Starting phenix.real_space_refine
on Sat May  2 11:58:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqm_45815/05_2026/9cqm_45815.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqm_45815/05_2026/9cqm_45815.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqm_45815/05_2026/9cqm_45815.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqm_45815/05_2026/9cqm_45815.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqm_45815/05_2026/9cqm_45815.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqm_45815/05_2026/9cqm_45815.cif"
  }
  resolution = 2.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
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: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      12      5.16       5
     C    2914      2.51       5
     N     764      2.21       5
     O    1096      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4790
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1050
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
    Chain: "B"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1110
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 1050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1050
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 1110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1110
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 137}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'HEM': 1, 'OXY': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 79
          Classifications: {'water': 79}
          Link IDs: {None: 78}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 62
          Classifications: {'water': 62}
          Link IDs: {None: 61}
    Chain: "C"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 86
          Classifications: {'water': 86}
          Link IDs: {None: 85}
    Chain: "D"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 63
          Classifications: {'water': 63}
          Link IDs: {None: 62}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   HOH B 334 " occ=0.66
  Time building chain proxies: 1.01, per 1000 atoms: 0.21
  Number of scatterers: 4790
  At special positions: 0
  Unit cell: (77.175, 72.03, 65.415, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      12     16.00
     O    1096      8.00
     N     764      7.00
     C    2914      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.24
  Conformation dependent library (CDL) restraints added in 96.0 milliseconds
  

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 0 sheets defined
      87.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
    Processing helix  chain 'A' and resid 17 through 19
      No H-bonds generated for 'chain 'A' and resid 17 through 19'
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 89
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 4.066A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 137
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.298A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 76
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.040A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 122
      No H-bonds generated for 'chain 'B' and resid 120 through 122'
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'B' and resid 143 through 146
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 17 through 19
      No H-bonds generated for 'chain 'C' and resid 17 through 19'
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 95 through 113
      removed outlier: 3.549A  pdb=" N   LYS C  99 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 3.852A  pdb=" N   LYS D  17 " --> pdb=" O   ALA D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 36 through 43
      removed outlier: 4.140A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 77
    Processing helix  chain 'D' and resid 80 through 85
    Processing helix  chain 'D' and resid 85 through 95
    Processing helix  chain 'D' and resid 100 through 119
      removed outlier: 3.661A  pdb=" N   ARG D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 120 through 122
      No H-bonds generated for 'chain 'D' and resid 120 through 122'
    Processing helix  chain 'D' and resid 123 through 142
    Processing helix  chain 'D' and resid 143 through 146

    333 hydrogen bonds defined for protein.
    942 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: 0.42

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.19 -     1.37: 1555
        1.37 -     1.56: 3049
        1.56 -     1.74: 0
        1.74 -     1.93: 19
        1.93 -     2.11: 15
  Bond restraints: 4638
  Sorted by residual:
  bond pdb=" O1  OXY B 202 "
       pdb=" O2  OXY B 202 "
    ideal  model  delta    sigma   weight residual
    1.109  1.206 -0.097 2.00e-02 2.50e+03 2.33e+01
  bond pdb=" O1  OXY D 202 "
       pdb=" O2  OXY D 202 "
    ideal  model  delta    sigma   weight residual
    1.109  1.205 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" O1  OXY A 202 "
       pdb=" O2  OXY A 202 "
    ideal  model  delta    sigma   weight residual
    1.109  1.204 -0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" O1  OXY C 202 "
       pdb=" O2  OXY C 202 "
    ideal  model  delta    sigma   weight residual
    1.109  1.203 -0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" C   VAL C  93 "
       pdb=" O   VAL C  93 "
