Starting phenix.real_space_refine
on Sat May 10 02:54:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqs_45821/05_2025/9cqs_45821.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqs_45821/05_2025/9cqs_45821.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqs_45821/05_2025/9cqs_45821.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqs_45821/05_2025/9cqs_45821.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqs_45821/05_2025/9cqs_45821.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqs_45821/05_2025/9cqs_45821.cif"
  }
  resolution = 2.52
  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=   0.023
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 13 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: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 78
          Classifications: {'water': 78}
          Link IDs: {None: 77}
    Chain: "B"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 59
          Classifications: {'water': 59}
          Link IDs: {None: 58}
    Chain: "C"
      Number of atoms: 92
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 92
          Classifications: {'water': 92}
          Link IDs: {None: 91}
    Chain: "D"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 61
          Classifications: {'water': 61}
          Link IDs: {None: 60}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   HOH B 331 " occ=0.78
  Time building chain proxies: 3.94, per 1000 atoms: 0.82
  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: 1.06
  Conformation dependent library (CDL) restraints added in 475.7 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:
      38 helices and 0 sheets defined
      87.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 18
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
      removed outlier: 3.683A  pdb=" N   THR A  41 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR A  42 " --> pdb=" O   THR A  39 " (cutoff:3.500A)
    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 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 4.105A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
      removed outlier: 3.761A  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 18
      removed outlier: 3.985A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   VAL B  18 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.370A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 3.809A  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 77
    Processing helix  chain 'B' and resid 80 through 85
    Processing helix  chain 'B' and resid 85 through 94
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.027A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.667A  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 18
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
      removed outlier: 3.597A  pdb=" N   THR C  41 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   TYR C  42 " --> pdb=" O   THR C  39 " (cutoff:3.500A)
    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 89
    Processing helix  chain 'C' and resid 94 through 113
      removed outlier: 4.100A  pdb=" N   PHE C  98 " --> pdb=" O   ASP C  94 " (cutoff:3.500A)
      removed outlier: 3.826A  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: 3.977A  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 46
      removed outlier: 4.092A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   SER D  44 " --> pdb=" O   PHE D  41 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (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
      removed outlier: 3.550A  pdb=" N   LYS D  95 " --> pdb=" O   LEU D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 119
      removed outlier: 3.739A  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.
    951 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: 1.01

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.20 -     1.38: 1627
        1.38 -     1.55: 2966
        1.55 -     1.72: 11
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4638
  Sorted by residual:
  bond pdb=" N   VAL B  18 "
       pdb=" CA  VAL B  18 "
    ideal  model  delta    sigma   weight residual
    1.458  1.497 -0.040 1.27e-02 6.20e+03 9.75e+00
  bond pdb=" N   VAL B  23 "
       pdb=" CA  VAL B  23 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.17e-02 7.31e+03 9.74e+00
  bond pdb=" N   ASN B  19 "
       pdb=" CA  ASN B  19 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.22e-02 6.72e+03 7.07e+00
  bond pdb=" N   TRP B  15 "
       pdb=" CA  TRP B  15 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 6.92e+00
  bond pdb=" N   LYS B  17 "
       pdb=" CA  LYS B  17 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 6.86e+00
  ... (remaining 4633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 6139
        1.78 -     3.56: 181
        3.56 -     5.34: 32
        5.34 -     7.12: 5
        7.12 -     8.90: 1
  Bond angle restraints: 6358
  Sorted by residual:
  angle pdb=" CA  LYS A  16 "
        pdb=" CB  LYS A  16 "
        pdb=" CG  LYS A  16 "
      ideal   model   delta    sigma   weight residual
     114.10  123.00   -8.90 2.00e+00 2.50e-01 1.98e+01
  angle pdb=" CA  LYS B  17 "
