Starting phenix.real_space_refine
on Thu Jun  5 01:29:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqs_45821/06_2025/9cqs_45821.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqs_45821/06_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_45821/06_2025/9cqs_45821.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqs_45821/06_2025/9cqs_45821.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqs_45821/06_2025/9cqs_45821.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqs_45821/06_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-5710/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: 4.18, per 1000 atoms: 0.87
  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: 1.27
  Conformation dependent library (CDL) restraints added in 506.6 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: 0.46
  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: 1.24

  Time building geometry restraints manager: 1.48 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:             2.600
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.200
  Find NCS groups from input model:        0.170
  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:13.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.240
-------------------------------------------------------------------------------
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  : 0.538 
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: 1.6026
  time to fit residues: 128.7375
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  : 0.428 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.9384

-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.144012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.122338 restraints weight = 4736.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3393 rms_B_bonded: 1.31
r_work: 0.3292 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.017   0.682   4642  Z= 0.166
  Angle     :  0.746  16.096   6358  Z= 0.279
  Chirality :  0.041   0.161    688
  Planarity :  0.006   0.051    794
  Dihedral  :  9.976  86.365    622
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.61
  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:  3.58 (0.37), residues: 560
  helix:  2.53 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.99 (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   0.015   0.002   TYR C  24 
 ARG   0.004   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04075 (  333)
  hydrogen bonds       : angle       3.76278 (  951)
  covalent geometry    : bond        0.00366 ( 4638)
  covalent geometry    : angle       0.74620 ( 6358)
  Misc. bond           : bond        0.58288 (    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
  88 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.478 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7777 (mttt) cc_final: 0.7193 (mptt)
REVERT: A   92 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7512 (mtp180)
REVERT: B   61 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7216 (tttm)
REVERT: B  120 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7942 (tttp)
REVERT: C   85 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7814 (m-30)
REVERT: C   90 LYS cc_start: 0.8290 (mptt) cc_final: 0.7734 (tttt)
REVERT: D   90 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7335 (tp30)
REVERT: D  120 LYS cc_start: 0.8388 (mtpp) cc_final: 0.7733 (ptmm)
  outliers start: 14
  outliers final: 3
  residues processed: 82
  average time/residue: 1.6379
  time to fit residues: 138.5339
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  : 0.520 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0170
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.4536

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.145899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.124357 restraints weight = 4805.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.32
r_work: 0.3317 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.1152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.193   4642  Z= 0.108
  Angle     :  0.697  15.228   6358  Z= 0.245
  Chirality :  0.038   0.159    688
  Planarity :  0.005   0.048    794
  Dihedral  :  9.628  87.102    620
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.42 %
    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:  3.94 (0.37), residues: 560
  helix:  2.81 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop :  2.05 (0.66), residues: 128