    ideal  model  delta    sigma   weight residual
    1.238  1.191  0.047 1.13e-02 7.83e+03 1.75e+01
  ... (remaining 4633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 5970
        1.26 -     2.52: 270
        2.52 -     3.77: 82
        3.77 -     5.03: 26
        5.03 -     6.29: 10
  Bond angle restraints: 6358
  Sorted by residual:
  angle pdb=" CA  ASP C  94 "
        pdb=" CB  ASP C  94 "
        pdb=" CG  ASP C  94 "
      ideal   model   delta    sigma   weight residual
     112.60  117.14   -4.54 1.00e+00 1.00e+00 2.06e+01
  angle pdb=" CA  LEU C  91 "
        pdb=" C   LEU C  91 "
        pdb=" O   LEU C  91 "
      ideal   model   delta    sigma   weight residual
     120.55  115.80    4.75 1.06e+00 8.90e-01 2.01e+01
  angle pdb=" C   ASP C  94 "
        pdb=" CA  ASP C  94 "
        pdb=" CB  ASP C  94 "
      ideal   model   delta    sigma   weight residual
     109.52  115.81   -6.29 1.58e+00 4.01e-01 1.59e+01
  angle pdb=" CA  LYS C 139 "
        pdb=" C   LYS C 139 "
        pdb=" O   LYS C 139 "
      ideal   model   delta    sigma   weight residual
     120.55  116.46    4.09 1.06e+00 8.90e-01 1.49e+01
  angle pdb=" C   ASP C  94 "
        pdb=" N   PRO C  95 "
        pdb=" CA  PRO C  95 "
      ideal   model   delta    sigma   weight residual
     119.05  123.24   -4.19 1.11e+00 8.12e-01 1.42e+01
  ... (remaining 6353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 2286
       17.96 -    35.91: 240
       35.91 -    53.87: 73
       53.87 -    71.83: 17
       71.83 -    89.78: 10
  Dihedral angle restraints: 2626
    sinusoidal: 998
      harmonic: 1628
  Sorted by residual:
  dihedral pdb=" C2B HEM C 201 "
           pdb=" C3B HEM C 201 "
           pdb=" CAB HEM C 201 "
           pdb=" CBB HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -69.82   69.82     2      1.00e+01 1.00e-02 4.23e+01
  dihedral pdb=" C2C HEM C 201 "
           pdb=" C3C HEM C 201 "
           pdb=" CAC HEM C 201 "
           pdb=" CBC HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -65.25   65.25     2      1.00e+01 1.00e-02 3.96e+01
  dihedral pdb=" C1A HEM C 201 "
           pdb=" C2A HEM C 201 "
           pdb=" CAA HEM C 201 "
           pdb=" CBA HEM C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   90.22   89.78     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 2623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 494
       0.038 -    0.076: 150
       0.076 -    0.114: 31
       0.114 -    0.152: 9
       0.152 -    0.191: 4
  Chirality restraints: 688
  Sorted by residual:
  chirality pdb=" CB  VAL B  60 "
            pdb=" CA  VAL B  60 "
            pdb=" CG1 VAL B  60 "
            pdb=" CG2 VAL B  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.08e-01
  chirality pdb=" CB  VAL C  93 "
            pdb=" CA  VAL C  93 "
            pdb=" CG1 VAL C  93 "
            pdb=" CG2 VAL C  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  LYS B  61 "
            pdb=" N   LYS B  61 "
            pdb=" C   LYS B  61 "
            pdb=" CB  LYS B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.37e-01
  ... (remaining 685 not shown)

  Planarity restraints: 794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  93 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.82e+00
        pdb=" C   VAL C  93 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   VAL C  93 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ASP C  94 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C  89 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.11e+00
        pdb=" C   HIS C  89 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   HIS C  89 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LYS C  90 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  94 "    0.028 5.00e-02 4.00e+02   4.33e-02 3.00e+00
        pdb=" N   PRO A  95 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.024 5.00e-02 4.00e+02
  ... (remaining 791 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 190
        2.70 -     3.25: 4641
        3.25 -     3.80: 8872
        3.80 -     4.35: 11643
        4.35 -     4.90: 17967
  Nonbonded interactions: 43313
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS D  92 "
            pdb="FE   HEM D 201 "
     model   vdw
     2.149 3.080
  nonbonded pdb=" NE2 HIS B  92 "
            pdb="FE   HEM B 201 "
     model   vdw
     2.174 3.080
  nonbonded pdb=" NE2 HIS A  87 "
            pdb="FE   HEM A 201 "
     model   vdw
     2.198 3.080
  nonbonded pdb=" O   HOH A 313 "
            pdb=" O   HOH A 367 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   HOH C 316 "
            pdb=" O   HOH C 372 "
     model   vdw
     2.215 3.040
  ... (remaining 43308 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 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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=0.66 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.130
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
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      :  0.010   0.315   4642  Z= 0.316
  Angle     :  0.705   6.291   6358  Z= 0.405
  Chirality :  0.040   0.191    688
  Planarity :  0.005   0.043    794
  Dihedral  : 17.703  89.782   1574
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.74 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.59 (0.37), residues: 560