        pdb=" C   LYS B  17 "
        pdb=" O   LYS B  17 "
      ideal   model   delta    sigma   weight residual
     120.55  116.92    3.63 1.06e+00 8.90e-01 1.17e+01
  angle pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
        pdb=" O   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     121.17  117.63    3.54 1.06e+00 8.90e-01 1.12e+01
  angle pdb=" CA  SER C 133 "
        pdb=" C   SER C 133 "
        pdb=" O   SER C 133 "
      ideal   model   delta    sigma   weight residual
     120.55  117.05    3.50 1.06e+00 8.90e-01 1.09e+01
  angle pdb=" CA  GLY B  24 "
        pdb=" C   GLY B  24 "
        pdb=" O   GLY B  24 "
      ideal   model   delta    sigma   weight residual
     120.75  117.57    3.18 1.03e+00 9.43e-01 9.53e+00
  ... (remaining 6353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 2247
       17.14 -    34.28: 262
       34.28 -    51.43: 90
       51.43 -    68.57: 19
       68.57 -    85.71: 8
  Dihedral angle restraints: 2626
    sinusoidal: 998
      harmonic: 1628
  Sorted by residual:
  dihedral pdb=" CA  LYS C  16 "
           pdb=" C   LYS C  16 "
           pdb=" N   VAL C  17 "
           pdb=" CA  VAL C  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.68   17.32     0      5.00e+00 4.00e-02 1.20e+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
       0.00   85.71  -85.71     2      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" C2D HEM D 201 "
           pdb=" C3D HEM D 201 "
           pdb=" CAD HEM D 201 "
           pdb=" CBD HEM D 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  100.77   79.23     2      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 2623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 616
       0.070 -    0.141: 64
       0.141 -    0.211: 6
       0.211 -    0.281: 1
       0.281 -    0.352: 1
  Chirality restraints: 688
  Sorted by residual:
  chirality pdb=" CB  VAL B  18 "
            pdb=" CA  VAL B  18 "
            pdb=" CG1 VAL B  18 "
            pdb=" CG2 VAL B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CA  VAL B  18 "
            pdb=" N   VAL B  18 "
            pdb=" C   VAL B  18 "
            pdb=" CB  VAL B  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.71   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  VAL C 132 "
            pdb=" N   VAL C 132 "
            pdb=" C   VAL C 132 "
            pdb=" CB  VAL C 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.33e-01
  ... (remaining 685 not shown)

  Planarity restraints: 794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  94 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO C  95 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  94 "    0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A  95 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  19 "    0.008 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   ASN B  19 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASN B  19 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL B  20 "    0.010 2.00e-02 2.50e+03
  ... (remaining 791 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 149
        2.66 -     3.22: 4300
        3.22 -     3.78: 8370
        3.78 -     4.34: 11759
        4.34 -     4.90: 18228
  Nonbonded interactions: 42806
  Sorted by model distance:
  nonbonded pdb=" O   VAL C  93 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" NE2 HIS D  92 "
            pdb="FE   HEM D 201 "
     model   vdw
     2.139 3.080
  nonbonded pdb=" NE2 HIS B  92 "
            pdb="FE   HEM B 201 "
     model   vdw
     2.145 3.080
  nonbonded pdb=" NE2 HIS A  87 "
            pdb="FE   HEM A 201 "
     model   vdw
     2.157 3.080
  nonbonded pdb=" O   HOH A 323 "
            pdb=" O   HOH A 366 "
     model   vdw
     2.161 3.040
  ... (remaining 42801 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=0.78 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:             2.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.760
  Find NCS groups from input model:        0.160
  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:10.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
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      :  0.013   0.580   4642  Z= 0.257
  Angle     :  0.710   8.899   6358  Z= 0.414
  Chirality :  0.048   0.352    688
  Planarity :  0.006   0.051    794
  Dihedral  : 17.313  85.710   1574
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 17.84 %
    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:  3.54 (0.37), residues: 560
  helix:  2.54 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.83 (0.68), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  15 
 HIS   0.006   0.001   HIS B 116 
 PHE   0.018   0.002   PHE D  45 
 TYR   0.010   0.002   TYR D  35 
 ARG   0.004   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09791 (  333)
  hydrogen bonds       : angle       4.05617 (  951)
  covalent geometry    : bond        0.00464 ( 4638)
  covalent geometry    : angle       0.71011 ( 6358)
  Misc. bond           : bond        0.42848 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7647 (mttt) cc_final: 0.6870 (mptt)
REVERT: A   76 MET cc_start: 0.7901 (mtt) cc_final: 0.7531 (mtt)
