Starting phenix.real_space_refine
on Sat May 10 02:44:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqn_45816/05_2025/9cqn_45816.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqn_45816/05_2025/9cqn_45816.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqn_45816/05_2025/9cqn_45816.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqn_45816/05_2025/9cqn_45816.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqn_45816/05_2025/9cqn_45816.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqn_45816/05_2025/9cqn_45816.cif"
  }
  resolution = 2.37
  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=   0.029
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): 0.01s

  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: 3.75, per 1000 atoms: 0.78
  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: 1.19
  Conformation dependent library (CDL) restraints added in 547.3 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: 0.46
  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: 1.21

  Time building geometry restraints manager: 1.39 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:             2.180
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.280
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  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:11.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
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
  102 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7777 (mmmm) cc_final: 0.7115 (tmtt)
REVERT: A   56 LYS cc_start: 0.8257 (mttt) cc_final: 0.7788 (mmpt)
REVERT: C   11 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7473 (mttp)
REVERT: C   56 LYS cc_start: 0.8247 (mttt) cc_final: 0.7848 (mmtt)
  outliers start: 6
  outliers final: 1
  residues processed: 99
  average time/residue: 1.6431
  time to fit residues: 167.3418
Evaluate side-chains
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   84 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 127 GLN
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.152877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.123257 restraints weight = 4029.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.38
r_work: 0.3190 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    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 = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.186   4642  Z= 0.142
  Angle     :  0.716  16.191   6358  Z= 0.277
  Chirality :  0.040   0.129    688
  Planarity :  0.005   0.046    794
  Dihedral  : 10.595  88.451    621
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.30 %
    Favored  : 82.16 %
  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 (0.37), residues: 560
  helix:  2.49 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  2.27 (0.65), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  14 
 HIS   0.005   0.001   HIS B  63 
 PHE   0.011   0.002   PHE A  36 
 TYR   0.010   0.002   TYR B 130 
 ARG   0.002   0.000   ARG D  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04179 (  333)
  hydrogen bonds       : angle       4.17536 (  942)
  covalent geometry    : bond        0.00315 ( 4638)
  covalent geometry    : angle       0.71608 ( 6358)
  Misc. bond           : bond        0.15028 (    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
  89 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7659 (mttm) cc_final: 0.7236 (mttp)
REVERT: A   56 LYS cc_start: 0.7789 (mttt) cc_final: 0.6931 (mmtt)
REVERT: A   92 ARG cc_start: 0.8366 (mtp85) cc_final: 0.8042 (mtt-85)
REVERT: C   11 LYS cc_start: 0.7546 (mtpp) cc_final: 0.6848 (mttp)
REVERT: C   56 LYS cc_start: 0.7775 (mttt) cc_final: 0.6957 (mmtt)
REVERT: D   43 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7045 (mt-10)
REVERT: D   61 LYS cc_start: 0.8015 (mttt) cc_final: 0.7666 (mttm)
  outliers start: 7
  outliers final: 1
  residues processed: 85
  average time/residue: 1.4860
  time to fit residues: 130.3905
Evaluate side-chains
  86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   43 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:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 36 optimal weight:    0.4980
   chunk 49 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   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
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.153199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.123147 restraints weight = 4032.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.40
r_work: 0.3187 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4642  Z= 0.132
  Angle     :  0.708  16.230   6358  Z= 0.266
  Chirality :  0.039   0.130    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.581  89.367    620
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.64 %
    Favored  : 82.16 %
  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:  3.71 (0.36), residues: 560
  helix:  2.55 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  2.37 (0.64), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.010   0.001   TYR B 130 
 ARG   0.003   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03902 (  333)
  hydrogen bonds       : angle       4.07864 (  942)
  covalent geometry    : bond        0.00299 ( 4638)
  covalent geometry    : angle       0.70774 ( 6358)
  Misc. bond           : bond        0.02731 (    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