  helix:  2.59 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  1.85 (0.66), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  31 
 TYR   0.010   0.002   TYR C 140 
 PHE   0.008   0.001   PHE A  36 
 TRP   0.008   0.001   TRP B  37 
 HIS   0.007   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00654 ( 4638)
  covalent geometry    : angle       0.70496 ( 6358)
  hydrogen bonds       : bond        0.10609 (  333)
  hydrogen bonds       : angle       4.56826 (  942)
  Misc. bond           : bond        0.24718 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8184 (mttt) cc_final: 0.7720 (mmpt)
REVERT: A   90 LYS cc_start: 0.8306 (mppt) cc_final: 0.7907 (ttmt)
REVERT: C   11 LYS cc_start: 0.8228 (mtpp) cc_final: 0.7980 (mttp)
REVERT: D   26 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7955 (mm-30)
REVERT: D   52 ASP cc_start: 0.8058 (m-30) cc_final: 0.7852 (m-30)
  outliers start: 6
  outliers final: 0
  residues processed: 96
  average time/residue: 0.5000
  time to fit residues: 49.3371
Evaluate side-chains
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0570
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
B 139 ASN
C  89 HIS
D  19 ASN
D  63 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.146256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.122286 restraints weight = 4489.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.22
r_work: 0.3166 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.158   4642  Z= 0.123
  Angle     :  0.718  17.259   6358  Z= 0.265
  Chirality :  0.038   0.131    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.732  86.437    620
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.08 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.80 (0.37), residues: 560
  helix:  2.63 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.35 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B  35 
 PHE   0.008   0.001   PHE C  36 
 TRP   0.004   0.001   TRP C  14 
 HIS   0.005   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4638)
  covalent geometry    : angle       0.71792 ( 6358)
  hydrogen bonds       : bond        0.03605 (  333)
  hydrogen bonds       : angle       3.94534 (  942)
  Misc. bond           : bond        0.09448 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7639 (tttt)
REVERT: A   92 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8041 (mtp85)
REVERT: B   26 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7172 (tm-30)
REVERT: B   43 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7065 (mp0)
REVERT: C   85 ASP cc_start: 0.7902 (m-30) cc_final: 0.7466 (t0)
REVERT: D   26 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7570 (mm-30)
REVERT: D  101 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7206 (tm-30)
REVERT: D  132 LYS cc_start: 0.8256 (mttt) cc_final: 0.8035 (mttt)
  outliers start: 9
  outliers final: 3
  residues processed: 75
  average time/residue: 0.4738
  time to fit residues: 36.6231
Evaluate side-chains
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    0.1980
   chunk 41 optimal weight:    0.0020
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS
B 139 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.146269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.122326 restraints weight = 4428.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.22
r_work: 0.3151 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.237   4642  Z= 0.111
  Angle     :  0.711  17.178   6358  Z= 0.251
  Chirality :  0.038   0.130    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.722  86.031    620
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.96 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.99 (0.37), residues: 560
  helix:  2.77 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.42 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.008   0.001   TYR D 130 
 PHE   0.007   0.001   PHE B 118 
 TRP   0.006   0.001   TRP A  14 
 HIS   0.003   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4638)
  covalent geometry    : angle       0.71120 ( 6358)
  hydrogen bonds       : bond        0.03272 (  333)
  hydrogen bonds       : angle       3.83909 (  942)
  Misc. bond           : bond        0.11850 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7701 (tttt)
REVERT: A   92 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8023 (mtp85)
REVERT: B   26 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7249 (tm-30)
REVERT: B   43 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6980 (mp0)
REVERT: C   56 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7297 (mttm)
REVERT: C   76 MET cc_start: 0.7238 (mtp) cc_final: 0.6978 (mtp)
REVERT: C   85 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7507 (t70)
REVERT: D   26 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7585 (mm-30)
REVERT: D   52 ASP cc_start: 0.7786 (m-30) cc_final: 0.7280 (m-30)
REVERT: D  101 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.6618 (tm-30)
REVERT: D  104 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7207 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8310 (mttt) cc_final: 0.8104 (mttt)
  outliers start: 7
  outliers final: 1
  residues processed: 72
  average time/residue: 0.4981
  time to fit residues: 36.9662
