Starting phenix.real_space_refine
on Fri Aug 22 14:21:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zrr_60403/08_2025/8zrr_60403.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zrr_60403/08_2025/8zrr_60403.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zrr_60403/08_2025/8zrr_60403.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zrr_60403/08_2025/8zrr_60403.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zrr_60403/08_2025/8zrr_60403.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zrr_60403/08_2025/8zrr_60403.cif"
  }
  resolution = 3.61
  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=   0.003 sd=   0.036
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      18      5.16       5
     C    2603      2.51       5
     N     686      2.21       5
     O     758      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4065
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "h"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 941
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "l"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 880
          Classifications: {'peptide': 114}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 106}
    Chain: "A"
      Number of atoms: 1118
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1118
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 11, 'TRANS': 128}
    Chain: "B"
      Number of atoms: 1126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1126
          Classifications: {'peptide': 141}
          Link IDs: {'PTRANS': 11, 'TRANS': 129}
  Time building chain proxies: 1.22, per 1000 atoms: 0.30
  Number of scatterers: 4065
  At special positions: 0
  Unit cell: (99.882, 69.81, 114.918, 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      18     16.00
     O     758      8.00
     N     686      7.00
     C    2603      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS h  22 " - pdb=" SG  CYS h  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS l  23 " - pdb=" SG  CYS l  93 " distance=2.04

  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: 0.24
  Conformation dependent library (CDL) restraints added in 132.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  958

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 6 sheets defined
      45.5% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'h' and resid 28 through 32
    Processing helix  chain 'h' and resid 87 through 91
      removed outlier: 3.750A  pdb=" N   THR h  91 " --> pdb=" O   ALA h  88 " (cutoff:3.500A)
    Processing helix  chain 'l' and resid 84 through 88
      removed outlier: 4.144A  pdb=" N   VAL l  88 " --> pdb=" O   ALA l  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 12 through 18
      removed outlier: 4.223A  pdb=" N   PHE A  18 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 43
      removed outlier: 3.503A  pdb=" N   LEU A  30 " --> pdb=" O   SER A  26 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   GLU A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   ALA A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 75
    Processing helix  chain 'A' and resid 78 through 92
      removed outlier: 3.672A  pdb=" N   ARG A  82 " --> pdb=" O   ASP A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 110
    Processing helix  chain 'A' and resid 111 through 128
      removed outlier: 4.008A  pdb=" N   GLY A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   TRP A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ARG A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 10
      removed outlier: 3.819A  pdb=" N   GLU B   8 " --> pdb=" O   PRO B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 18
      removed outlier: 3.928A  pdb=" N   LEU B  16 " --> pdb=" O   SER B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 44
      removed outlier: 3.524A  pdb=" N   ARG B  39 " --> pdb=" O   SER B  35 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   GLU B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ALA B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  39 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   SER B  44 " --> pdb=" O   GLU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 75
      removed outlier: 3.898A  pdb=" N   THR B  53 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 91
      removed outlier: 4.091A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 111
      removed outlier: 4.197A  pdb=" N   ILE B  97 " --> pdb=" O   MET B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 128
      removed outlier: 3.652A  pdb=" N   VAL B 115 " --> pdb=" O   GLY B 111 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 116 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   GLU B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   THR B 128 " --> pdb=" O   VAL B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 133
      removed outlier: 3.506A  pdb=" N   TYR B 132 " --> pdb=" O   PRO B 129 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'h' and resid 3 through 7
      removed outlier: 4.121A  pdb=" N   GLN h   3 " --> pdb=" O   SER h  25 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER h  25 " --> pdb=" O   GLN h   3 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU h  81 " --> pdb=" O   LEU h  20 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   CYS h  22 " --> pdb=" O   LEU h  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'h' and resid 10 through 12
      removed outlier: 7.100A  pdb=" N   MET h  34 " --> pdb=" O   TYR h  50 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   TYR h  50 " --> pdb=" O   MET h  34 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   TRP h  36 " --> pdb=" O   LEU h  48 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   TYR h  50 " --> pdb=" O   ASP h  59 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP h  59 " --> pdb=" O   TYR h  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'h' and resid 10 through 12
    Processing sheet with id=AA4, first strand: chain 'l' and resid 4 through 7
      removed outlier: 3.574A  pdb=" N   PHE l  76 " --> pdb=" O   CYS l  23 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR l  77 " --> pdb=" O   SER l  70 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER l  70 " --> pdb=" O   THR l  77 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'l' and resid 10 through 12
      removed outlier: 3.696A  pdb=" N   LEU l  11 " --> pdb=" O   LYS l 108 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU l 110 " --> pdb=" O   LEU l  11 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   MET l  94 " --> pdb=" O   SER l  39 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER l  39 " --> pdb=" O   MET l  94 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   PHE l  38 " --> pdb=" O   TYR l  54 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   TYR l  54 " --> pdb=" O   PHE l  38 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   TRP l  40 " --> pdb=" O   LEU l  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'l' and resid 10 through 12
      removed outlier: 3.696A  pdb=" N   LEU l  11 " --> pdb=" O   LYS l 108 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU l 110 " --> pdb=" O   LEU l  11 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   THR l 102 " --> pdb=" O   GLN l  95 " (cutoff:3.500A)

    206 hydrogen bonds defined for protein.