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   0.007   0.001   PHE B 118 
 TYR   0.011   0.001   TYR C  24 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03039 (  333)
  hydrogen bonds       : angle       3.54030 (  951)
  covalent geometry    : bond        0.00257 ( 4638)
  covalent geometry    : angle       0.69672 ( 6358)
  Misc. bond           : bond        0.14373 (    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
  83 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7649 (mttt) cc_final: 0.7104 (mptt)
REVERT: A   92 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7539 (mtp180)
REVERT: B  120 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7629 (mttt)
REVERT: C   16 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7451 (tmtm)
REVERT: C   85 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7727 (m-30)
REVERT: C   90 LYS cc_start: 0.8297 (mptt) cc_final: 0.7713 (tttt)
REVERT: C  116 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7498 (mp0)
REVERT: D   90 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7304 (tp30)
REVERT: D  120 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7660 (ptmm)
  outliers start: 11
  outliers final: 1
  residues processed: 79
  average time/residue: 1.5752
  time to fit residues: 128.3306
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  : 0.516 
-------------------------------------------------------------------------------
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   16 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:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   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  50 HIS
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 127 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.148492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.126794 restraints weight = 4874.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.32
r_work: 0.3335 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.130   4642  Z= 0.136
  Angle     :  0.754  15.996   6358  Z= 0.265
  Chirality :  0.040   0.174    688
  Planarity :  0.005   0.048    794
  Dihedral  :  9.728  85.338    620
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.52 %
    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:  3.71 (0.36), residues: 560
  helix:  2.63 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  2.01 (0.66), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C  14 
 HIS   0.005   0.001   HIS B 116 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.012   0.001   TYR C  24 
 ARG   0.004   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  333)
  hydrogen bonds       : angle       3.64767 (  951)
  covalent geometry    : bond        0.00328 ( 4638)
  covalent geometry    : angle       0.75357 ( 6358)
  Misc. bond           : bond        0.10913 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7730 (mttt) cc_final: 0.7214 (mptt)
REVERT: A   76 MET cc_start: 0.7948 (mtt) cc_final: 0.7541 (mtt)
REVERT: A   92 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7635 (mtp180)
REVERT: B  120 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7616 (tttm)
REVERT: C   85 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7845 (m-30)
REVERT: C   90 LYS cc_start: 0.8314 (mptt) cc_final: 0.7810 (tttt)
REVERT: C  116 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7675 (mp0)
REVERT: D   90 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7336 (tp30)
REVERT: D  120 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7728 (ptmm)
  outliers start: 14
  outliers final: 3
  residues processed: 74
  average time/residue: 1.7019
  time to fit residues: 129.6540
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
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   14 LEU
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:    0.1980
   chunk 5 optimal weight:    0.0040
   chunk 44 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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**
C  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.150164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.128470 restraints weight = 4919.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.34
r_work: 0.3353 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092   4642  Z= 0.112
  Angle     :  0.726  15.783   6358  Z= 0.250
  Chirality :  0.038   0.172    688
  Planarity :  0.005   0.047    794
  Dihedral  :  9.582  86.182    620
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.62 %
    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:  3.90 (0.36), residues: 560
  helix:  2.79 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop :  2.01 (0.66), residues: 128

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   0.010   0.001   TYR C  24 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03167 (  333)
  hydrogen bonds       : angle       3.53667 (  951)
  covalent geometry    : bond        0.00270 ( 4638)
  covalent geometry    : angle       0.72617 ( 6358)
  Misc. bond           : bond        0.06918 (    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: 9
    poor density    : 66
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7652 (mttt) cc_final: 0.7144 (mptt)
REVERT: A   92 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7639 (mtp180)
REVERT: B  120 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7623 (tttm)
REVERT: C   85 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7772 (m-30)
REVERT: C   90 LYS cc_start: 0.8297 (mptt) cc_final: 0.7799 (tttt)
REVERT: D   55 MET cc_start: 0.8626 (mmm) cc_final: 0.8377 (mmm)
REVERT: D   90 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7328 (tp30)
REVERT: D  120 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7691 (ptmm)
  outliers start: 9
  outliers final: 1
  residues processed: 72
  average time/residue: 1.6277
  time to fit residues: 120.8261
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
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 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:    0.0370
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.7260