REVERT: B   61 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7126 (tttm)
REVERT: C   90 LYS cc_start: 0.8264 (mptt) cc_final: 0.7726 (tttt)
REVERT: D  120 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7610 (ptmm)
  outliers start: 4
  outliers final: 1
  residues processed: 78
  average time/residue: 1.6513
  time to fit residues: 132.6107
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   83 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
A  68 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.143957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.122273 restraints weight = 4733.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.32
r_work: 0.3289 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.0821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.018   0.684   4642  Z= 0.167
  Angle     :  0.734  15.355   6358  Z= 0.279
  Chirality :  0.041   0.162    688
  Planarity :  0.006   0.051    794
  Dihedral  :  9.993  86.254    622
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 13.66 %
    Favored  : 83.26 %
  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:  3.56 (0.37), residues: 560
  helix:  2.53 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.98 (0.67), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  14 
 HIS   0.005   0.001   HIS B 116 
 PHE   0.013   0.002   PHE D  45 
 TYR   0.016   0.002   TYR C  24 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04101 (  333)
  hydrogen bonds       : angle       3.76565 (  951)
  covalent geometry    : bond        0.00372 ( 4638)
  covalent geometry    : angle       0.73393 ( 6358)
  Misc. bond           : bond        0.58647 (    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: 14
    poor density    : 75
  time to evaluate  : 0.555 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7786 (mttt) cc_final: 0.7191 (mptt)
REVERT: A   92 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7521 (mtp180)
REVERT: B   61 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7217 (tttm)
REVERT: B  120 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7938 (tttp)
REVERT: C   85 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7824 (m-30)
REVERT: C   90 LYS cc_start: 0.8279 (mptt) cc_final: 0.7726 (tttt)
REVERT: D   90 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7274 (tp30)
REVERT: D  120 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7729 (ptmm)
  outliers start: 14
  outliers final: 3
  residues processed: 83
  average time/residue: 1.5777
  time to fit residues: 134.9088
Evaluate side-chains
  76 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   61 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   14 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0040
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.145061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.123425 restraints weight = 4803.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.32
r_work: 0.3302 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.252   4642  Z= 0.115
  Angle     :  0.706  15.145   6358  Z= 0.251
  Chirality :  0.038   0.167    688
  Planarity :  0.005   0.048    794
  Dihedral  :  9.696  86.941    620
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.86 %
    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:  3.85 (0.37), residues: 560
  helix:  2.75 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop :  2.00 (0.66), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C 103 
 PHE   0.008   0.001   PHE B 118 
 TYR   0.012   0.001   TYR C  24 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03242 (  333)
  hydrogen bonds       : angle       3.57981 (  951)
  covalent geometry    : bond        0.00277 ( 4638)
  covalent geometry    : angle       0.70607 ( 6358)
  Misc. bond           : bond        0.17353 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7675 (mttt) cc_final: 0.7111 (mptt)
REVERT: A   92 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7531 (mtp180)
REVERT: B  120 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7628 (mttt)
REVERT: C   16 LYS cc_start: 0.8161 (tmtm) cc_final: 0.7949 (mmmt)
REVERT: C   85 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7741 (m-30)
REVERT: C   90 LYS cc_start: 0.8298 (mptt) cc_final: 0.7723 (tttt)
REVERT: C  116 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7557 (mp0)
REVERT: D   90 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7291 (tp30)
REVERT: D  120 LYS cc_start: 0.8372 (mtpp) cc_final: 0.7665 (ptmm)
  outliers start: 9
  outliers final: 2
  residues processed: 78
  average time/residue: 1.5839
  time to fit residues: 127.4698
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0670
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.144015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.122045 restraints weight = 4845.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.34
r_work: 0.3291 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.101   4642  Z= 0.122
  Angle     :  0.738  15.878   6358  Z= 0.257
  Chirality :  0.039   0.169    688
  Planarity :  0.005   0.047    794
  Dihedral  :  9.643  85.600    620
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.96 %