    540 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: 0.44

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 669
        1.30 -     1.43: 1175
        1.43 -     1.56: 2305
        1.56 -     1.69: 2
        1.69 -     1.81: 26
  Bond restraints: 4177
  Sorted by residual:
  bond pdb=" C   ARG B  98 "
       pdb=" N   GLN B  99 "
    ideal  model  delta    sigma   weight residual
    1.335  1.440 -0.106 1.25e-02 6.40e+03 7.18e+01
  bond pdb=" C   GLY h  26 "
       pdb=" N   PHE h  27 "
    ideal  model  delta    sigma   weight residual
    1.330  1.230  0.100 1.26e-02 6.30e+03 6.26e+01
  bond pdb=" C   LEU A 119 "
       pdb=" N   VAL A 120 "
    ideal  model  delta    sigma   weight residual
    1.333  1.237  0.097 1.24e-02 6.50e+03 6.11e+01
  bond pdb=" C   CYS B  48 "
       pdb=" N   SER B  49 "
    ideal  model  delta    sigma   weight residual
    1.331  1.419 -0.087 1.18e-02 7.18e+03 5.49e+01
  bond pdb=" C   SER A  26 "
       pdb=" N   ILE A  27 "
    ideal  model  delta    sigma   weight residual
    1.334  1.421 -0.087 1.22e-02 6.72e+03 5.03e+01
  ... (remaining 4172 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 5272
        1.69 -     3.37: 312
        3.37 -     5.06: 79
        5.06 -     6.74: 27
        6.74 -     8.43: 4
  Bond angle restraints: 5694
  Sorted by residual:
  angle pdb=" CA  CYS B  48 "
        pdb=" C   CYS B  48 "
        pdb=" N   SER B  49 "
      ideal   model   delta    sigma   weight residual
     119.52  113.93    5.59 7.90e-01 1.60e+00 5.00e+01
  angle pdb=" N   GLU A  77 "
        pdb=" CA  GLU A  77 "
        pdb=" C   GLU A  77 "
      ideal   model   delta    sigma   weight residual
     111.28  117.54   -6.26 1.09e+00 8.42e-01 3.30e+01
  angle pdb=" CA  ARG B  98 "
        pdb=" C   ARG B  98 "
        pdb=" N   GLN B  99 "
      ideal   model   delta    sigma   weight residual
     117.30  110.74    6.56 1.16e+00 7.43e-01 3.20e+01
  angle pdb=" C   SER B  49 "
        pdb=" N   PRO B  50 "
        pdb=" CA  PRO B  50 "
      ideal   model   delta    sigma   weight residual
     119.28  125.45   -6.17 1.10e+00 8.26e-01 3.14e+01
  angle pdb=" O   ARG B  98 "
        pdb=" C   ARG B  98 "
        pdb=" N   GLN B  99 "
      ideal   model   delta    sigma   weight residual
     122.12  127.92   -5.80 1.06e+00 8.90e-01 3.00e+01
  ... (remaining 5689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.32: 2094
       16.32 -    32.64: 251
       32.64 -    48.97: 83
       48.97 -    65.29: 22
       65.29 -    81.61: 4
  Dihedral angle restraints: 2454
    sinusoidal: 962
      harmonic: 1492
  Sorted by residual:
  dihedral pdb=" C   ASP B  78 "
           pdb=" N   ASP B  78 "
           pdb=" CA  ASP B  78 "
           pdb=" CB  ASP B  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.14   -8.46     0      2.50e+00 1.60e-01 1.15e+01
  dihedral pdb=" CA  GLN h  39 "
           pdb=" C   GLN h  39 "
           pdb=" N   VAL h  40 "
           pdb=" CA  VAL h  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.71   16.29     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  LEU A  37 "
           pdb=" C   LEU A  37 "
           pdb=" N   TYR A  38 "
           pdb=" CA  TYR A  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.36  -15.64     0      5.00e+00 4.00e-02 9.79e+00
  ... (remaining 2451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 445
       0.045 -    0.090: 106
       0.090 -    0.134: 59
       0.134 -    0.179: 6
       0.179 -    0.224: 8
  Chirality restraints: 624
  Sorted by residual:
  chirality pdb=" CA  LEU A  31 "
            pdb=" N   LEU A  31 "
            pdb=" C   LEU A  31 "
            pdb=" CB  LEU A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE A  97 "
            pdb=" N   ILE A  97 "
            pdb=" C   ILE A  97 "
            pdb=" CB  ILE A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  GLN l  95 "
            pdb=" N   GLN l  95 "
            pdb=" C   GLN l  95 "
            pdb=" CB  GLN l  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 621 not shown)

  Planarity restraints: 731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR l  14 "   -0.074 5.00e-02 4.00e+02   1.08e-01 1.85e+01
        pdb=" N   PRO l  15 "    0.186 5.00e-02 4.00e+02
        pdb=" CA  PRO l  15 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO l  15 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  74 "   -0.019 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" C   SER B  74 "    0.066 2.00e-02 2.50e+03
        pdb=" O   SER B  74 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ASN B  75 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY h  99 "   -0.013 2.00e-02 2.50e+03   2.72e-02 7.39e+00
        pdb=" C   GLY h  99 "    0.047 2.00e-02 2.50e+03
        pdb=" O   GLY h  99 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   PHE h 100 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 728 not shown)

  Histogram of nonbonded interaction distances:
        1.34 -     2.06: 3
        2.06 -     2.77: 750
        2.77 -     3.48: 5707
        3.48 -     4.19: 8607
        4.19 -     4.90: 14908
  Nonbonded interactions: 29975
  Sorted by model distance:
  nonbonded pdb=" OH  TYR h  53 "
            pdb=" OE1 GLU B  83 "
     model   vdw
     1.345 3.040
  nonbonded pdb=" OD1 ASN l  33 "
            pdb=" CD1 LEU A  84 "
     model   vdw
     1.710 3.460
  nonbonded pdb=" OH  TYR h  53 "
            pdb=" CD  GLU B  83 "
     model   vdw
     2.039 3.270
  nonbonded pdb=" O   ALA A  80 "
            pdb=" N   GLU A  83 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" OD2 ASP A  78 "
            pdb=" N   SER A  81 "
     model   vdw
     2.284 3.120
  ... (remaining 29970 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 3 through 142)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.710
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
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      :  0.008   0.106   4179  Z= 0.600