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.148924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.127396 restraints weight = 4821.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.31
r_work: 0.3342 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   4642  Z= 0.128
  Angle     :  0.754  16.099   6358  Z= 0.261
  Chirality :  0.040   0.178    688
  Planarity :  0.005   0.046    794
  Dihedral  :  9.631  85.128    620
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.18 %
    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:  3.76 (0.36), residues: 560
  helix:  2.69 (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   0.009   0.001   TRP C  14 
 HIS   0.004   0.001   HIS B 116 
 PHE   0.009   0.001   PHE D 118 
 TYR   0.009   0.001   TYR C  24 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  333)
  hydrogen bonds       : angle       3.60652 (  951)
  covalent geometry    : bond        0.00306 ( 4638)
  covalent geometry    : angle       0.75438 ( 6358)
  Misc. bond           : bond        0.08757 (    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
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7718 (mttt) cc_final: 0.7191 (mptt)
REVERT: A   76 MET cc_start: 0.7904 (mtt) cc_final: 0.7699 (mtt)
REVERT: A   92 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7638 (mtp180)
REVERT: B  120 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7777 (mttt)
REVERT: C   85 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7830 (m-30)
REVERT: C   90 LYS cc_start: 0.8303 (mptt) cc_final: 0.7826 (tttt)
REVERT: D   90 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7363 (tp30)
REVERT: D  120 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7731 (ptmm)
  outliers start: 11
  outliers final: 4
  residues processed: 72
  average time/residue: 2.1704
  time to fit residues: 161.1131
Evaluate side-chains
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.3689 r_free = 0.3689 target = 0.148964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.127569 restraints weight = 4760.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.30
r_work: 0.3343 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.179   4642  Z= 0.128
  Angle     :  0.756  16.196   6358  Z= 0.260
  Chirality :  0.040   0.184    688
  Planarity :  0.005   0.047    794
  Dihedral  :  9.605  85.237    620
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.62 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.75 (0.36), residues: 560
  helix:  2.70 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.88 (0.65), 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   0.009   0.001   PHE D 118 
 TYR   0.009   0.001   TYR C  24 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03487 (  333)
  hydrogen bonds       : angle       3.61448 (  951)
  covalent geometry    : bond        0.00307 ( 4638)
  covalent geometry    : angle       0.75576 ( 6358)
  Misc. bond           : bond        0.11176 (    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
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.487 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7760 (mttt) cc_final: 0.7205 (mptt)
REVERT: A   76 MET cc_start: 0.7940 (mtt) cc_final: 0.7581 (mtt)
REVERT: A   92 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7625 (mtp180)
REVERT: B   43 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7115 (mp0)
REVERT: B  120 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7815 (mttt)
REVERT: C   85 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7828 (m-30)
REVERT: C   90 LYS cc_start: 0.8324 (mptt) cc_final: 0.7842 (tttt)
REVERT: D   55 MET cc_start: 0.8674 (mmm) cc_final: 0.8385 (mmm)
REVERT: D   90 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7397 (tp30)
REVERT: D  120 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7724 (ptmm)
  outliers start: 11
  outliers final: 3
  residues processed: 70
  average time/residue: 1.6166
  time to fit residues: 116.6505
Evaluate side-chains
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
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   43 GLU
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   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:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  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 = 0.3678 r_free = 0.3678 target = 0.148272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.126659 restraints weight = 4808.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.33
r_work: 0.3339 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.178   4642  Z= 0.129
  Angle     :  0.761  16.181   6358  Z= 0.262
  Chirality :  0.040   0.188    688
  Planarity :  0.006   0.046    794
  Dihedral  :  9.591  84.721    620
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.84 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.74 (0.36), residues: 560
  helix:  2.69 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.86 (0.65), 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   0.009   0.001   PHE D 118 
 TYR   0.008   0.001   TYR C  24 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  333)
  hydrogen bonds       : angle       3.61068 (  951)
  covalent geometry    : bond        0.00309 ( 4638)
  covalent geometry    : angle       0.76072 ( 6358)
  Misc. bond           : bond        0.11302 (    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
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7759 (mttt) cc_final: 0.7198 (mptt)
REVERT: A   76 MET cc_start: 0.7940 (mtt) cc_final: 0.7575 (mtt)
REVERT: A   92 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7636 (mtp180)
REVERT: B  120 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7776 (mttt)
REVERT: C   85 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7831 (m-30)
REVERT: C   90 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7835 (tttt)
REVERT: D   90 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7385 (tp30)
REVERT: D  120 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7730 (ptmm)
  outliers start: 11
  outliers final: 4
  residues processed: 67
