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

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

  Found model, /net/cci-nas-00/data/ceres_data/9cqt_45822/06_2025/9cqt_45822.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cqt_45822/06_2025/9cqt_45822.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cqt_45822/06_2025/9cqt_45822.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cqt_45822/06_2025/9cqt_45822.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cqt_45822/06_2025/9cqt_45822.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cqt_45822/06_2025/9cqt_45822.cif"
  }
  resolution = 2.37
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.027
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 21 residue(s): 0.03s

  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: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 79
          Classifications: {'water': 79}
          Link IDs: {None: 78}
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 61
          Classifications: {'water': 61}
          Link IDs: {None: 60}
    Chain: "C"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 87
          Classifications: {'water': 87}
          Link IDs: {None: 86}
    Chain: "D"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 63
          Classifications: {'water': 63}
          Link IDs: {None: 62}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" O   HOH B 318 " occ=0.59
  Time building chain proxies: 4.32, per 1000 atoms: 0.90
  Number of scatterers: 4790
  At special positions: 0
  Unit cell: (77.175, 72.765, 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 545.5 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
      87.5% 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
    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 95 through 113
      removed outlier: 3.789A  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 17
      removed outlier: 3.925A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 4.180A  pdb=" N   GLU B  43 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   SER B  44 " --> pdb=" O   PHE B  41 " (cutoff:3.500A)
      removed outlier: 4.107A  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 95
    Processing helix  chain 'B' and resid 99 through 119
      removed outlier: 4.040A  pdb=" N   PHE B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.664A  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: 3.506A  pdb=" N   THR C  41 " --> pdb=" O   THR C  38 " (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 90
    Processing helix  chain 'C' and resid 95 through 113
      removed outlier: 3.809A  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: 3.887A  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: 4.121A  pdb=" N   GLU D  43 " --> pdb=" O   ARG D  40 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   SER D  44 " --> pdb=" O   PHE D  41 " (cutoff:3.500A)
      removed outlier: 4.195A  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: 3.544A  pdb=" N   LYS D  95 " --> pdb=" O   LEU D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 119
      removed outlier: 3.749A  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

    338 hydrogen bonds defined for protein.
    957 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: 1.49 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: 1560
        1.38 -     1.55: 3034
        1.55 -     1.72: 10
        1.72 -     1.89: 18
        1.89 -     2.06: 16
  Bond restraints: 4638
  Sorted by residual:
  bond pdb=" N   THR C  39 "
       pdb=" CA  THR C  39 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.25e-02 6.40e+03 9.82e+00
  bond pdb=" N   VAL A  93 "
       pdb=" CA  VAL A  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.24e-02 6.50e+03 9.58e+00
  bond pdb=" N   LYS C  40 "
       pdb=" CA  LYS C  40 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.90e+00
  bond pdb=" N   LEU A  91 "
       pdb=" CA  LEU A  91 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.23e-02 6.61e+03 7.50e+00
  bond pdb=" N   THR C  41 "
       pdb=" CA  THR C  41 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 6.80e+00
  ... (remaining 4633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 6014
        1.20 -     2.40: 227
        2.40 -     3.60: 74
        3.60 -     4.80: 31
        4.80 -     6.00: 12
  Bond angle restraints: 6358
  Sorted by residual:
  angle pdb=" C   PHE C  36 "
        pdb=" N   PRO C  37 "
        pdb=" CA  PRO C  37 "
      ideal   model   delta    sigma   weight residual
     119.56  124.15   -4.59 1.02e+00 9.61e-01 2.02e+01
  angle pdb=" C   ALA A  88 "
        pdb=" N   HIS A  89 "
        pdb=" CA  HIS A  89 "
      ideal   model   delta    sigma   weight residual
     122.42  116.74    5.68 1.55e+00 4.16e-01 1.34e+01
  angle pdb=" CA  PHE C  43 "
        pdb=" CB  PHE C  43 "
        pdb=" CG  PHE C  43 "
      ideal   model   delta    sigma   weight residual
     113.80  117.40   -3.60 1.00e+00 1.00e+00 1.30e+01
  angle pdb=" CA  THR C  41 "
        pdb=" C   THR C  41 "
        pdb=" O   THR C  41 "
      ideal   model   delta    sigma   weight residual
     120.55  116.97    3.58 1.06e+00 8.90e-01 1.14e+01
  angle pdb=" CA  LEU A  91 "
        pdb=" C   LEU A  91 "
        pdb=" O   LEU A  91 "
      ideal   model   delta    sigma   weight residual
     120.42  116.89    3.53 1.06e+00 8.90e-01 1.11e+01
  ... (remaining 6353 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 2259
       17.75 -    35.49: 251
       35.49 -    53.24: 82
       53.24 -    70.99: 25
       70.99 -    88.73: 9
  Dihedral angle restraints: 2626
    sinusoidal: 998
      harmonic: 1628
  Sorted by residual:
  dihedral pdb=" C1A HEM A 201 "
           pdb=" C2A HEM A 201 "
           pdb=" CAA HEM A 201 "
           pdb=" CBA HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   93.16   86.84     2      2.00e+01 2.50e-03 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
     180.00   94.37   85.63     2      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" C1A HEM B 201 "
           pdb=" C2A HEM B 201 "
           pdb=" CAA HEM B 201 "
           pdb=" CBA HEM B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.08  -80.08     2      2.00e+01 2.50e-03 1.16e+01
  ... (remaining 2623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 505
       0.043 -    0.086: 141
       0.086 -    0.129: 34
       0.129 -    0.172: 5
       0.172 -    0.214: 3
  Chirality restraints: 688
  Sorted by residual:
  chirality pdb=" CA  PHE C  43 "
            pdb=" N   PHE C  43 "
            pdb=" C   PHE C  43 "
            pdb=" CB  PHE C  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CB  THR A 134 "
            pdb=" CA  THR A 134 "
            pdb=" OG1 THR A 134 "
            pdb=" CG2 THR A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 7.92e-01
  chirality pdb=" CB  THR C 134 "
            pdb=" CA  THR C 134 "
            pdb=" OG1 THR C 134 "
            pdb=" CG2 THR C 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.48e-01
  ... (remaining 685 not shown)