  Angle     :  0.992   8.431   5698  Z= 0.694
  Chirality :  0.053   0.224    624
  Planarity :  0.007   0.108    731
  Dihedral  : 16.463  81.610   1490
  Min Nonbonded Distance : 1.345

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  3.54 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 27.13 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.38), residues: 508
  helix:  1.03 (0.38), residues: 173
  sheet:  1.02 (0.59), residues: 81
  loop : -0.31 (0.41), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  56 
 TYR   0.015   0.002   TYR A   6 
 PHE   0.029   0.002   PHE l  38 
 TRP   0.015   0.002   TRP B  71 
 HIS   0.004   0.001   HIS h  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00824 ( 4177)
  covalent geometry    : angle       0.99143 ( 5694)
  SS BOND              : bond        0.00652 (    2)
  SS BOND              : angle       1.51588 (    4)
  hydrogen bonds       : bond        0.22649 (  197)
  hydrogen bonds       : angle       8.44558 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: h   36 TRP cc_start: 0.7281 (m100) cc_final: 0.7057 (m100)
REVERT: h   38 ARG cc_start: 0.6982 (tmm-80) cc_final: 0.6739 (ttp-170)
REVERT: h   39 GLN cc_start: 0.7120 (tt0) cc_final: 0.6877 (tm-30)
REVERT: h   47 TRP cc_start: 0.8430 (t60) cc_final: 0.7896 (t60)
REVERT: h   69 THR cc_start: 0.7607 (t) cc_final: 0.7304 (p)
REVERT: h   83 MET cc_start: 0.7099 (mtm) cc_final: 0.6618 (mtm)
REVERT: l   68 SER cc_start: 0.8016 (t) cc_final: 0.7594 (p)
REVERT: l   78 LEU cc_start: 0.8672 (tp) cc_final: 0.8373 (tp)
REVERT: A   31 LEU cc_start: 0.8283 (mm) cc_final: 0.7922 (mm)
REVERT: A  124 VAL cc_start: 0.8249 (t) cc_final: 0.8036 (p)
REVERT: B   19 LEU cc_start: 0.8123 (tp) cc_final: 0.7777 (tp)
REVERT: B   38 TYR cc_start: 0.7284 (m-80) cc_final: 0.6905 (m-10)
REVERT: B   42 LEU cc_start: 0.8095 (tt) cc_final: 0.7882 (tp)
REVERT: B   66 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7233 (mmt)
REVERT: B  103 PHE cc_start: 0.8418 (t80) cc_final: 0.8064 (t80)
  outliers start: 17
  outliers final: 7
  residues processed: 178
  average time/residue: 0.0453
  time to fit residues: 10.4828
Evaluate side-chains
  162 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 154
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue  106 LEU
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   78 ASP
Chi-restraints excluded: chain B residue  108 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    0.0470
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 19 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0020
   overall best weight:    0.3086

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

Flipped N/Q/H residues before XYZ refinement:
l  95 GLN
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.136949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.119652 restraints weight = 8327.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.123827 restraints weight = 4489.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.126723 restraints weight = 2778.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.128796 restraints weight = 1880.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.130231 restraints weight = 1355.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4179  Z= 0.135
  Angle     :  0.658   6.630   5698  Z= 0.336
  Chirality :  0.043   0.138    624
  Planarity :  0.005   0.056    731
  Dihedral  :  6.789  59.533    581
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 23.99 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.38), residues: 508
  helix:  1.89 (0.39), residues: 177
  sheet:  0.57 (0.57), residues: 92
  loop : -0.04 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG h  38 
 TYR   0.022   0.002   TYR h 101 
 PHE   0.013   0.002   PHE l  67 
 TRP   0.009   0.002   TRP B  71 
 HIS   0.006   0.001   HIS B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4177)
  covalent geometry    : angle       0.65806 ( 5694)
  SS BOND              : bond        0.00337 (    2)
  SS BOND              : angle       0.55119 (    4)
  hydrogen bonds       : bond        0.04504 (  197)
  hydrogen bonds       : angle       5.79270 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: h   47 TRP cc_start: 0.8233 (t60) cc_final: 0.7900 (t60)
REVERT: h   70 ILE cc_start: 0.8524 (tt) cc_final: 0.8272 (tt)
REVERT: h   83 MET cc_start: 0.6718 (mtm) cc_final: 0.6327 (ttm)
REVERT: h  111 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7478 (tm-30)
REVERT: l   33 ASN cc_start: 0.7270 (t0) cc_final: 0.7057 (t0)
REVERT: l   68 SER cc_start: 0.8189 (t) cc_final: 0.7758 (p)
REVERT: l   78 LEU cc_start: 0.8740 (tp) cc_final: 0.8461 (tp)
REVERT: l   94 MET cc_start: 0.7035 (tmt) cc_final: 0.6793 (tmt)
REVERT: l   95 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7105 (tm-30)
REVERT: A   37 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7824 (tp)
REVERT: A   61 CYS cc_start: 0.8755 (m) cc_final: 0.8019 (m)
REVERT: A   66 MET cc_start: 0.7524 (tpp) cc_final: 0.7198 (mpp)
REVERT: A  108 LEU cc_start: 0.8573 (tp) cc_final: 0.8128 (tp)
REVERT: B   19 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7815 (tp)
REVERT: B   38 TYR cc_start: 0.7663 (m-80) cc_final: 0.7372 (m-10)
REVERT: B   83 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5861 (mt-10)
  outliers start: 23
  outliers final: 9
  residues processed: 161
  average time/residue: 0.0456
  time to fit residues: 9.6619
Evaluate side-chains
  162 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue  115 VAL
Chi-restraints excluded: chain h residue  116 ILE
Chi-restraints excluded: chain l residue   95 GLN
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0050