  90 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7809 (mttt) cc_final: 0.6943 (mmtt)
REVERT: A   90 LYS cc_start: 0.8390 (mppt) cc_final: 0.8104 (mppt)
REVERT: B   95 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.6832 (tmtt)
REVERT: C   11 LYS cc_start: 0.7528 (mtpp) cc_final: 0.6790 (mttt)
REVERT: C   56 LYS cc_start: 0.7770 (mttt) cc_final: 0.6946 (mmtt)
REVERT: D   43 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7065 (mt-10)
REVERT: D   61 LYS cc_start: 0.8004 (mttt) cc_final: 0.7657 (mttm)
  outliers start: 10
  outliers final: 3
  residues processed: 84
  average time/residue: 1.5158
  time to fit residues: 131.3876
Evaluate side-chains
  85 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   95 LYS
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 1 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0370
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.154552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.124415 restraints weight = 4059.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.41
r_work: 0.3207 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3065
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3065 r_free = 0.3065    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3065
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4642  Z= 0.115
  Angle     :  0.689  16.112   6358  Z= 0.252
  Chirality :  0.038   0.123    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.312  88.465    620
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.52 %
    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:  3.88 (0.36), residues: 560
  helix:  2.74 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.19 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.008   0.001   PHE D 118 
 TYR   0.009   0.001   TYR B 130 
 ARG   0.005   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03441 (  333)
  hydrogen bonds       : angle       3.93808 (  942)
  covalent geometry    : bond        0.00264 ( 4638)
  covalent geometry    : angle       0.68885 ( 6358)
  Misc. bond           : bond        0.02437 (    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
  92 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7568 (mttm) cc_final: 0.7210 (mttp)
REVERT: A   56 LYS cc_start: 0.7771 (mttt) cc_final: 0.6869 (mmpt)
REVERT: A   90 LYS cc_start: 0.8333 (mppt) cc_final: 0.8112 (mppt)
REVERT: B   95 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.6785 (tmtt)
REVERT: C   11 LYS cc_start: 0.7533 (mtpp) cc_final: 0.6817 (mttp)
REVERT: C   56 LYS cc_start: 0.7733 (mttt) cc_final: 0.6933 (mmtt)
REVERT: D   43 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7023 (mt-10)
REVERT: D   61 LYS cc_start: 0.7975 (mttt) cc_final: 0.7631 (mttm)
  outliers start: 10
  outliers final: 3
  residues processed: 88
  average time/residue: 1.5568
  time to fit residues: 141.0855
Evaluate side-chains
  87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   95 LYS
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 5 optimal weight:    0.4980
   chunk 44 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 10 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
C  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.153536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.123276 restraints weight = 4103.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.41
r_work: 0.3189 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3050 r_free = 0.3050    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 = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4642  Z= 0.124
  Angle     :  0.696  16.032   6358  Z= 0.259
  Chirality :  0.039   0.127    688
  Planarity :  0.005   0.044    794
  Dihedral  : 10.506  89.660    620
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 (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:  3.83 (0.36), residues: 560
  helix:  2.70 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.18 (0.62), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.009   0.001   PHE C  98 
 TYR   0.010   0.001   TYR B 130 
 ARG   0.003   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  333)
  hydrogen bonds       : angle       3.99603 (  942)
  covalent geometry    : bond        0.00284 ( 4638)
  covalent geometry    : angle       0.69624 ( 6358)
  Misc. bond           : bond        0.02189 (    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
  94 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.470 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7613 (mttm) cc_final: 0.7136 (mttp)
REVERT: A   56 LYS cc_start: 0.7782 (mttt) cc_final: 0.6885 (mmpt)
REVERT: B   93 CYS cc_start: 0.6755 (m) cc_final: 0.5899 (t)
REVERT: C   11 LYS cc_start: 0.7560 (mtpp) cc_final: 0.6846 (mttp)
REVERT: C   56 LYS cc_start: 0.7766 (mttt) cc_final: 0.6922 (mmpt)
REVERT: D   61 LYS cc_start: 0.7994 (mttt) cc_final: 0.7652 (mttm)
  outliers start: 12
  outliers final: 4
  residues processed: 89
  average time/residue: 1.4893
  time to fit residues: 136.7674
Evaluate side-chains
  87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain D residue   11 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0970
   chunk 24 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
B  63 HIS