    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:  3.80 (0.37), residues: 560
  helix:  2.71 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.98 (0.66), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B 116 
 PHE   0.008   0.001   PHE D 118 
 TYR   0.010   0.001   TYR C  24 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03475 (  333)
  hydrogen bonds       : angle       3.58856 (  951)
  covalent geometry    : bond        0.00292 ( 4638)
  covalent geometry    : angle       0.73810 ( 6358)
  Misc. bond           : bond        0.08278 (    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
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7728 (mttt) cc_final: 0.7150 (mptt)
REVERT: A   76 MET cc_start: 0.7904 (mtt) cc_final: 0.7554 (mtt)
REVERT: A   92 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7570 (mtp180)
REVERT: B  120 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7570 (tttm)
REVERT: C   85 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7753 (m-30)
REVERT: C   90 LYS cc_start: 0.8311 (mptt) cc_final: 0.7772 (tttt)
REVERT: C  116 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7667 (mp0)
REVERT: D   90 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7335 (tp30)
REVERT: D  120 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7666 (ptmm)
  outliers start: 11
  outliers final: 2
  residues processed: 75
  average time/residue: 1.5703
  time to fit residues: 121.3673
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0270
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.149311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127811 restraints weight = 4915.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.32
r_work: 0.3347 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   4642  Z= 0.123
  Angle     :  0.745  16.041   6358  Z= 0.258
  Chirality :  0.039   0.176    688
  Planarity :  0.005   0.046    794
  Dihedral  :  9.619  85.427    620
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.96 %
    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:  3.81 (0.36), residues: 560
  helix:  2.73 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.93 (0.65), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C  14 
 HIS   0.004   0.001   HIS B 116 
 PHE   0.008   0.001   PHE D 118 
 TYR   0.010   0.001   TYR C  24 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  333)
  hydrogen bonds       : angle       3.59375 (  951)
  covalent geometry    : bond        0.00296 ( 4638)
  covalent geometry    : angle       0.74458 ( 6358)
  Misc. bond           : bond        0.07459 (    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
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7699 (mttt) cc_final: 0.7172 (mptt)
REVERT: A   92 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7628 (mtp180)
REVERT: B   82 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7460 (mptt)
REVERT: B  120 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7582 (tttm)
REVERT: C   85 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7788 (m-30)
REVERT: C   90 LYS cc_start: 0.8304 (mptt) cc_final: 0.7819 (tttt)
REVERT: D   55 MET cc_start: 0.8665 (mmm) cc_final: 0.8385 (mmm)
REVERT: D   90 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7362 (tp30)
REVERT: D  120 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7715 (ptmm)
  outliers start: 11
  outliers final: 3
  residues processed: 72
  average time/residue: 1.6712
  time to fit residues: 123.8587
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.143470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.120777 restraints weight = 4810.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.38
r_work: 0.3299 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.265   4642  Z= 0.190
  Angle     :  0.806  16.270   6358  Z= 0.297
  Chirality :  0.044   0.189    688
  Planarity :  0.006   0.046    794
  Dihedral  :  9.953  84.382    620
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.96 %
    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:  3.31 (0.36), residues: 560
  helix:  2.38 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.73 (0.65), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  14 
 HIS   0.007   0.002   HIS B 116 
 PHE   0.013   0.002   PHE D 118 
 TYR   0.012   0.002   TYR C  24 
 ARG   0.004   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04521 (  333)
  hydrogen bonds       : angle       3.82135 (  951)
  covalent geometry    : bond        0.00461 ( 4638)
  covalent geometry    : angle       0.80647 ( 6358)
  Misc. bond           : bond        0.15494 (    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
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7845 (mttt) cc_final: 0.7260 (mptt)
REVERT: A   76 MET cc_start: 0.8007 (mtt) cc_final: 0.7658 (mtt)
REVERT: A   92 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7629 (mtp180)
REVERT: B  120 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7821 (mttt)
REVERT: C   85 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7875 (m-30)
REVERT: C   90 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7854 (tttt)
REVERT: D   95 LYS cc_start: 0.7976 (tttm) cc_final: 0.7416 (mmtp)