   chunk 26 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.133577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.115725 restraints weight = 8137.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.119973 restraints weight = 4346.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.122812 restraints weight = 2686.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.124865 restraints weight = 1833.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.126310 restraints weight = 1336.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4179  Z= 0.132
  Angle     :  0.609   7.322   5698  Z= 0.310
  Chirality :  0.043   0.260    624
  Planarity :  0.005   0.042    731
  Dihedral  :  5.794  59.392    571
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 24.44 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.38), residues: 508
  helix:  2.38 (0.38), residues: 176
  sheet:  0.51 (0.56), residues: 92
  loop :  0.06 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG l  66 
 TYR   0.015   0.002   TYR l  54 
 PHE   0.019   0.002   PHE B 103 
 TRP   0.019   0.002   TRP h  36 
 HIS   0.004   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4177)
  covalent geometry    : angle       0.60909 ( 5694)
  SS BOND              : bond        0.00348 (    2)
  SS BOND              : angle       0.57246 (    4)
  hydrogen bonds       : bond        0.04269 (  197)
  hydrogen bonds       : angle       5.14459 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: h   38 ARG cc_start: 0.7333 (ttp-170) cc_final: 0.7120 (ttp-170)
REVERT: h   43 LYS cc_start: 0.8663 (mmtt) cc_final: 0.8335 (mmtt)
REVERT: h   47 TRP cc_start: 0.8258 (t60) cc_final: 0.7900 (t60)
REVERT: h   70 ILE cc_start: 0.8509 (tt) cc_final: 0.8223 (tt)
REVERT: h   83 MET cc_start: 0.7090 (mtm) cc_final: 0.6867 (mtm)
REVERT: h  111 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7490 (tm-30)
REVERT: l   33 ASN cc_start: 0.7438 (t0) cc_final: 0.7101 (t0)
REVERT: l   68 SER cc_start: 0.8160 (t) cc_final: 0.7701 (p)
REVERT: l   78 LEU cc_start: 0.8715 (tp) cc_final: 0.8464 (tp)
REVERT: l   94 MET cc_start: 0.7158 (tmt) cc_final: 0.6798 (tmt)
REVERT: A   37 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7810 (tp)
REVERT: A   66 MET cc_start: 0.7577 (tpp) cc_final: 0.7290 (tpp)
REVERT: A  101 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8094 (mp)
REVERT: A  108 LEU cc_start: 0.8579 (tp) cc_final: 0.8147 (tp)
REVERT: A  110 PHE cc_start: 0.8547 (m-80) cc_final: 0.8275 (m-80)
REVERT: B   19 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7825 (tp)
REVERT: B   39 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.7072 (mtp-110)
REVERT: B   83 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5909 (mt-10)
  outliers start: 23
  outliers final: 13
  residues processed: 153
  average time/residue: 0.0527
  time to fit residues: 10.2888
Evaluate side-chains
  163 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue   71 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue   75 SER
Chi-restraints excluded: chain A residue   28 ARG
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   39 ARG
Chi-restraints excluded: chain B residue   64 GLU
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  139 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.124733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.107121 restraints weight = 8131.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.111205 restraints weight = 4438.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.114015 restraints weight = 2780.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.115959 restraints weight = 1907.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.117418 restraints weight = 1404.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4179  Z= 0.246
  Angle     :  0.700   7.202   5698  Z= 0.376
  Chirality :  0.047   0.185    624
  Planarity :  0.006   0.061    731
  Dihedral  :  6.409  58.248    571
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 24.22 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.37), residues: 508
  helix:  1.80 (0.36), residues: 175
  sheet:  0.22 (0.54), residues: 96
  loop : -0.01 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  39 
 TYR   0.016   0.003   TYR B  38 
 PHE   0.014   0.002   PHE A  18 
 TRP   0.015   0.002   TRP B 125 
 HIS   0.005   0.002   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 4177)
  covalent geometry    : angle       0.69993 ( 5694)
  SS BOND              : bond        0.00692 (    2)
  SS BOND              : angle       1.21810 (    4)
  hydrogen bonds       : bond        0.06389 (  197)
  hydrogen bonds       : angle       5.48569 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: h   43 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8308 (mmtt)
REVERT: h   46 GLU cc_start: 0.6954 (tt0) cc_final: 0.6742 (tt0)
REVERT: h   47 TRP cc_start: 0.8323 (t60) cc_final: 0.8062 (t60)
REVERT: h   70 ILE cc_start: 0.8622 (tt) cc_final: 0.8293 (tt)
REVERT: h  111 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7471 (tm-30)
REVERT: l   33 ASN cc_start: 0.7590 (t0) cc_final: 0.7101 (t0)
REVERT: l   68 SER cc_start: 0.8241 (t) cc_final: 0.7784 (p)
REVERT: l   78 LEU cc_start: 0.8685 (tp) cc_final: 0.8467 (tp)
REVERT: l   94 MET cc_start: 0.7234 (tmt) cc_final: 0.7006 (tmt)
REVERT: l  114 THR cc_start: 0.7909 (p) cc_final: 0.7588 (t)
REVERT: A    6 TYR cc_start: 0.8195 (m-80) cc_final: 0.7876 (m-80)
REVERT: A   66 MET cc_start: 0.7742 (tpp) cc_final: 0.7461 (tpp)
REVERT: A   84 LEU cc_start: 0.8361 (tp) cc_final: 0.8156 (tp)
REVERT: B   19 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7871 (tp)
REVERT: B   24 PHE cc_start: 0.9011 (m-10) cc_final: 0.8801 (m-10)
REVERT: B   27 ILE cc_start: 0.7415 (pt) cc_final: 0.7163 (mm)
REVERT: B   71 TRP cc_start: 0.8295 (t60) cc_final: 0.7521 (t60)
REVERT: B   83 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6073 (mt-10)
REVERT: B   90 ASN cc_start: 0.8068 (t0) cc_final: 0.7749 (m-40)
REVERT: B  103 PHE cc_start: 0.8916 (t80) cc_final: 0.8433 (t80)
  outliers start: 28
  outliers final: 18
  residues processed: 168
  average time/residue: 0.0442
  time to fit residues: 9.8973
