Starting phenix.real_space_refine
on Sat May 10 02:40:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqm_45815/05_2025/9cqm_45815.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqm_45815/05_2025/9cqm_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_2025/9cqm_45815.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqm_45815/05_2025/9cqm_45815.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqm_45815/05_2025/9cqm_45815.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqm_45815/05_2025/9cqm_45815.cif"
  }
  resolution = 2.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.09, per 1000 atoms: 0.85
  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: 1.29
  Conformation dependent library (CDL) restraints added in 551.0 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: 0.47
  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: 1.26

  Time building geometry restraints manager: 1.47 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=" 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
  bond pdb=" C   PRO B  58 "
       pdb=" O   PRO B  58 "
    ideal  model  delta    sigma   weight residual
    1.237  1.197  0.040 1.16e-02 7.43e+03 1.18e+01
  bond pdb=" N   VAL C  93 "
       pdb=" CA  VAL C  93 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.19e-02 7.06e+03 1.12e+01
  bond pdb=" C3B HEM C 201 "
       pdb=" CAB HEM C 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.478  0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" N   VAL C  96 "
       pdb=" CA  VAL C  96 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.01e+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: 0.01
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:             2.880
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.910
  Find NCS groups from input model:        0.170
  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:13.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.540
-------------------------------------------------------------------------------
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      :  0.009   0.315   4642  Z= 0.283
  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 : 5.83
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.59 (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
 TRP   0.008   0.001   TRP B  37 
 HIS   0.007   0.001   HIS B  63 
 PHE   0.008   0.001   PHE A  36 
 TYR   0.010   0.002   TYR C 140 
 ARG   0.003   0.001   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10609 (  333)
  hydrogen bonds       : angle       4.56826 (  942)
  covalent geometry    : bond        0.00591 ( 4638)
  covalent geometry    : angle       0.70496 ( 6358)
  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  : 0.575 
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: 1.5304
  time to fit residues: 151.3110
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  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9980
   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  63 HIS
B 139 ASN
C  89 HIS
D  19 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.144043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.120132 restraints weight = 4414.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.21
r_work: 0.3139 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2988
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2988 r_free = 0.2988    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2988 r_free = 0.2988    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2988
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.208   4642  Z= 0.144
  Angle     :  0.729  16.518   6358  Z= 0.279
  Chirality :  0.040   0.141    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.954  86.607    620
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.30 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.60 (0.36), residues: 560
  helix:  2.47 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.34 (0.65), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.006   0.001   HIS B  63 
 PHE   0.011   0.002   PHE B 118 
 TYR   0.010   0.001   TYR B  35 
 ARG   0.003   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  333)
  hydrogen bonds       : angle       4.06373 (  942)
  covalent geometry    : bond        0.00339 ( 4638)
  covalent geometry    : angle       0.72919 ( 6358)
  Misc. bond           : bond        0.13359 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7704 (tttt)
REVERT: A   92 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8074 (mtp85)
REVERT: B   26 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7278 (tm-30)
REVERT: B   43 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7104 (mp0)
REVERT: D   26 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7618 (mm-30)
REVERT: D   52 ASP cc_start: 0.7781 (m-30) cc_final: 0.7467 (m-30)
REVERT: D  101 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7282 (tm-30)
REVERT: D  132 LYS cc_start: 0.8316 (mttt) cc_final: 0.8107 (mttt)
  outliers start: 9
  outliers final: 3
  residues processed: 77
  average time/residue: 1.4296
  time to fit residues: 113.8875
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  : 0.704 
-------------------------------------------------------------------------------
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 28 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 5 optimal weight:    0.3980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.144210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.120086 restraints weight = 4438.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.21
r_work: 0.3135 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2987 r_free = 0.2987    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.255   4642  Z= 0.122
  Angle     :  0.720  17.416   6358  Z= 0.259
  Chirality :  0.038   0.137    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.765  85.727    620
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.96 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.82 (0.36), residues: 560
  helix:  2.64 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.41 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  14 
 HIS   0.003   0.001   HIS A 112 
 PHE   0.008   0.001   PHE B 118 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03485 (  333)
  hydrogen bonds       : angle       3.91524 (  942)
  covalent geometry    : bond        0.00288 ( 4638)
  covalent geometry    : angle       0.72024 ( 6358)