REVERT: D  120 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7739 (ptmm)
  outliers start: 13
  outliers final: 2
  residues processed: 69
  average time/residue: 1.6558
  time to fit residues: 117.8595
Evaluate side-chains
  67 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3667 r_free = 0.3667 target = 0.146523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.124488 restraints weight = 4699.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.33
r_work: 0.3328 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.212   4642  Z= 0.136
  Angle     :  0.768  16.515   6358  Z= 0.266
  Chirality :  0.040   0.179    688
  Planarity :  0.006   0.045    794
  Dihedral  :  9.734  86.408    620
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.74 %
    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:  3.54 (0.36), residues: 560
  helix:  2.57 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.72 (0.64), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C  14 
 HIS   0.005   0.001   HIS B 116 
 PHE   0.010   0.001   PHE D 118 
 TYR   0.008   0.001   TYR C  24 
 ARG   0.004   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  333)
  hydrogen bonds       : angle       3.67965 (  951)
  covalent geometry    : bond        0.00328 ( 4638)
  covalent geometry    : angle       0.76791 ( 6358)
  Misc. bond           : bond        0.12714 (    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
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7794 (mttt) cc_final: 0.7233 (mptt)
REVERT: A   76 MET cc_start: 0.7962 (mtt) cc_final: 0.7707 (mtt)
REVERT: A   92 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7644 (mtp180)
REVERT: B  120 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7840 (mttt)
REVERT: C   85 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7868 (m-30)
REVERT: C   90 LYS cc_start: 0.8322 (mptt) cc_final: 0.7853 (tttt)
REVERT: D  120 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7727 (ptmm)
  outliers start: 14
  outliers final: 4
  residues processed: 71
  average time/residue: 1.5858
  time to fit residues: 116.1249
Evaluate side-chains
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   59 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  120 LYS
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:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 1 optimal weight:    0.3980
   chunk 28 optimal weight:    0.0030
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3667 r_free = 0.3667 target = 0.147120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.124693 restraints weight = 4756.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.37
r_work: 0.3350 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.124   4642  Z= 0.111
  Angle     :  0.735  15.980   6358  Z= 0.251
  Chirality :  0.038   0.179    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.542  86.474    620
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.28 %
    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:  3.89 (0.36), residues: 560
  helix:  2.80 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.92 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  14 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.007   0.001   PHE D 118 
 TYR   0.007   0.001   TYR B 130 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03166 (  333)
  hydrogen bonds       : angle       3.56290 (  951)
  covalent geometry    : bond        0.00267 ( 4638)
  covalent geometry    : angle       0.73515 ( 6358)
  Misc. bond           : bond        0.08125 (    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
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7741 (mttt) cc_final: 0.7183 (mptt)
REVERT: A   76 MET cc_start: 0.7938 (mtt) cc_final: 0.7599 (mtt)
REVERT: A   92 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7640 (mtp180)
REVERT: B   82 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7449 (mptt)
REVERT: B  120 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7817 (mttt)
REVERT: C   85 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7825 (m-30)
REVERT: C   90 LYS cc_start: 0.8320 (mptt) cc_final: 0.7835 (tttt)
REVERT: D  120 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7718 (ptmm)
  outliers start: 9
  outliers final: 2
  residues processed: 69
  average time/residue: 1.6393
  time to fit residues: 116.7087
Evaluate side-chains
  67 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   82 LYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   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  97 ASN ** 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 = 0.3623 r_free = 0.3623 target = 0.145952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.121419 restraints weight = 4650.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 1.47
r_work: 0.3203 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.189   4642  Z= 0.130
  Angle     :  0.763  16.252   6358  Z= 0.264
  Chirality :  0.040   0.188    688
  Planarity :  0.006   0.044    794
  Dihedral  :  9.599  85.238    620
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 18.72 %
    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:  3.70 (0.36), residues: 560