Evaluate side-chains
  181 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   11 VAL
Chi-restraints excluded: chain h residue   18 LEU
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue  116 ILE
Chi-restraints excluded: chain l residue   21 ILE
Chi-restraints excluded: chain l residue   57 SER
Chi-restraints excluded: chain l residue   75 SER
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  139 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0570
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    0.3980
   chunk 6 optimal weight:    0.0670
   chunk 3 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
** l  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.128869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.111306 restraints weight = 8090.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.115381 restraints weight = 4454.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.118212 restraints weight = 2801.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.120220 restraints weight = 1930.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.121681 restraints weight = 1413.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4179  Z= 0.123
  Angle     :  0.626   8.731   5698  Z= 0.314
  Chirality :  0.043   0.186    624
  Planarity :  0.005   0.049    731
  Dihedral  :  5.940  59.217    569
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 28.03 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.38), residues: 508
  helix:  2.25 (0.38), residues: 175
  sheet:  0.29 (0.55), residues: 97
  loop :  0.18 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG l  24 
 TYR   0.024   0.002   TYR B 118 
 PHE   0.011   0.002   PHE h  95 
 TRP   0.014   0.001   TRP l  40 
 HIS   0.004   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4177)
  covalent geometry    : angle       0.62548 ( 5694)
  SS BOND              : bond        0.00489 (    2)
  SS BOND              : angle       1.08969 (    4)
  hydrogen bonds       : bond        0.04583 (  197)
  hydrogen bonds       : angle       4.90315 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: h   43 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8259 (mmtt)
REVERT: h   47 TRP cc_start: 0.8269 (t60) cc_final: 0.7878 (t60)
REVERT: h   70 ILE cc_start: 0.8593 (tt) cc_final: 0.8237 (tt)
REVERT: h   81 LEU cc_start: 0.7590 (tp) cc_final: 0.7276 (tp)
REVERT: h   83 MET cc_start: 0.7304 (mtm) cc_final: 0.6618 (mtm)
REVERT: h  111 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7454 (tm-30)
REVERT: l   68 SER cc_start: 0.8193 (t) cc_final: 0.7872 (t)
REVERT: l  114 THR cc_start: 0.7803 (p) cc_final: 0.7486 (t)
REVERT: A   66 MET cc_start: 0.7636 (tpp) cc_final: 0.7430 (tpp)
REVERT: A  103 PHE cc_start: 0.8358 (t80) cc_final: 0.8088 (t80)
REVERT: B   19 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7630 (tt)
REVERT: B   24 PHE cc_start: 0.8974 (m-10) cc_final: 0.8619 (m-10)
REVERT: B   64 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7689 (pt0)
REVERT: B   71 TRP cc_start: 0.8300 (t60) cc_final: 0.7898 (t-100)
REVERT: B   90 ASN cc_start: 0.7993 (t0) cc_final: 0.7732 (m-40)
REVERT: B  103 PHE cc_start: 0.8773 (t80) cc_final: 0.8343 (t80)
  outliers start: 23
  outliers final: 19
  residues processed: 172
  average time/residue: 0.0575
  time to fit residues: 12.9530
Evaluate side-chains
  187 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue   45 LEU
Chi-restraints excluded: chain h residue   48 LEU
Chi-restraints excluded: chain h residue   69 THR
Chi-restraints excluded: chain h residue   71 SER
Chi-restraints excluded: chain h residue  116 ILE
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue   10 SER
Chi-restraints excluded: chain l residue   21 ILE
Chi-restraints excluded: chain l residue   50 GLN
Chi-restraints excluded: chain l residue   75 SER
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   64 GLU
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  139 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0980
   chunk 26 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0980
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
l  32 ASN
l  33 ASN
** l  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.128401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.110980 restraints weight = 8243.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.115108 restraints weight = 4499.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.117934 restraints weight = 2818.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.119884 restraints weight = 1921.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.121313 restraints weight = 1407.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
moved from start:          0.4389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4179  Z= 0.109
  Angle     :  0.634   9.567   5698  Z= 0.309
  Chirality :  0.043   0.170    624
  Planarity :  0.004   0.039    731
  Dihedral  :  5.641  59.702    569
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 28.70 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.38), residues: 508
  helix:  2.39 (0.38), residues: 176
  sheet:  0.26 (0.54), residues: 98
  loop :  0.24 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  56 
 TYR   0.029   0.002   TYR B 118 
 PHE   0.012   0.001   PHE A 110 
 TRP   0.013   0.001   TRP A 102 
 HIS   0.003   0.001   HIS B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 4177)
  covalent geometry    : angle       0.63331 ( 5694)
  SS BOND              : bond        0.00322 (    2)
  SS BOND              : angle       1.01142 (    4)
  hydrogen bonds       : bond        0.03915 (  197)
  hydrogen bonds       : angle       4.63785 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: h   43 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8206 (mmtt)
REVERT: h   47 TRP cc_start: 0.8234 (t60) cc_final: 0.7845 (t60)
REVERT: h   70 ILE cc_start: 0.8590 (tt) cc_final: 0.8228 (tt)