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  104 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.143517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.119374 restraints weight = 4433.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.22
r_work: 0.3112 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2968
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2968 r_free = 0.2968    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.353   4642  Z= 0.136
  Angle     :  0.732  17.321   6358  Z= 0.266
  Chirality :  0.040   0.142    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.949  89.752    620
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.64 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.78 (0.36), residues: 560
  helix:  2.62 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.33 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.009   0.001   TYR B  35 
 PHE   0.010   0.001   PHE B 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4638)
  covalent geometry    : angle       0.73151 ( 6358)
  hydrogen bonds       : bond        0.03829 (  333)
  hydrogen bonds       : angle       3.98647 (  942)
  Misc. bond           : bond        0.18079 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7868 (mttt) cc_final: 0.7020 (mptt)
REVERT: A   90 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7807 (tttt)
REVERT: A   92 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8092 (mtp85)
REVERT: A  116 GLU cc_start: 0.7735 (mp0) cc_final: 0.7090 (pp20)
REVERT: B   26 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7271 (tm-30)
REVERT: C   20 HIS cc_start: 0.7656 (m-70) cc_final: 0.7425 (m90)
REVERT: C   76 MET cc_start: 0.7233 (mtp) cc_final: 0.6976 (mtp)
REVERT: D   26 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7614 (mm-30)
REVERT: D  101 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.6779 (tm-30)
REVERT: D  132 LYS cc_start: 0.8420 (mttt) cc_final: 0.8176 (mttt)
  outliers start: 13
  outliers final: 3
  residues processed: 76
  average time/residue: 0.4551
  time to fit residues: 35.6758
Evaluate side-chains
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 44 optimal weight:    0.2980
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.144893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.121149 restraints weight = 4432.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.21
r_work: 0.3120 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.327   4642  Z= 0.126
  Angle     :  0.718  17.067   6358  Z= 0.259
  Chirality :  0.039   0.138    688
  Planarity :  0.005   0.046    794
  Dihedral  :  9.687  88.504    620
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.64 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.87 (0.36), residues: 560
  helix:  2.70 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.31 (0.63), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4638)
  covalent geometry    : angle       0.71833 ( 6358)
  hydrogen bonds       : bond        0.03472 (  333)
  hydrogen bonds       : angle       3.90502 (  942)
  Misc. bond           : bond        0.16685 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7776 (tttt)
REVERT: A   92 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8061 (mtp85)
REVERT: B   26 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7221 (tm-30)
REVERT: B   43 GLU cc_start: 0.7691 (mt-10) cc_final: 0.6974 (mp0)
REVERT: C   20 HIS cc_start: 0.7639 (m-70) cc_final: 0.7435 (m90)
REVERT: C   56 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7267 (mttm)
REVERT: C   76 MET cc_start: 0.7204 (mtp) cc_final: 0.6947 (mtp)
REVERT: C   85 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7497 (t0)
REVERT: D   26 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7604 (mm-30)
REVERT: D  101 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6798 (tm-30)
REVERT: D  132 LYS cc_start: 0.8401 (mttt) cc_final: 0.8175 (mttt)
  outliers start: 12
  outliers final: 4
  residues processed: 75
  average time/residue: 0.4063
  time to fit residues: 31.5128
Evaluate side-chains
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.140191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.116039 restraints weight = 4555.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.23
r_work: 0.3095 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.566   4642  Z= 0.191
  Angle     :  0.765  16.387   6358  Z= 0.296
  Chirality :  0.043   0.160    688
  Planarity :  0.006   0.047    794
  Dihedral  : 10.223  87.009    620
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.86 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.40 (0.36), residues: 560
  helix:  2.36 (0.24), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.16 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  40 
 TYR   0.011   0.002   TYR B  35 
 PHE   0.014   0.002   PHE B 118 
 TRP   0.007   0.001   TRP A  14 
 HIS   0.005   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 4638)
  covalent geometry    : angle       0.76478 ( 6358)
  hydrogen bonds       : bond        0.04550 (  333)
  hydrogen bonds       : angle       4.19313 (  942)
  Misc. bond           : bond        0.28689 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7897 (mttt) cc_final: 0.7059 (mptt)
REVERT: A   90 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7890 (tttt)
REVERT: A  116 GLU cc_start: 0.7534 (mp0) cc_final: 0.7060 (pp20)