  Misc. bond           : bond        0.13308 (    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
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.526 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7703 (tttt)
REVERT: A   92 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8016 (mtp85)
REVERT: B   26 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7244 (tm-30)
REVERT: B   43 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6988 (mp0)
REVERT: C   56 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7240 (mttm)
REVERT: C   76 MET cc_start: 0.7225 (mtp) cc_final: 0.6954 (mtp)
REVERT: C   85 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7462 (t0)
REVERT: D   26 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7551 (mm-30)
REVERT: D  101 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.6577 (tm-30)
REVERT: D  104 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7188 (mtt-85)
REVERT: D  132 LYS cc_start: 0.8327 (mttt) cc_final: 0.8108 (mttt)
  outliers start: 8
  outliers final: 2
  residues processed: 73
  average time/residue: 1.4799
  time to fit residues: 111.6779
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
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   11 VAL
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 4 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   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 = 0.3547 r_free = 0.3547 target = 0.143130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.118971 restraints weight = 4476.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.23
r_work: 0.3111 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
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 = 0.45   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 = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.345   4642  Z= 0.137
  Angle     :  0.728  17.061   6358  Z= 0.266
  Chirality :  0.040   0.143    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.943  89.580    620
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.75 (0.36), residues: 560
  helix:  2.58 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.38 (0.64), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.009   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03823 (  333)
  hydrogen bonds       : angle       4.00853 (  942)
  covalent geometry    : bond        0.00324 ( 4638)
  covalent geometry    : angle       0.72846 ( 6358)
  Misc. bond           : bond        0.18145 (    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
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7846 (mttt) cc_final: 0.7008 (mptt)
REVERT: A   90 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7796 (tttt)
REVERT: A   92 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8081 (mtp85)
REVERT: B   26 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7307 (tm-30)
REVERT: C   76 MET cc_start: 0.7218 (mtp) cc_final: 0.6943 (mtp)
REVERT: D   26 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7617 (mm-30)
REVERT: D  101 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6746 (tm-30)
REVERT: D  132 LYS cc_start: 0.8422 (mttt) cc_final: 0.8177 (mttt)
  outliers start: 12
  outliers final: 4
  residues processed: 79
  average time/residue: 1.4101
  time to fit residues: 115.2858
Evaluate side-chains
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
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 D residue   14 LEU
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 20 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0270
   chunk 18 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.1242

-------------------------------------------------------------------------------
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  20 HIS
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.141663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.117895 restraints weight = 4528.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.22
r_work: 0.3077 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2918
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2918 r_free = 0.2918    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2918
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.518   4642  Z= 0.173
  Angle     :  0.761  16.827   6358  Z= 0.289
  Chirality :  0.042   0.158    688
  Planarity :  0.006   0.046    794
  Dihedral  : 10.147  87.018    620
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.45 (0.36), residues: 560
  helix:  2.37 (0.24), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.26 (0.63), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 
 PHE   0.012   0.002   PHE B 118 
 TYR   0.010   0.002   TYR B  35 
 ARG   0.002   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  333)
  hydrogen bonds       : angle       4.17379 (  942)
  covalent geometry    : bond        0.00410 ( 4638)
  covalent geometry    : angle       0.76133 ( 6358)
  Misc. bond           : bond        0.26919 (    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
  89 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7904 (mttt) cc_final: 0.7055 (mptt)
REVERT: A   90 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7891 (tttt)
REVERT: B   26 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7343 (tm-30)
REVERT: B   43 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7123 (mp0)
REVERT: C   56 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7200 (mptt)
REVERT: C   76 MET cc_start: 0.7211 (mtp) cc_final: 0.6950 (mtp)
REVERT: C   90 LYS cc_start: 0.8096 (mttt) cc_final: 0.7559 (ttpt)
REVERT: D   26 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7694 (mm-30)
REVERT: D   52 ASP cc_start: 0.7826 (m-30) cc_final: 0.7362 (m-30)
REVERT: D  101 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.6875 (tm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 83
  average time/residue: 1.4584
  time to fit residues: 124.9674
Evaluate side-chains
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
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   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 1 optimal weight:    0.0070
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    0.9602

-------------------------------------------------------------------------------
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  20 HIS
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.141451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.117604 restraints weight = 4485.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.22
