   0.001   PHE A  97 
 TRP   0.009   0.001   TRP A 125 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4207)
  covalent geometry    : angle       0.55881 ( 5737)
  SS BOND              : bond        0.00469 (    3)
  SS BOND              : angle       1.37448 (    6)
  hydrogen bonds       : bond        0.05166 (  198)
  hydrogen bonds       : angle       5.32862 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 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: 18
    poor density    : 49
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8495 (t) cc_final: 0.8190 (m)
REVERT: A  100 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6357 (mp)
REVERT: L   55 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7805 (mtm-85)
  outliers start: 18
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0737
  time to fit residues: 5.8650
Evaluate side-chains
  60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue  112 GLU
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   64 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0980
   chunk 37 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.137303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.101046 restraints weight = 4984.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.77
r_work: 0.2868 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4210  Z= 0.122
  Angle     :  0.518   7.940   5743  Z= 0.268
  Chirality :  0.038   0.126    628
  Planarity :  0.004   0.042    736
  Dihedral  :  3.983  16.230    576
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 24.94 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.39), residues: 511
  helix:  1.01 (0.37), residues: 205
  sheet:  0.72 (0.57), residues: 96
  loop :  1.08 (0.47), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  55 
 TYR   0.007   0.001   TYR B  38 
 PHE   0.007   0.001   PHE A  18 
 TRP   0.006   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4207)
  covalent geometry    : angle       0.51652 ( 5737)
  SS BOND              : bond        0.00444 (    3)
  SS BOND              : angle       1.34291 (    6)
  hydrogen bonds       : bond        0.04521 (  198)
  hydrogen bonds       : angle       4.85413 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8485 (t) cc_final: 0.8180 (m)
REVERT: A   37 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6878 (mt)
REVERT: A  100 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6163 (mp)
REVERT: H   51 MET cc_start: 0.7977 (ttm) cc_final: 0.7758 (ttt)
REVERT: L   55 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7793 (mtm-85)
  outliers start: 16
  outliers final: 9
  residues processed: 62
  average time/residue: 0.0764
  time to fit residues: 5.9513
Evaluate side-chains
  60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  112 GLU
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0570
   chunk 38 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.137054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.101401 restraints weight = 4988.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 2.71
r_work: 0.2870 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4210  Z= 0.125
  Angle     :  0.509   7.890   5743  Z= 0.263
  Chirality :  0.038   0.123    628
  Planarity :  0.004   0.042    736
  Dihedral  :  3.938  15.861    576
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 23.58 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.39), residues: 511
  helix:  1.11 (0.37), residues: 205
  sheet:  0.94 (0.54), residues: 106
  loop :  1.14 (0.48), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  55 
 TYR   0.010   0.001   TYR B  38 
 PHE   0.007   0.001   PHE A  18 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4207)
  covalent geometry    : angle       0.50767 ( 5737)
  SS BOND              : bond        0.00678 (    3)
  SS BOND              : angle       1.05010 (    6)
  hydrogen bonds       : bond        0.04274 (  198)
  hydrogen bonds       : angle       4.69724 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 51
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8497 (t) cc_final: 0.8182 (m)
REVERT: A  100 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6185 (mp)
REVERT: H   51 MET cc_start: 0.7929 (ttm) cc_final: 0.7715 (ttt)
  outliers start: 20
  outliers final: 13
  residues processed: 68
  average time/residue: 0.0730
  time to fit residues: 6.3518
Evaluate side-chains
  65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASP
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  112 GLU
Chi-restraints excluded: chain H residue  118 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 46 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.133149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.097963 restraints weight = 5063.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.61
r_work: 0.2825 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4210  Z= 0.208
  Angle     :  0.577   8.332   5743  Z= 0.299
  Chirality :  0.041   0.124    628
  Planarity :  0.004   0.044    736
  Dihedral  :  4.062  16.146    576
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 24.04 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.39), residues: 511
  helix:  1.02 (0.36), residues: 202
  sheet:  0.97 (0.54), residues: 105
  loop :  0.98 (0.47), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  56 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.012   0.001   PHE A  18 
 TRP   0.008   0.001   TRP B 125 
 HIS   0.005   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 4207)
  covalent geometry    : angle       0.57655 ( 5737)
  SS BOND              : bond        0.00620 (    3)
  SS BOND              : angle       1.15823 (    6)
  hydrogen bonds       : bond        0.05199 (  198)
  hydrogen bonds       : angle       4.86237 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 49
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8545 (t) cc_final: 0.8215 (m)
REVERT: A   76 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7129 (mp)
REVERT: A  100 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6293 (mp)