  Planarity restraints: 794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  50 "    0.044 5.00e-02 4.00e+02   6.62e-02 7.00e+00
        pdb=" N   PRO B  51 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B  51 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  51 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  94 "    0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO C  95 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A  87 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   HIS A  87 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   HIS A  87 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A  88 "    0.011 2.00e-02 2.50e+03
  ... (remaining 791 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 136
        2.65 -     3.21: 4258
        3.21 -     3.78: 8510
        3.78 -     4.34: 11898
        4.34 -     4.90: 18118
  Nonbonded interactions: 42920
  Sorted by model distance:
  nonbonded pdb=" O   VAL C  93 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" NE2 HIS D  92 "
            pdb="FE   HEM D 201 "
     model   vdw
     2.145 3.080
  nonbonded pdb=" NE2 HIS B  92 "
            pdb="FE   HEM B 201 "
     model   vdw
     2.146 3.080
  nonbonded pdb=" OD1 ASP C  85 "
            pdb=" O   HOH C 301 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" O   HOH C 357 "
            pdb=" O   HOH D 346 "
     model   vdw
     2.189 3.040
  ... (remaining 42915 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=0.59 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:             2.590
  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:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.580
  Find NCS groups from input model:        0.190
  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:12.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
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      :  0.014   0.588   4642  Z= 0.221
  Angle     :  0.684   6.005   6358  Z= 0.378
  Chirality :  0.043   0.214    688
  Planarity :  0.006   0.066    794
  Dihedral  : 18.270  88.735   1574
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 19.82 %
    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:  3.48 (0.37), residues: 560
  helix:  2.50 (0.24), residues: 428
  sheet:  None (None), residues: 0
  loop :  1.87 (0.67), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.013   0.002   PHE C  43 
 TYR   0.011   0.002   TYR C  42 
 ARG   0.004   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10178 (  338)
  hydrogen bonds       : angle       4.29880 (  957)
  covalent geometry    : bond        0.00396 ( 4638)
  covalent geometry    : angle       0.68415 ( 6358)
  Misc. bond           : bond        0.45647 (    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
  82 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7955 (mmmm) cc_final: 0.7662 (tptm)
REVERT: A   90 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7543 (tttt)
REVERT: B   84 THR cc_start: 0.8113 (m) cc_final: 0.7894 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 81
  average time/residue: 1.4764
  time to fit residues: 123.5375
Evaluate side-chains
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.153228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.130681 restraints weight = 4201.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.10
r_work: 0.3315 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.0672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.020   0.774   4642  Z= 0.164
  Angle     :  0.723  14.101   6358  Z= 0.284
  Chirality :  0.041   0.168    688
  Planarity :  0.006   0.060    794
  Dihedral  : 10.393  86.443    624
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.32 %
    Favored  : 83.04 %
  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:  3.30 (0.36), residues: 560
  helix:  2.33 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.89 (0.66), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  14 
 HIS   0.005   0.001   HIS D  63 
 PHE   0.011   0.002   PHE B 118 
 TYR   0.010   0.002   TYR D  35 
 ARG   0.003   0.001   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04285 (  338)
  hydrogen bonds       : angle       3.96967 (  957)
  covalent geometry    : bond        0.00339 ( 4638)
  covalent geometry    : angle       0.72331 ( 6358)
  Misc. bond           : bond        0.66084 (    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
  91 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A   85 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7761 (t70)
REVERT: A   90 LYS cc_start: 0.8130 (mppt) cc_final: 0.7635 (tttt)
REVERT: B   84 THR cc_start: 0.8060 (m) cc_final: 0.7838 (m)
REVERT: C   38 THR cc_start: 0.8360 (p) cc_final: 0.8116 (t)
REVERT: C   60 LYS cc_start: 0.8437 (tttm) cc_final: 0.7837 (ttmp)
REVERT: C  126 ASP cc_start: 0.8078 (t70) cc_final: 0.7797 (t70)
  outliers start: 12
  outliers final: 1
  residues processed: 82
  average time/residue: 1.5426
  time to fit residues: 130.4562
Evaluate side-chains
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain C residue  127 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    0.3980
   chunk 0 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0050
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.3594