  average time/residue: 1.9773
  time to fit residues: 136.6120
Evaluate side-chains
  68 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
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 C residue   90 LYS
Chi-restraints excluded: chain D residue   14 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:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   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 = 0.3626 r_free = 0.3626 target = 0.146204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121696 restraints weight = 4652.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.47
r_work: 0.3207 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.191   4642  Z= 0.130
  Angle     :  0.765  16.273   6358  Z= 0.264
  Chirality :  0.040   0.183    688
  Planarity :  0.006   0.046    794
  Dihedral  :  9.604  84.897    620
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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:  3.71 (0.36), residues: 560
  helix:  2.68 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.83 (0.65), 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   0.009   0.001   PHE D 118 
 TYR   0.008   0.001   TYR C  24 
 ARG   0.006   0.001   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  333)
  hydrogen bonds       : angle       3.62147 (  951)
  covalent geometry    : bond        0.00314 ( 4638)
  covalent geometry    : angle       0.76464 ( 6358)
  Misc. bond           : bond        0.11552 (    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
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 1.488 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7608 (mttt) cc_final: 0.6785 (mptt)
REVERT: A   76 MET cc_start: 0.7810 (mtt) cc_final: 0.7421 (mtt)
REVERT: A   92 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7489 (mtp180)
REVERT: B  120 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7646 (mttt)
REVERT: C   85 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7706 (m-30)
REVERT: C   90 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7740 (tttt)
REVERT: D   90 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7199 (tp30)
REVERT: D  120 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7534 (ptmm)
  outliers start: 9
  outliers final: 4
  residues processed: 66
  average time/residue: 2.2410
  time to fit residues: 154.2119
Evaluate side-chains
  69 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
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 C residue   90 LYS
Chi-restraints excluded: chain D residue   14 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:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0670
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 2 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.147324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.123003 restraints weight = 4626.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.46
r_work: 0.3223 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.129   4642  Z= 0.113
  Angle     :  0.740  15.943   6358  Z= 0.253
  Chirality :  0.039   0.176    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.495  85.212    620
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.37
  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:  3.91 (0.36), residues: 560
  helix:  2.81 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.96 (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   0.008   0.001   PHE D 118 
 TYR   0.007   0.001   TYR D  35 
 ARG   0.005   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  333)
  hydrogen bonds       : angle       3.54944 (  951)
  covalent geometry    : bond        0.00272 ( 4638)
  covalent geometry    : angle       0.73997 ( 6358)
  Misc. bond           : bond        0.08524 (    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
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.614 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.7548 (mttt) cc_final: 0.6742 (mptt)
REVERT: A   92 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7508 (mtp180)
REVERT: B  120 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7608 (mttt)
REVERT: C   85 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7661 (m-30)
REVERT: C   90 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7724 (tttt)
REVERT: D   90 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7156 (tp30)
REVERT: D  120 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7517 (ptmm)
  outliers start: 9
  outliers final: 3
  residues processed: 67
  average time/residue: 2.7387
  time to fit residues: 190.0524
Evaluate side-chains
  67 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
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   14 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 6 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0970
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0670
   overall best weight:    0.4716

-------------------------------------------------------------------------------
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 = 0.148217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.123829 restraints weight = 4619.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.46
r_work: 0.3232 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.105   4642  Z= 0.107
  Angle     :  0.723  15.749   6358  Z= 0.248
  Chirality :  0.038   0.179    688
  Planarity :  0.005   0.045    794
  Dihedral  :  9.401  85.328    620
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.84 %
    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:  4.02 (0.37), residues: 560
  helix:  2.89 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.00 (0.66), 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        0.03063 (  333)
  hydrogen bonds       : angle       3.51558 (  951)
  covalent geometry    : bond        0.00259 ( 4638)
  covalent geometry    : angle       0.72265 ( 6358)
  Misc. bond           : bond        0.07272 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4345.98 seconds
wall clock time: 77 minutes 8.74 seconds (4628.74 seconds total)