REVERT: h   81 LEU cc_start: 0.7444 (tp) cc_final: 0.7165 (tp)
REVERT: h   83 MET cc_start: 0.7217 (mtm) cc_final: 0.6615 (mtm)
REVERT: l   68 SER cc_start: 0.8183 (t) cc_final: 0.7841 (t)
REVERT: l  114 THR cc_start: 0.7723 (p) cc_final: 0.7406 (t)
REVERT: A   61 CYS cc_start: 0.8572 (m) cc_final: 0.7596 (t)
REVERT: A   68 LEU cc_start: 0.7584 (tp) cc_final: 0.7381 (tp)
REVERT: B   19 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7674 (tt)
REVERT: B   24 PHE cc_start: 0.8951 (m-10) cc_final: 0.8600 (m-10)
REVERT: B   27 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7122 (mm)
REVERT: B   64 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7652 (pt0)
REVERT: B   71 TRP cc_start: 0.8358 (t60) cc_final: 0.7973 (t-100)
REVERT: B   90 ASN cc_start: 0.7976 (t0) cc_final: 0.7730 (m-40)
  outliers start: 21
  outliers final: 17
  residues processed: 162
  average time/residue: 0.0576
  time to fit residues: 12.1408
Evaluate side-chains
  174 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   11 VAL
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue   48 LEU
Chi-restraints excluded: chain h residue   69 THR
Chi-restraints excluded: chain h residue   71 SER
Chi-restraints excluded: chain h residue  121 SER
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue   33 ASN
Chi-restraints excluded: chain l residue   75 SER
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   64 GLU
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  139 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
l  36 ASN
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.126475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.108636 restraints weight = 8370.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.112842 restraints weight = 4568.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.115664 restraints weight = 2867.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.117693 restraints weight = 1963.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.119132 restraints weight = 1435.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4179  Z= 0.169
  Angle     :  0.640  11.001   5698  Z= 0.321
  Chirality :  0.044   0.162    624
  Planarity :  0.005   0.040    731
  Dihedral  :  5.623  59.902    569
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 27.35 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.38), residues: 508
  helix:  2.35 (0.38), residues: 176
  sheet:  0.29 (0.53), residues: 97
  loop :  0.28 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 127 
 TYR   0.018   0.002   TYR B 118 
 PHE   0.020   0.002   PHE B 103 
 TRP   0.012   0.002   TRP A  62 
 HIS   0.005   0.001   HIS l  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4177)
  covalent geometry    : angle       0.64069 ( 5694)
  SS BOND              : bond        0.00939 (    2)
  SS BOND              : angle       0.26092 (    4)
  hydrogen bonds       : bond        0.04528 (  197)
  hydrogen bonds       : angle       4.74676 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: h   47 TRP cc_start: 0.8276 (t60) cc_final: 0.7916 (t60)
REVERT: h   70 ILE cc_start: 0.8603 (tt) cc_final: 0.8240 (tt)
REVERT: h   81 LEU cc_start: 0.7497 (tp) cc_final: 0.7189 (tp)
REVERT: h   83 MET cc_start: 0.7235 (mtm) cc_final: 0.6641 (mtm)
REVERT: h  111 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7421 (tm-30)
REVERT: l   68 SER cc_start: 0.8203 (t) cc_final: 0.7866 (t)
REVERT: l  114 THR cc_start: 0.7802 (p) cc_final: 0.7505 (t)
REVERT: A   61 CYS cc_start: 0.8527 (m) cc_final: 0.7579 (t)
REVERT: A   66 MET cc_start: 0.7795 (tpp) cc_final: 0.7432 (mpp)
REVERT: B   19 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7681 (tt)
REVERT: B   24 PHE cc_start: 0.8936 (m-10) cc_final: 0.8574 (m-10)
REVERT: B   64 GLU cc_start: 0.7966 (pt0) cc_final: 0.7670 (pt0)
REVERT: B   71 TRP cc_start: 0.8355 (t60) cc_final: 0.7964 (t-100)
REVERT: B   83 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6047 (mt-10)
REVERT: B   90 ASN cc_start: 0.8013 (t0) cc_final: 0.7771 (m-40)
REVERT: B  103 PHE cc_start: 0.8772 (t80) cc_final: 0.8323 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 170
  average time/residue: 0.0558
  time to fit residues: 12.3509
Evaluate side-chains
  180 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   11 VAL
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue   61 VAL
Chi-restraints excluded: chain h residue   69 THR
Chi-restraints excluded: chain l residue   10 SER
Chi-restraints excluded: chain l residue   33 ASN
Chi-restraints excluded: chain l residue   50 GLN
Chi-restraints excluded: chain l residue   75 SER
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain l residue  105 GLN
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  139 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0670
   chunk 26 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 43 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0370
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.128166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.110803 restraints weight = 8046.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.114942 restraints weight = 4382.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.117788 restraints weight = 2746.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.119766 restraints weight = 1872.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.121154 restraints weight = 1361.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7194
moved from start:          0.4710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4179  Z= 0.110
  Angle     :  0.662  14.391   5698  Z= 0.313
  Chirality :  0.044   0.169    624
  Planarity :  0.004   0.039    731
  Dihedral  :  5.273  56.535    569
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 27.80 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.38), residues: 508
  helix:  2.33 (0.38), residues: 176
  sheet:  0.37 (0.54), residues: 97