REVERT: H   51 MET cc_start: 0.8013 (ttm) cc_final: 0.7745 (ttt)
REVERT: L   55 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7811 (mtm-85)
  outliers start: 24
  outliers final: 19
  residues processed: 68
  average time/residue: 0.0678
  time to fit residues: 5.9419
Evaluate side-chains
  72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASP
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  112 GLU
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   29 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    0.1980
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0070
   chunk 40 optimal weight:    0.0770
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.3356

-------------------------------------------------------------------------------
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 = 0.3449 r_free = 0.3449 target = 0.138479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.102519 restraints weight = 5044.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.76
r_work: 0.2887 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   4210  Z= 0.105
  Angle     :  0.509   7.538   5743  Z= 0.261
  Chirality :  0.038   0.143    628
  Planarity :  0.004   0.043    736
  Dihedral  :  3.920  15.465    576
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 25.85 %
    Favored  : 70.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.39), residues: 511
  helix:  1.17 (0.37), residues: 205
  sheet:  1.18 (0.55), residues: 105
  loop :  1.10 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.007   0.001   PHE B   9 
 TRP   0.008   0.001   TRP B 102 
 HIS   0.002   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 4207)
  covalent geometry    : angle       0.50815 ( 5737)
  SS BOND              : bond        0.00729 (    3)
  SS BOND              : angle       1.06678 (    6)
  hydrogen bonds       : bond        0.03846 (  198)
  hydrogen bonds       : angle       4.54033 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 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: 17
    poor density    : 50
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8549 (t) cc_final: 0.8245 (m)
REVERT: A  100 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6227 (mp)
REVERT: H   51 MET cc_start: 0.7838 (ttm) cc_final: 0.7578 (ttt)
REVERT: L   55 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.7767 (mtm-85)
  outliers start: 17
  outliers final: 14
  residues processed: 65
  average time/residue: 0.0706
  time to fit residues: 5.7472
Evaluate side-chains
  65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASP
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  112 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.136589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.100506 restraints weight = 5120.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.77
r_work: 0.2861 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4210  Z= 0.138
  Angle     :  0.524   7.895   5743  Z= 0.267
  Chirality :  0.039   0.122    628
  Planarity :  0.004   0.043    736
  Dihedral  :  3.894  15.232    576
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 24.26 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.39), residues: 511
  helix:  1.16 (0.37), residues: 205
  sheet:  1.16 (0.55), residues: 105
  loop :  1.06 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.008   0.001   PHE A  18 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.004   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4207)
  covalent geometry    : angle       0.52314 ( 5737)
  SS BOND              : bond        0.00535 (    3)
  SS BOND              : angle       0.99896 (    6)
  hydrogen bonds       : bond        0.04261 (  198)
  hydrogen bonds       : angle       4.56712 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8493 (t) cc_final: 0.8177 (m)
REVERT: A   76 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6809 (mp)
REVERT: A  100 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6205 (mp)
REVERT: H   51 MET cc_start: 0.7877 (ttm) cc_final: 0.7598 (ttt)
REVERT: L   55 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7775 (mtm-85)
  outliers start: 20
  outliers final: 17
  residues processed: 62
  average time/residue: 0.0737
  time to fit residues: 5.8561
Evaluate side-chains
  67 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASP
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  112 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.136351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.100483 restraints weight = 5029.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.72
r_work: 0.2860 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4210  Z= 0.140
  Angle     :  0.533   7.898   5743  Z= 0.273
  Chirality :  0.039   0.161    628
  Planarity :  0.004   0.043    736
  Dihedral  :  3.906  14.986    576
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 24.26 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.39), residues: 511
  helix:  1.18 (0.37), residues: 205
  sheet:  1.19 (0.55), residues: 105
  loop :  1.06 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.008   0.001   PHE B   9 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4207)
  covalent geometry    : angle       0.53191 ( 5737)
  SS BOND              : bond        0.00493 (    3)
  SS BOND              : angle       0.98318 (    6)
  hydrogen bonds       : bond        0.04306 (  198)
  hydrogen bonds       : angle       4.54558 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8503 (t) cc_final: 0.8191 (m)
REVERT: A   76 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6929 (mp)
REVERT: A  100 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6221 (mp)
REVERT: H   18 MET cc_start: 0.7047 (tpt) cc_final: 0.6722 (tpt)
REVERT: H   51 MET cc_start: 0.7872 (ttm) cc_final: 0.7594 (ttt)
REVERT: H   90 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7303 (t0)
REVERT: L   55 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.7771 (mtm-85)
  outliers start: 21
  outliers final: 17
  residues processed: 63
  average time/residue: 0.0703