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.157089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.135036 restraints weight = 4262.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.07
r_work: 0.3361 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3227
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3227 r_free = 0.3227    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3227
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.246   4642  Z= 0.107
  Angle     :  0.693  14.909   6358  Z= 0.248
  Chirality :  0.037   0.163    688
  Planarity :  0.005   0.058    794
  Dihedral  :  9.897  84.795    620
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.08 %
    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 (0.36), residues: 560
  helix:  2.74 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.06 (0.65), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  14 
 HIS   0.002   0.001   HIS D  63 
 PHE   0.006   0.001   PHE B 118 
 TYR   0.008   0.001   TYR B 130 
 ARG   0.003   0.000   ARG C  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03095 (  338)
  hydrogen bonds       : angle       3.72973 (  957)
  covalent geometry    : bond        0.00251 ( 4638)
  covalent geometry    : angle       0.69337 ( 6358)
  Misc. bond           : bond        0.20487 (    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
  87 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.500 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8443 (tttm) cc_final: 0.7846 (ttmp)
REVERT: A   90 LYS cc_start: 0.8109 (mppt) cc_final: 0.7608 (tttt)
REVERT: B  120 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7703 (ttmm)
REVERT: C   38 THR cc_start: 0.8323 (p) cc_final: 0.8089 (t)
REVERT: C   60 LYS cc_start: 0.8407 (tttm) cc_final: 0.7804 (ttmp)
REVERT: D   99 ASP cc_start: 0.8041 (t70) cc_final: 0.7825 (t70)
  outliers start: 8
  outliers final: 0
  residues processed: 81
  average time/residue: 1.5840
  time to fit residues: 132.3275
Evaluate side-chains
  71 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.155489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.131274 restraints weight = 4309.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.19
r_work: 0.3324 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.130   4642  Z= 0.133
  Angle     :  0.760  16.384   6358  Z= 0.271
  Chirality :  0.040   0.179    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.117  86.260    620
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.74 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.63 (0.36), residues: 560
  helix:  2.56 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.06 (0.65), residues: 130