  loop :  0.44 (0.43), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 127 
 TYR   0.017   0.001   TYR B 118 
 PHE   0.018   0.001   PHE B 103 
 TRP   0.012   0.001   TRP A 102 
 HIS   0.003   0.001   HIS A 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 4177)
  covalent geometry    : angle       0.66212 ( 5694)
  SS BOND              : bond        0.00605 (    2)
  SS BOND              : angle       0.28788 (    4)
  hydrogen bonds       : bond        0.03902 (  197)
  hydrogen bonds       : angle       4.54516 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: h    2 VAL cc_start: 0.8888 (m) cc_final: 0.8611 (t)
REVERT: h   47 TRP cc_start: 0.8232 (t60) cc_final: 0.7849 (t60)
REVERT: h   70 ILE cc_start: 0.8581 (tt) cc_final: 0.8221 (tt)
REVERT: h   81 LEU cc_start: 0.7340 (tp) cc_final: 0.7073 (tp)
REVERT: h   83 MET cc_start: 0.7226 (mtm) cc_final: 0.6632 (mtm)
REVERT: l   68 SER cc_start: 0.8126 (t) cc_final: 0.7789 (t)
REVERT: l  114 THR cc_start: 0.7740 (p) cc_final: 0.7451 (t)
REVERT: A   37 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7762 (tp)
REVERT: A   61 CYS cc_start: 0.8505 (m) cc_final: 0.7603 (t)
REVERT: A   66 MET cc_start: 0.7820 (tpp) cc_final: 0.7540 (mpp)
REVERT: B   19 LEU cc_start: 0.8295 (tp) cc_final: 0.7666 (tt)
REVERT: B   24 PHE cc_start: 0.8908 (m-10) cc_final: 0.8609 (m-10)
REVERT: B   64 GLU cc_start: 0.8030 (pt0) cc_final: 0.7726 (pt0)
REVERT: B   71 TRP cc_start: 0.8335 (t60) cc_final: 0.7969 (t-100)
REVERT: B   90 ASN cc_start: 0.7997 (t0) cc_final: 0.7747 (m-40)
REVERT: B   93 MET cc_start: 0.8014 (ttm) cc_final: 0.7732 (ttm)
REVERT: B  103 PHE cc_start: 0.8699 (t80) cc_final: 0.8199 (t80)
REVERT: B  127 ARG cc_start: 0.2341 (OUTLIER) cc_final: 0.2008 (tmt170)
  outliers start: 24
  outliers final: 19
  residues processed: 170
  average time/residue: 0.0650
  time to fit residues: 14.0770
Evaluate side-chains
  183 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue   48 LEU
Chi-restraints excluded: chain h residue   69 THR
Chi-restraints excluded: chain l residue   10 SER
Chi-restraints excluded: chain l residue   21 ILE
Chi-restraints excluded: chain l residue   33 ASN
Chi-restraints excluded: chain l residue   50 GLN
Chi-restraints excluded: chain l residue   75 SER
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain A residue   22 ASP
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  139 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 49 optimal weight:    0.0030
   chunk 8 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.0994

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

Flipped N/Q/H residues before XYZ refinement:
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.126263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.108686 restraints weight = 8364.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.112808 restraints weight = 4554.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.115633 restraints weight = 2871.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.117631 restraints weight = 1971.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.119042 restraints weight = 1445.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4179  Z= 0.145
  Angle     :  0.690  13.273   5698  Z= 0.332
  Chirality :  0.046   0.254    624
  Planarity :  0.005   0.040    731
  Dihedral  :  4.897  59.774    567
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 28.70 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.38), residues: 508
  helix:  2.16 (0.37), residues: 176
  sheet:  0.05 (0.52), residues: 102
  loop :  0.50 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG h  87 
 TYR   0.011   0.002   TYR B 118 
 PHE   0.016   0.002   PHE B 103 
 TRP   0.014   0.002   TRP A 102 
 HIS   0.004   0.001   HIS B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4177)
  covalent geometry    : angle       0.68987 ( 5694)
  SS BOND              : bond        0.00520 (    2)
  SS BOND              : angle       0.30168 (    4)
  hydrogen bonds       : bond        0.04586 (  197)
  hydrogen bonds       : angle       4.68983 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: h    2 VAL cc_start: 0.8899 (m) cc_final: 0.8647 (t)
REVERT: h   46 GLU cc_start: 0.6885 (tt0) cc_final: 0.6619 (tt0)
REVERT: h   47 TRP cc_start: 0.8268 (t60) cc_final: 0.7900 (t60)
REVERT: h   70 ILE cc_start: 0.8604 (tt) cc_final: 0.8233 (tt)
REVERT: h   81 LEU cc_start: 0.7399 (tp) cc_final: 0.7101 (tp)
REVERT: h   83 MET cc_start: 0.7233 (mtm) cc_final: 0.6617 (mtm)
REVERT: h  111 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7405 (tm-30)
REVERT: l   43 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7557 (tm-30)
REVERT: l   68 SER cc_start: 0.8188 (t) cc_final: 0.7838 (t)
REVERT: l   95 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7314 (tm-30)
REVERT: A   61 CYS cc_start: 0.8455 (m) cc_final: 0.7579 (t)
REVERT: A   66 MET cc_start: 0.7815 (tpp) cc_final: 0.7555 (mpp)
REVERT: B   19 LEU cc_start: 0.8286 (tp) cc_final: 0.7703 (tt)
REVERT: B   24 PHE cc_start: 0.8909 (m-10) cc_final: 0.8588 (m-10)
REVERT: B   64 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7710 (pt0)
REVERT: B   71 TRP cc_start: 0.8403 (t60) cc_final: 0.7997 (t-100)
REVERT: B   83 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6111 (mt-10)
REVERT: B   90 ASN cc_start: 0.8050 (t0) cc_final: 0.7776 (m-40)
REVERT: B   93 MET cc_start: 0.7979 (ttm) cc_final: 0.7774 (ttm)
REVERT: B  103 PHE cc_start: 0.8725 (t80) cc_final: 0.8240 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 167
  average time/residue: 0.0639
  time to fit residues: 13.8113
Evaluate side-chains
  177 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   11 VAL
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue   69 THR
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue   10 SER
Chi-restraints excluded: chain l residue   21 ILE
Chi-restraints excluded: chain l residue   33 ASN
Chi-restraints excluded: chain l residue   50 GLN