REVERT: B   26 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7322 (tm-30)
REVERT: B   43 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7098 (mp0)
REVERT: C   20 HIS cc_start: 0.7665 (m-70) cc_final: 0.7440 (m90)
REVERT: C   56 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7193 (mptt)
REVERT: C   76 MET cc_start: 0.7208 (mtp) cc_final: 0.6946 (mtp)
REVERT: C   90 LYS cc_start: 0.8059 (mttt) cc_final: 0.7556 (ttpt)
REVERT: D   26 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7683 (mm-30)
REVERT: D   52 ASP cc_start: 0.7809 (m-30) cc_final: 0.7345 (m-30)
REVERT: D  101 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.6860 (tm-30)
REVERT: D  104 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8125 (ttp-110)
  outliers start: 12
  outliers final: 5
  residues processed: 85
  average time/residue: 0.4116
  time to fit residues: 36.0988
Evaluate side-chains
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Chi-restraints excluded: chain D residue  104 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.142203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.118420 restraints weight = 4472.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.21
r_work: 0.3127 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.403   4642  Z= 0.132
  Angle     :  0.727  17.262   6358  Z= 0.263
  Chirality :  0.039   0.146    688
  Planarity :  0.005   0.046    794
  Dihedral  :  9.700  85.843    620
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.18 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.65 (0.36), residues: 560
  helix:  2.55 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.21 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4638)
  covalent geometry    : angle       0.72677 ( 6358)
  hydrogen bonds       : bond        0.03631 (  333)
  hydrogen bonds       : angle       4.00932 (  942)
  Misc. bond           : bond        0.20426 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7791 (tttt)
REVERT: A  116 GLU cc_start: 0.7489 (mp0) cc_final: 0.7111 (pp20)
REVERT: B   26 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7227 (tm-30)
REVERT: C   20 HIS cc_start: 0.7642 (m-70) cc_final: 0.7418 (m90)
REVERT: C   56 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7113 (mptt)
REVERT: C   76 MET cc_start: 0.7192 (mtp) cc_final: 0.6939 (mtp)
REVERT: C   90 LYS cc_start: 0.8052 (mttt) cc_final: 0.7496 (ttpt)
REVERT: D   26 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7570 (mm-30)
REVERT: D  101 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6746 (tm-30)
REVERT: D  132 LYS cc_start: 0.8415 (mttp) cc_final: 0.8159 (mttt)
  outliers start: 10
  outliers final: 6
  residues processed: 73
  average time/residue: 0.4022
  time to fit residues: 30.3400
Evaluate side-chains
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    0.2980
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.143411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.119652 restraints weight = 4530.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.22
r_work: 0.3158 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.300   4642  Z= 0.117
  Angle     :  0.706  17.071   6358  Z= 0.252
  Chirality :  0.038   0.134    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.535  86.100    620
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.52 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.85 (0.36), residues: 560
  helix:  2.70 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.23 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.007   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.003   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4638)
  covalent geometry    : angle       0.70551 ( 6358)
  hydrogen bonds       : bond        0.03289 (  333)
  hydrogen bonds       : angle       3.90053 (  942)
  Misc. bond           : bond        0.15219 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.094 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7741 (ttmt)
REVERT: A  116 GLU cc_start: 0.7479 (mp0) cc_final: 0.7162 (pp20)
REVERT: B   26 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7222 (tm-30)
REVERT: C   56 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7110 (mptt)
REVERT: C   76 MET cc_start: 0.7200 (mtp) cc_final: 0.6930 (mtp)
REVERT: C   85 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7472 (t0)
REVERT: C   90 LYS cc_start: 0.8035 (mttt) cc_final: 0.7488 (ttpt)
REVERT: D   26 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7557 (mm-30)
REVERT: D   52 ASP cc_start: 0.7776 (m-30) cc_final: 0.7248 (m-30)
REVERT: D  101 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6756 (tm-30)
REVERT: D  132 LYS cc_start: 0.8393 (mttp) cc_final: 0.8143 (mttt)
  outliers start: 12
  outliers final: 6
  residues processed: 70
  average time/residue: 0.3739
  time to fit residues: 27.1092
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 ASN
C  68 ASN
C  72 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.142166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.118475 restraints weight = 4471.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 1.21
r_work: 0.3100 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.375   4642  Z= 0.136
  Angle     :  0.725  16.939   6358  Z= 0.265
  Chirality :  0.039   0.143    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.735  86.418    620