r_work: 0.3086 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.450   4642  Z= 0.155
  Angle     :  0.742  17.064   6358  Z= 0.276
  Chirality :  0.041   0.154    688
  Planarity :  0.006   0.047    794
  Dihedral  :  9.899  86.318    620
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 16.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.49 (0.36), residues: 560
  helix:  2.42 (0.24), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.22 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 
 PHE   0.010   0.002   PHE B 118 
 TYR   0.009   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  333)
  hydrogen bonds       : angle       4.10676 (  942)
  covalent geometry    : bond        0.00368 ( 4638)
  covalent geometry    : angle       0.74199 ( 6358)
  Misc. bond           : bond        0.23382 (    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
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7885 (mttt) cc_final: 0.7025 (mptt)
REVERT: A   90 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7868 (tttt)
REVERT: B   26 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7308 (tm-30)
REVERT: B   43 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7112 (mp0)
REVERT: C   56 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7170 (mptt)
REVERT: C   76 MET cc_start: 0.7180 (mtp) cc_final: 0.6911 (mtp)
REVERT: C   90 LYS cc_start: 0.8071 (mttt) cc_final: 0.7535 (ttpt)
REVERT: D   26 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7663 (mm-30)
REVERT: D   52 ASP cc_start: 0.7818 (m-30) cc_final: 0.7349 (m-30)
REVERT: D  101 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6822 (tm-30)
REVERT: D  132 LYS cc_start: 0.8446 (mttp) cc_final: 0.8178 (mttt)
  outliers start: 12
  outliers final: 6
  residues processed: 78
  average time/residue: 1.3762
  time to fit residues: 111.1617
Evaluate side-chains
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
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   26 GLU
Chi-restraints excluded: chain D residue  101 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C  20 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.144027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.120482 restraints weight = 4401.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.21
r_work: 0.3115 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2965
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2965 r_free = 0.2965    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 = 0.2965 r_free = 0.2965    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2965
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.317   4642  Z= 0.122
  Angle     :  0.711  17.087   6358  Z= 0.257
  Chirality :  0.038   0.139    688
  Planarity :  0.005   0.046    794
  Dihedral  :  9.579  85.994    620
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.62 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.74 (0.36), residues: 560
  helix:  2.62 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.22 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 
 PHE   0.007   0.001   PHE B 118 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  333)
  hydrogen bonds       : angle       3.94781 (  942)
  covalent geometry    : bond        0.00291 ( 4638)
  covalent geometry    : angle       0.71146 ( 6358)
  Misc. bond           : bond        0.16536 (    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
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7772 (tttt)
REVERT: B   26 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7260 (tm-30)
REVERT: B   43 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7053 (mp0)
REVERT: C   56 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7109 (mptt)
REVERT: C   76 MET cc_start: 0.7163 (mtp) cc_final: 0.6900 (mtp)
REVERT: C   90 LYS cc_start: 0.8065 (mttt) cc_final: 0.7486 (ttpt)
REVERT: D   26 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7583 (mm-30)
REVERT: D  101 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6747 (tm-30)
REVERT: D  132 LYS cc_start: 0.8410 (mttp) cc_final: 0.8149 (mttt)
  outliers start: 10
  outliers final: 5
  residues processed: 78
  average time/residue: 1.3658
  time to fit residues: 110.2385
Evaluate side-chains
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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   26 GLU
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 25 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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  20 HIS
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.141674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.117949 restraints weight = 4475.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.21
r_work: 0.3096 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    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 = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.354   4642  Z= 0.133
  Angle     :  0.722  17.040   6358  Z= 0.263
  Chirality :  0.039   0.141    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.709  86.192    620
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.68 (0.36), residues: 560
  helix:  2.57 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.23 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 
 PHE   0.008   0.001   PHE C  98 
 TYR   0.009   0.001   TYR B  35 
 ARG   0.001   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (  333)
  hydrogen bonds       : angle       4.00560 (  942)
  covalent geometry    : bond        0.00314 ( 4638)
  covalent geometry    : angle       0.72154 ( 6358)
  Misc. bond           : bond        0.18507 (    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
  81 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7865 (mttt) cc_final: 0.6996 (mptt)
REVERT: A   90 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7791 (tttt)
REVERT: B   26 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7290 (tm-30)
REVERT: B   43 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7038 (mp0)
REVERT: B  144 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6360 (mptm)
REVERT: C   56 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7138 (mptt)
REVERT: C   76 MET cc_start: 0.7166 (mtp) cc_final: 0.6902 (mtp)
REVERT: C   90 LYS cc_start: 0.8061 (mttt) cc_final: 0.7521 (ttpt)
REVERT: D   26 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7574 (mm-30)
REVERT: D   52 ASP cc_start: 0.7767 (m-30) cc_final: 0.7279 (m-30)
REVERT: D  101 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6744 (tm-30)