C  89 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.154415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.124374 restraints weight = 4027.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.40
r_work: 0.3205 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3068 r_free = 0.3068    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.1275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4642  Z= 0.117
  Angle     :  0.689  15.936   6358  Z= 0.253
  Chirality :  0.038   0.124    688
  Planarity :  0.005   0.044    794
  Dihedral  : 10.295  89.598    620
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.52 %
    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:  3.90 (0.36), residues: 560
  helix:  2.77 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.15 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.010   0.001   PHE B 118 
 TYR   0.009   0.001   TYR D 130 
 ARG   0.004   0.001   ARG A  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  333)
  hydrogen bonds       : angle       3.91342 (  942)
  covalent geometry    : bond        0.00269 ( 4638)
  covalent geometry    : angle       0.68904 ( 6358)
  Misc. bond           : bond        0.01471 (    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: 8
    poor density    : 82
  time to evaluate  : 0.513 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7571 (mttm) cc_final: 0.7086 (mttp)
REVERT: A   56 LYS cc_start: 0.7783 (mttt) cc_final: 0.6898 (mmpt)
REVERT: B   43 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7004 (mt-10)
REVERT: B   93 CYS cc_start: 0.6697 (m) cc_final: 0.5888 (t)
REVERT: C   11 LYS cc_start: 0.7541 (mtpp) cc_final: 0.6826 (mttp)
REVERT: C   56 LYS cc_start: 0.7745 (mttt) cc_final: 0.6926 (mmpt)
REVERT: D   61 LYS cc_start: 0.7975 (mttt) cc_final: 0.7638 (mttm)
  outliers start: 8
  outliers final: 4
  residues processed: 88
  average time/residue: 1.4581
  time to fit residues: 132.5009
Evaluate side-chains
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain D residue   11 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.152903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.122959 restraints weight = 3987.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.39
r_work: 0.3186 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4642  Z= 0.137
  Angle     :  0.706  15.928   6358  Z= 0.268
  Chirality :  0.040   0.131    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.643  88.858    620
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.96 %
    Favored  : 81.06 %
  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:  3.73 (0.36), residues: 560
  helix:  2.61 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  2.23 (0.63), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D 116 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.011   0.002   TYR B 130 
 ARG   0.004   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03999 (  333)
  hydrogen bonds       : angle       4.04325 (  942)
  covalent geometry    : bond        0.00312 ( 4638)
  covalent geometry    : angle       0.70565 ( 6358)
  Misc. bond           : bond        0.02126 (    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
  89 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.536 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7608 (mttm) cc_final: 0.7116 (mttp)
REVERT: A   56 LYS cc_start: 0.7787 (mttt) cc_final: 0.6889 (mmpt)
REVERT: B   43 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7089 (mt-10)
REVERT: B   93 CYS cc_start: 0.6739 (m) cc_final: 0.5920 (t)
REVERT: C   11 LYS cc_start: 0.7549 (mtpp) cc_final: 0.6798 (mttt)
REVERT: C   56 LYS cc_start: 0.7812 (mttt) cc_final: 0.6945 (mmpt)
REVERT: D   61 LYS cc_start: 0.8014 (mttt) cc_final: 0.7670 (mttm)
  outliers start: 9
  outliers final: 4
  residues processed: 86
  average time/residue: 1.4667
  time to fit residues: 130.2332
Evaluate side-chains
  86 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain D residue   11 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.153220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.123240 restraints weight = 4002.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.39
r_work: 0.3191 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   4642  Z= 0.135
  Angle     :  0.697  15.698   6358  Z= 0.265
  Chirality :  0.040   0.128    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.547  89.032    620
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  3.74 (0.36), residues: 560
  helix:  2.62 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  2.17 (0.62), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D 116 
 PHE   0.011   0.001   PHE B 118 
 TYR   0.011   0.001   TYR D 130 
 ARG   0.004   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  333)
  hydrogen bonds       : angle       4.03348 (  942)
  covalent geometry    : bond        0.00307 ( 4638)
  covalent geometry    : angle       0.69704 ( 6358)
  Misc. bond           : bond        0.03099 (    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
  88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.551 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7576 (mttm) cc_final: 0.7089 (mttp)
REVERT: A   56 LYS cc_start: 0.7809 (mttt) cc_final: 0.6905 (mmpt)
REVERT: B   93 CYS cc_start: 0.6731 (m) cc_final: 0.5921 (t)
REVERT: C   11 LYS cc_start: 0.7543 (mtpp) cc_final: 0.6790 (mttt)
REVERT: C   56 LYS cc_start: 0.7800 (mttt) cc_final: 0.6982 (mmtt)