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.96 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.72 (0.36), residues: 560
  helix:  2.61 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.20 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  31 
 TYR   0.009   0.001   TYR B  35 
 PHE   0.009   0.001   PHE B 118 
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4638)
  covalent geometry    : angle       0.72539 ( 6358)
  hydrogen bonds       : bond        0.03721 (  333)
  hydrogen bonds       : angle       3.99613 (  942)
  Misc. bond           : bond        0.19076 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7860 (mttt) cc_final: 0.7017 (mptt)
REVERT: A   90 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7814 (tttt)
REVERT: A  116 GLU cc_start: 0.7499 (mp0) cc_final: 0.7193 (pp20)
REVERT: B   26 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7314 (tm-30)
REVERT: C   56 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7158 (mptt)
REVERT: C   76 MET cc_start: 0.7198 (mtp) cc_final: 0.6924 (mtp)
REVERT: C   90 LYS cc_start: 0.8073 (mttt) cc_final: 0.7536 (ttpt)
REVERT: D   26 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7610 (mm-30)
REVERT: D   52 ASP cc_start: 0.7786 (m-30) cc_final: 0.7264 (m-30)
REVERT: D   82 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7505 (mptt)
REVERT: D  101 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.6796 (tm-30)
REVERT: D  132 LYS cc_start: 0.8445 (mttp) cc_final: 0.8186 (mttt)
  outliers start: 14
  outliers final: 6
  residues processed: 74
  average time/residue: 0.3944
  time to fit residues: 30.1682
Evaluate side-chains
  78 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 22 optimal weight:    0.3980
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0980
   chunk 43 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.144005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.120291 restraints weight = 4482.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.21
r_work: 0.3152 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3011 r_free = 0.3011    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.288   4642  Z= 0.114
  Angle     :  0.700  16.937   6358  Z= 0.250
  Chirality :  0.038   0.131    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.472  86.257    620
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.84 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.88 (0.36), residues: 560
  helix:  2.74 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.18 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.007   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4638)
  covalent geometry    : angle       0.69978 ( 6358)
  hydrogen bonds       : bond        0.03220 (  333)
  hydrogen bonds       : angle       3.88144 (  942)
  Misc. bond           : bond        0.14638 (    4)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7733 (ttmt)
REVERT: A  116 GLU cc_start: 0.7555 (mp0) cc_final: 0.7147 (pp20)
REVERT: B   26 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7229 (tm-30)
REVERT: C   56 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7104 (mptt)
REVERT: C   76 MET cc_start: 0.7185 (mtp) cc_final: 0.6922 (mtp)
REVERT: C   90 LYS cc_start: 0.8048 (mttt) cc_final: 0.7490 (ttpt)
REVERT: D   26 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7558 (mm-30)
REVERT: D   52 ASP cc_start: 0.7768 (m-30) cc_final: 0.7260 (m-30)
REVERT: D   82 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7498 (mptt)
REVERT: D  101 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6758 (tm-30)
REVERT: D  132 LYS cc_start: 0.8393 (mttp) cc_final: 0.8148 (mttt)
  outliers start: 11
  outliers final: 6
  residues processed: 72
  average time/residue: 0.3842
  time to fit residues: 28.6195
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   90 LYS
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0870
   chunk 43 optimal weight:    0.0060
   chunk 42 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.4774

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  72 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.144298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.120597 restraints weight = 4476.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.21
r_work: 0.3129 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2992 r_free = 0.2992    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.261   4642  Z= 0.112
  Angle     :  0.694  16.725   6358  Z= 0.248
  Chirality :  0.038   0.128    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.471  86.517    620
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.84 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.92 (0.36), residues: 560
  helix:  2.79 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.13 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  31 
 TYR   0.008   0.001   TYR B 130 
 PHE   0.006   0.001   PHE D 118 
 TRP   0.008   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4638)
  covalent geometry    : angle       0.69431 ( 6358)
  hydrogen bonds       : bond        0.03177 (  333)
  hydrogen bonds       : angle       3.83897 (  942)
  Misc. bond           : bond        0.13334 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1219.88 seconds
wall clock time: 23 minutes 35.80 seconds (1415.80 seconds total)