REVERT: D  132 LYS cc_start: 0.8432 (mttp) cc_final: 0.8158 (mttt)
  outliers start: 12
  outliers final: 6
  residues processed: 76
  average time/residue: 1.4887
  time to fit residues: 117.0604
Evaluate side-chains
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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 B residue  144 LYS
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 27 optimal weight:    7.9990
   chunk 29 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0470
   chunk 33 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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  20 HIS
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 = 0.3543 r_free = 0.3543 target = 0.142891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.119197 restraints weight = 4497.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 1.21
r_work: 0.3116 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.296   4642  Z= 0.119
  Angle     :  0.706  16.972   6358  Z= 0.255
  Chirality :  0.038   0.135    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.514  86.284    620
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.16
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.80 (0.36), residues: 560
  helix:  2.67 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.21 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.004   0.001   HIS C  20 
 PHE   0.007   0.001   PHE C  98 
 TYR   0.008   0.001   TYR B 130 
 ARG   0.001   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03343 (  333)
  hydrogen bonds       : angle       3.92708 (  942)
  covalent geometry    : bond        0.00283 ( 4638)
  covalent geometry    : angle       0.70639 ( 6358)
  Misc. bond           : bond        0.15457 (    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
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A   90 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7754 (tttt)
REVERT: A  116 GLU cc_start: 0.7365 (mp0) cc_final: 0.6971 (pp20)
REVERT: B   26 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7244 (tm-30)
REVERT: B   43 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7018 (mp0)
REVERT: B  144 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6358 (mptm)
REVERT: C   56 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7080 (mptt)
REVERT: C   76 MET cc_start: 0.7141 (mtp) cc_final: 0.6880 (mtp)
REVERT: C   90 LYS cc_start: 0.8052 (mttt) cc_final: 0.7494 (ttpt)
REVERT: D   26 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7550 (mm-30)
REVERT: D  101 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6715 (tm-30)
REVERT: D  132 LYS cc_start: 0.8384 (mttp) cc_final: 0.8129 (mttt)
  outliers start: 11
  outliers final: 6
  residues processed: 72
  average time/residue: 1.4335
  time to fit residues: 106.9473
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  : 0.534 
-------------------------------------------------------------------------------
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 B residue  144 LYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 139 ASN
C  20 HIS
C  72 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.141607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.118020 restraints weight = 4481.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.21
r_work: 0.3136 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.349   4642  Z= 0.134
  Angle     :  0.721  16.935   6358  Z= 0.265
  Chirality :  0.039   0.141    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.676  86.446    620
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.84 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.69 (0.36), residues: 560
  helix:  2.59 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.16 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 
 PHE   0.008   0.001   PHE B 118 
 TYR   0.009   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  333)
  hydrogen bonds       : angle       3.98043 (  942)
  covalent geometry    : bond        0.00317 ( 4638)
  covalent geometry    : angle       0.72149 ( 6358)
  Misc. bond           : bond        0.18259 (    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: 12
    poor density    : 65
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7861 (mttt) cc_final: 0.7001 (mptt)
REVERT: A   90 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7789 (ttmt)
REVERT: B   26 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7284 (tm-30)
REVERT: B   43 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7032 (mp0)
REVERT: C   56 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7091 (mptt)
REVERT: C   76 MET cc_start: 0.7178 (mtp) cc_final: 0.6910 (mtp)
REVERT: C   90 LYS cc_start: 0.8061 (mttt) cc_final: 0.7535 (ttpt)
REVERT: D   26 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7577 (mm-30)
REVERT: D  101 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6754 (tm-30)
REVERT: D  132 LYS cc_start: 0.8439 (mttp) cc_final: 0.8163 (mttt)
  outliers start: 12
  outliers final: 6
  residues processed: 71
  average time/residue: 1.4264
  time to fit residues: 105.2848
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
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  101 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  20 HIS
C  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.141846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.118107 restraints weight = 4474.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.21
r_work: 0.3128 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.361   4642  Z= 0.134
  Angle     :  0.720  16.989   6358  Z= 0.264
  Chirality :  0.039   0.141    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.642  86.389    620
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.84 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.68 (0.36), residues: 560
  helix:  2.59 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.16 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  14 
 HIS   0.005   0.001   HIS C  20 
 PHE   0.008   0.001   PHE B 118 
 TYR   0.009   0.001   TYR B  35 
 ARG   0.002   0.000   ARG C  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  333)
  hydrogen bonds       : angle       3.97656 (  942)
  covalent geometry    : bond        0.00317 ( 4638)
  covalent geometry    : angle       0.72017 ( 6358)
  Misc. bond           : bond        0.18882 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3966.07 seconds
wall clock time: 70 minutes 0.18 seconds (4200.18 seconds total)