Chi-restraints excluded: chain l residue   75 SER
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue   64 GLU
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  139 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0030
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.127063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.109786 restraints weight = 8197.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.113841 restraints weight = 4477.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.116567 restraints weight = 2816.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.118574 restraints weight = 1945.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.120012 restraints weight = 1427.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.5085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4179  Z= 0.125
  Angle     :  0.718  16.027   5698  Z= 0.339
  Chirality :  0.046   0.301    624
  Planarity :  0.004   0.040    731
  Dihedral  :  4.757  58.152    567
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 28.48 %
    Favored  : 66.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.38), residues: 508
  helix:  2.04 (0.38), residues: 177
  sheet:  0.02 (0.52), residues: 102
  loop :  0.63 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG h  87 
 TYR   0.013   0.001   TYR A  38 
 PHE   0.017   0.001   PHE B 103 
 TRP   0.014   0.002   TRP A 102 
 HIS   0.005   0.001   HIS B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4177)
  covalent geometry    : angle       0.71867 ( 5694)
  SS BOND              : bond        0.00496 (    2)
  SS BOND              : angle       0.29784 (    4)
  hydrogen bonds       : bond        0.04175 (  197)
  hydrogen bonds       : angle       4.60483 (  540)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: h    2 VAL cc_start: 0.8896 (m) cc_final: 0.8674 (t)
REVERT: h   46 GLU cc_start: 0.6910 (tt0) cc_final: 0.6654 (tt0)
REVERT: h   47 TRP cc_start: 0.8249 (t60) cc_final: 0.7856 (t60)
REVERT: h   70 ILE cc_start: 0.8590 (tt) cc_final: 0.8210 (tt)
REVERT: h   81 LEU cc_start: 0.7307 (tp) cc_final: 0.7041 (tp)
REVERT: h   83 MET cc_start: 0.7170 (mtm) cc_final: 0.6600 (mtm)
REVERT: l   68 SER cc_start: 0.8160 (t) cc_final: 0.7826 (t)
REVERT: A    7 LYS cc_start: 0.8451 (tppt) cc_final: 0.8244 (tppt)
REVERT: A   12 SER cc_start: 0.8707 (t) cc_final: 0.8408 (p)
REVERT: A   37 LEU cc_start: 0.8210 (tp) cc_final: 0.7904 (tp)
REVERT: A   61 CYS cc_start: 0.8447 (m) cc_final: 0.7611 (t)
REVERT: A   66 MET cc_start: 0.7827 (tpp) cc_final: 0.7583 (mpp)
REVERT: B   19 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7697 (tt)
REVERT: B   24 PHE cc_start: 0.8909 (m-10) cc_final: 0.8610 (m-10)
REVERT: B   64 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7522 (pt0)
REVERT: B   71 TRP cc_start: 0.8404 (t60) cc_final: 0.8013 (t-100)
REVERT: B   83 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6137 (mt-10)
REVERT: B   90 ASN cc_start: 0.8043 (t0) cc_final: 0.7773 (m-40)
REVERT: B   93 MET cc_start: 0.7987 (ttm) cc_final: 0.7763 (ttm)
REVERT: B  103 PHE cc_start: 0.8669 (t80) cc_final: 0.8160 (t80)
  outliers start: 23
  outliers final: 17
  residues processed: 178
  average time/residue: 0.0559
  time to fit residues: 13.0177
Evaluate side-chains
  189 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain h residue   11 VAL
Chi-restraints excluded: chain h residue   30 ASN
Chi-restraints excluded: chain h residue   69 THR
Chi-restraints excluded: chain l residue    4 MET
Chi-restraints excluded: chain l residue   10 SER
Chi-restraints excluded: chain l residue   21 ILE
Chi-restraints excluded: chain l residue   33 ASN
Chi-restraints excluded: chain l residue   50 GLN
Chi-restraints excluded: chain l residue   75 SER
Chi-restraints excluded: chain l residue   94 MET
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   22 ASP
Chi-restraints excluded: chain B residue   64 GLU
Chi-restraints excluded: chain B residue   66 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  114 THR
Chi-restraints excluded: chain B residue  139 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 36 optimal weight:    0.0470
   chunk 13 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.7680

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

Flipped N/Q/H residues before XYZ refinement:
h  57 ASN
B  51 HIS
B 104 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.126955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.109413 restraints weight = 8207.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.113480 restraints weight = 4509.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.116293 restraints weight = 2847.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.118321 restraints weight = 1966.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.119691 restraints weight = 1444.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4179  Z= 0.129
  Angle     :  0.731  15.753   5698  Z= 0.346
  Chirality :  0.046   0.304    624
  Planarity :  0.004   0.041    731
  Dihedral  :  4.077  16.327    565
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 28.70 %
    Favored  : 66.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.38), residues: 508
  helix:  1.98 (0.38), residues: 177
  sheet:  0.04 (0.52), residues: 102
  loop :  0.69 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG h  87 
 TYR   0.015   0.001   TYR A  38 
 PHE   0.016   0.002   PHE B 103 
 TRP   0.016   0.001   TRP A 102 
 HIS   0.004   0.001   HIS B 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4177)
  covalent geometry    : angle       0.73108 ( 5694)
  SS BOND              : bond        0.00499 (    2)
  SS BOND              : angle       0.29765 (    4)
  hydrogen bonds       : bond        0.04121 (  197)
  hydrogen bonds       : angle       4.59000 (  540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 880.54 seconds
wall clock time: 15 minutes 57.73 seconds (957.73 seconds total)