  time to fit residues: 5.6629
Evaluate side-chains
  67 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 47
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASP
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  112 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3423 r_free = 0.3423 target = 0.136297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.100327 restraints weight = 5088.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 2.73
r_work: 0.2858 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4210  Z= 0.137
  Angle     :  0.527   7.897   5743  Z= 0.270
  Chirality :  0.039   0.144    628
  Planarity :  0.004   0.043    736
  Dihedral  :  3.888  14.898    576
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 24.04 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.39), residues: 511
  helix:  1.18 (0.37), residues: 205
  sheet:  1.17 (0.55), residues: 105
  loop :  1.09 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.009   0.001   PHE B   9 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 4207)
  covalent geometry    : angle       0.52676 ( 5737)
  SS BOND              : bond        0.00499 (    3)
  SS BOND              : angle       0.99897 (    6)
  hydrogen bonds       : bond        0.04282 (  198)
  hydrogen bonds       : angle       4.53232 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 49
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8492 (t) cc_final: 0.8179 (m)
REVERT: A   76 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6941 (mp)
REVERT: A  100 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6203 (mp)
REVERT: H   18 MET cc_start: 0.6918 (tpt) cc_final: 0.6586 (tpt)
REVERT: H   51 MET cc_start: 0.7868 (ttm) cc_final: 0.7579 (ttt)
REVERT: H   90 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7316 (t0)
REVERT: L   55 ARG cc_start: 0.8317 (mtm-85) cc_final: 0.7759 (mtm-85)
  outliers start: 23
  outliers final: 18
  residues processed: 66
  average time/residue: 0.0626
  time to fit residues: 5.3390
Evaluate side-chains
  70 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 49
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASP
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  112 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.136380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.100754 restraints weight = 4933.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.69
r_work: 0.2862 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   4210  Z= 0.134
  Angle     :  0.528   7.900   5743  Z= 0.271
  Chirality :  0.039   0.173    628
  Planarity :  0.004   0.043    736
  Dihedral  :  3.875  14.888    576
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 24.49 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.39), residues: 511
  helix:  1.22 (0.37), residues: 205
  sheet:  1.19 (0.55), residues: 105
  loop :  1.11 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  55 
 TYR   0.011   0.001   TYR B  38 
 PHE   0.009   0.001   PHE B   9 
 TRP   0.006   0.001   TRP A  62 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 4207)
  covalent geometry    : angle       0.52746 ( 5737)
  SS BOND              : bond        0.00484 (    3)
  SS BOND              : angle       1.00361 (    6)
  hydrogen bonds       : bond        0.04246 (  198)
  hydrogen bonds       : angle       4.50957 (  558)

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

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

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1022 Ramachandran restraints generated.
    511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   17 SER cc_start: 0.8549 (t) cc_final: 0.8246 (m)
REVERT: A   76 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6889 (mp)
REVERT: A  100 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6162 (mp)
REVERT: H   18 MET cc_start: 0.6875 (tpt) cc_final: 0.6553 (tpt)
REVERT: H   51 MET cc_start: 0.7856 (ttm) cc_final: 0.7563 (ttt)
REVERT: H   90 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7312 (t0)
REVERT: L   55 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.7755 (mtm-85)
REVERT: L   64 SER cc_start: 0.7230 (m) cc_final: 0.6354 (p)
  outliers start: 21
  outliers final: 18
  residues processed: 64
  average time/residue: 0.0704
  time to fit residues: 5.7896
Evaluate side-chains
  69 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ASP
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain B residue   18 PHE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain H residue    2 LEU
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   17 HIS
Chi-restraints excluded: chain H residue   28 THR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain H residue  112 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0370
   chunk 12 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.3441 r_free = 0.3441 target = 0.137985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.101990 restraints weight = 5023.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.73
r_work: 0.2881 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   4210  Z= 0.116
  Angle     :  0.520   7.763   5743  Z= 0.266
  Chirality :  0.038   0.171    628
  Planarity :  0.004   0.043    736
  Dihedral  :  3.837  14.795    576
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 25.62 %
    Favored  : 70.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.39), residues: 511
  helix:  1.25 (0.37), residues: 205
  sheet:  1.22 (0.55), residues: 105
  loop :  1.16 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.012   0.001   TYR B  38 
 PHE   0.009   0.001   PHE B   9 
 TRP   0.006   0.001   TRP B 102 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4207)
  covalent geometry    : angle       0.51887 ( 5737)
  SS BOND              : bond        0.00445 (    3)
  SS BOND              : angle       0.97286 (    6)
  hydrogen bonds       : bond        0.03979 (  198)
  hydrogen bonds       : angle       4.41544 (  558)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1099.17 seconds
wall clock time: 19 minutes 30.91 seconds (1170.91 seconds total)