  helix:  2.67 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.84 (0.65), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C  14 
 HIS   0.004   0.001   HIS B 116 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.008   0.001   TYR D  35 
 ARG   0.004   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03597 (  333)
  hydrogen bonds       : angle       3.63529 (  951)
  covalent geometry    : bond        0.00313 ( 4638)
  covalent geometry    : angle       0.76256 ( 6358)
  Misc. bond           : bond        0.11834 (    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
  66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7603 (mttt) cc_final: 0.6762 (mptt)
REVERT: A   76 MET cc_start: 0.7834 (mtt) cc_final: 0.7548 (mtt)
REVERT: A   92 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7521 (mtp180)
REVERT: B  120 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7614 (mttt)
REVERT: C   85 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7686 (m-30)
REVERT: C   90 LYS cc_start: 0.8349 (mptt) cc_final: 0.7730 (tttt)
REVERT: D  120 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7509 (ptmm)
  outliers start: 7
  outliers final: 2
  residues processed: 64
  average time/residue: 2.0119
  time to fit residues: 132.8009
Evaluate side-chains
  65 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain D residue  120 LYS
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:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 25 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   chunk 2 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.147383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.122998 restraints weight = 4627.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 1.47
r_work: 0.3227 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.120   4642  Z= 0.110
  Angle     :  0.736  16.017   6358  Z= 0.252
  Chirality :  0.038   0.178    688
  Planarity :  0.005   0.044    794
  Dihedral  :  9.505  85.994    620
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.72 %
    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:  3.94 (0.36), residues: 560
  helix:  2.83 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.98 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  14 
 HIS   0.003   0.001   HIS D 116 
 PHE   0.007   0.001   PHE D 118 
 TYR   0.007   0.001   TYR B 130 
 ARG   0.005   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03132 (  333)
  hydrogen bonds       : angle       3.56225 (  951)
  covalent geometry    : bond        0.00266 ( 4638)
  covalent geometry    : angle       0.73582 ( 6358)
  Misc. bond           : bond        0.07966 (    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
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7539 (mttt) cc_final: 0.6731 (mptt)
REVERT: A   76 MET cc_start: 0.7824 (mtt) cc_final: 0.7475 (mtt)
REVERT: A   92 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7530 (mtp180)
REVERT: B  120 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7645 (mttt)
REVERT: C   85 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7662 (m-30)
REVERT: C   90 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7711 (tttt)
REVERT: D   26 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7644 (tt0)
REVERT: D  120 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7478 (ptmm)
  outliers start: 8
  outliers final: 2
  residues processed: 64
  average time/residue: 1.5778
  time to fit residues: 104.2732
Evaluate side-chains
  66 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ARG
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue   85 ASP
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue   90 LYS
Chi-restraints excluded: chain D residue  120 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0870
   chunk 26 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:    0.1980
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 ASN ** 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 = 0.3649 r_free = 0.3649 target = 0.148233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.123999 restraints weight = 4621.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 1.46
r_work: 0.3237 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.095   4642  Z= 0.105
  Angle     :  0.717  15.578   6358  Z= 0.248
  Chirality :  0.038   0.180    688
  Planarity :  0.005   0.043    794
  Dihedral  :  9.380  85.788    620
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.72 %
    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:  4.05 (0.36), residues: 560
  helix:  2.91 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.04 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  14 
 HIS   0.003   0.001   HIS C 103 
 PHE   0.006   0.001   PHE B 118 
 TYR   0.007   0.001   TYR B 130 
 ARG   0.006   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02981 (  333)
  hydrogen bonds       : angle       3.51126 (  951)
  covalent geometry    : bond        0.00254 ( 4638)
  covalent geometry    : angle       0.71696 ( 6358)
  Misc. bond           : bond        0.06642 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3849.87 seconds
wall clock time: 67 minutes 9.59 seconds (4029.59 seconds total)