REVERT: D   61 LYS cc_start: 0.8006 (mttt) cc_final: 0.7667 (mttm)
  outliers start: 8
  outliers final: 4
  residues processed: 85
  average time/residue: 1.4948
  time to fit residues: 131.3169
Evaluate side-chains
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain D residue   11 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0970
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A  89 HIS
D  63 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.154783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.124907 restraints weight = 4017.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.39
r_work: 0.3212 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4642  Z= 0.113
  Angle     :  0.683  15.917   6358  Z= 0.250
  Chirality :  0.038   0.122    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.240  89.676    620
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 17.84 %
    Favored  : 81.06 %
  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:  3.89 (0.36), residues: 560
  helix:  2.79 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.03 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.011   0.001   PHE B 118 
 TYR   0.010   0.001   TYR D 130 
 ARG   0.005   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03371 (  333)
  hydrogen bonds       : angle       3.89600 (  942)
  covalent geometry    : bond        0.00260 ( 4638)
  covalent geometry    : angle       0.68271 ( 6358)
  Misc. bond           : bond        0.01256 (    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
  87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7611 (mttm) cc_final: 0.7132 (mttp)
REVERT: A   56 LYS cc_start: 0.7791 (mttt) cc_final: 0.6902 (mmpt)
REVERT: A  116 GLU cc_start: 0.7629 (mp0) cc_final: 0.6736 (mm-30)
REVERT: B   93 CYS cc_start: 0.6658 (m) cc_final: 0.5942 (t)
REVERT: C   11 LYS cc_start: 0.7563 (mtpp) cc_final: 0.6854 (mttp)
REVERT: C   56 LYS cc_start: 0.7750 (mttt) cc_final: 0.6961 (mmtt)
REVERT: D   61 LYS cc_start: 0.7969 (mttt) cc_final: 0.7636 (mttm)
REVERT: D  120 LYS cc_start: 0.8198 (mtpp) cc_final: 0.7004 (mmpt)
  outliers start: 5
  outliers final: 3
  residues processed: 85
  average time/residue: 1.6401
  time to fit residues: 143.8371
Evaluate side-chains
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.153800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.123816 restraints weight = 4000.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.38
r_work: 0.3199 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4642  Z= 0.125
  Angle     :  0.693  15.987   6358  Z= 0.259
  Chirality :  0.039   0.126    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.425  88.681    620
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 18.72 %
    Favored  : 80.40 %
  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:  3.81 (0.36), residues: 560
  helix:  2.72 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop :  2.02 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.012   0.001   PHE B 118 
 TYR   0.009   0.001   TYR D 130 
 ARG   0.005   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03697 (  333)
  hydrogen bonds       : angle       3.95700 (  942)
  covalent geometry    : bond        0.00285 ( 4638)
  covalent geometry    : angle       0.69268 ( 6358)
  Misc. bond           : bond        0.01986 (    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
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.541 
Fit side-chains
REVERT: A   11 LYS cc_start: 0.7557 (mttm) cc_final: 0.7065 (mttp)
REVERT: A   56 LYS cc_start: 0.7801 (mttt) cc_final: 0.6904 (mmpt)
REVERT: A  116 GLU cc_start: 0.7620 (mp0) cc_final: 0.6700 (mm-30)
REVERT: B   93 CYS cc_start: 0.6698 (m) cc_final: 0.5966 (t)
REVERT: C   11 LYS cc_start: 0.7587 (mtpp) cc_final: 0.6852 (mttt)
REVERT: C   56 LYS cc_start: 0.7764 (mttt) cc_final: 0.6962 (mmtt)
REVERT: D   61 LYS cc_start: 0.7995 (mttt) cc_final: 0.7658 (mttm)
  outliers start: 4
  outliers final: 3
  residues processed: 83
  average time/residue: 1.6030
  time to fit residues: 137.2468
Evaluate side-chains
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain B residue   11 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.152781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.122893 restraints weight = 4009.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.39
r_work: 0.3191 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4642  Z= 0.135
  Angle     :  0.700  15.661   6358  Z= 0.267
  Chirality :  0.040   0.129    688
  Planarity :  0.005   0.045    794
  Dihedral  : 10.568  88.294    620
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 18.50 %
    Favored  : 80.40 %
  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:  2.61 (0.25), residues: 428
  sheet:  None (None), residues: 0
  loop :  2.07 (0.62), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D 116 
 PHE   0.013   0.001   PHE B 118 
 TYR   0.010   0.001   TYR D 130 
 ARG   0.004   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03937 (  333)
  hydrogen bonds       : angle       4.02867 (  942)
  covalent geometry    : bond        0.00308 ( 4638)
  covalent geometry    : angle       0.70003 ( 6358)
  Misc. bond           : bond        0.03289 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4475.80 seconds
wall clock time: 77 minutes 38.94 seconds (4658.94 seconds total)