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03988 (  338)
  hydrogen bonds       : angle       3.84731 (  957)
  covalent geometry    : bond        0.00307 ( 4638)
  covalent geometry    : angle       0.75989 ( 6358)
  Misc. bond           : bond        0.10575 (    4)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8419 (tttm) cc_final: 0.7779 (ttmp)
REVERT: A   85 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7692 (t70)
REVERT: A   90 LYS cc_start: 0.8135 (mppt) cc_final: 0.7585 (tttt)
REVERT: C   38 THR cc_start: 0.8342 (p) cc_final: 0.8130 (t)
REVERT: C   60 LYS cc_start: 0.8409 (tttm) cc_final: 0.7771 (ttmp)
REVERT: C  126 ASP cc_start: 0.8033 (t70) cc_final: 0.7698 (t70)
REVERT: D   95 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7247 (tmtt)
  outliers start: 7
  outliers final: 0
  residues processed: 81
  average time/residue: 1.4979
  time to fit residues: 125.2857
Evaluate side-chains
  72 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.155732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.131533 restraints weight = 4349.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.20
r_work: 0.3330 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092   4642  Z= 0.125
  Angle     :  0.754  16.787   6358  Z= 0.265
  Chirality :  0.040   0.180    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.046  85.630    620
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.40 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.65 (0.36), residues: 560
  helix:  2.60 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.98 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS B 116 
 PHE   0.009   0.001   PHE B 118 
 TYR   0.008   0.001   TYR D  35 
 ARG   0.001   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  338)
  hydrogen bonds       : angle       3.80885 (  957)
  covalent geometry    : bond        0.00290 ( 4638)
  covalent geometry    : angle       0.75387 ( 6358)
  Misc. bond           : bond        0.07513 (    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
  84 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7783 (ttmp)
REVERT: A   85 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7684 (t70)
REVERT: A   90 LYS cc_start: 0.8108 (mppt) cc_final: 0.7565 (tttt)
REVERT: C   60 LYS cc_start: 0.8420 (tttm) cc_final: 0.7769 (ttmp)
REVERT: C  126 ASP cc_start: 0.8012 (t70) cc_final: 0.7711 (t70)
REVERT: D   95 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7246 (tmtt)
  outliers start: 7
  outliers final: 1
  residues processed: 80
  average time/residue: 1.5746
  time to fit residues: 130.0017
Evaluate side-chains
  73 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 0 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 27 optimal weight:    6.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.155074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.130939 restraints weight = 4270.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.19
r_work: 0.3322 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.148   4642  Z= 0.131
  Angle     :  0.769  17.057   6358  Z= 0.269
  Chirality :  0.040   0.184    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.099  85.890    620
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.40 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.62 (0.36), residues: 560
  helix:  2.57 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  1.99 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.009   0.002   PHE B 118 
 TYR   0.008   0.001   TYR D  35 
 ARG   0.002   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  338)
  hydrogen bonds       : angle       3.81252 (  957)
  covalent geometry    : bond        0.00302 ( 4638)
  covalent geometry    : angle       0.76875 ( 6358)
  Misc. bond           : bond        0.09732 (    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
  80 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7789 (ttmp)
REVERT: A   85 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7727 (t70)
REVERT: C   60 LYS cc_start: 0.8422 (tttm) cc_final: 0.7776 (ttmp)
REVERT: C  126 ASP cc_start: 0.8007 (t70) cc_final: 0.7676 (t70)
REVERT: D   95 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7222 (tmtt)
  outliers start: 8
  outliers final: 2
  residues processed: 76
  average time/residue: 1.9146
  time to fit residues: 150.2647
Evaluate side-chains
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.154500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.130517 restraints weight = 4221.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.17
r_work: 0.3316 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3196
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3196 r_free = 0.3196    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3196
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.179   4642  Z= 0.139
  Angle     :  0.783  17.218   6358  Z= 0.275
  Chirality :  0.041   0.191    688
  Planarity :  0.006   0.055    794
  Dihedral  : 10.155  85.874    620
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.18 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.52 (0.36), residues: 560
  helix:  2.50 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.94 (0.65), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.010   0.002   PHE B 118 
 TYR   0.009   0.001   TYR D  35 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04010 (  338)
  hydrogen bonds       : angle       3.85164 (  957)
  covalent geometry    : bond        0.00319 ( 4638)
  covalent geometry    : angle       0.78302 ( 6358)
  Misc. bond           : bond        0.14260 (    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
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7791 (ttmp)
REVERT: A   85 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7721 (t70)
REVERT: C   60 LYS cc_start: 0.8425 (tttm) cc_final: 0.7780 (ttmp)
REVERT: C  126 ASP cc_start: 0.7996 (t70) cc_final: 0.7663 (t70)
REVERT: D   95 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7272 (tmtt)
  outliers start: 9
  outliers final: 3
  residues processed: 74
  average time/residue: 1.5020
  time to fit residues: 114.8365
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   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  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.154902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.130877 restraints weight = 4239.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.17
r_work: 0.3321 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.160   4642  Z= 0.134
  Angle     :  0.778  17.267   6358  Z= 0.271
  Chirality :  0.040   0.191    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.116  85.751    620
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 18.50 %
    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:  3.61 (0.36), residues: 560
  helix:  2.56 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.01 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.009   0.002   PHE B 118 
 TYR   0.009   0.001   TYR C 140 
 ARG   0.002   0.000   ARG D 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03875 (  338)
  hydrogen bonds       : angle       3.80796 (  957)
  covalent geometry    : bond        0.00308 ( 4638)
  covalent geometry    : angle       0.77771 ( 6358)
  Misc. bond           : bond        0.14701 (    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
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.498 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7827 (ttmp)
REVERT: A   85 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7726 (t70)
REVERT: C   60 LYS cc_start: 0.8422 (tttm) cc_final: 0.7775 (ttmp)
REVERT: C  126 ASP cc_start: 0.8008 (t70) cc_final: 0.7673 (t70)
REVERT: D   95 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7202 (tmtt)
  outliers start: 7
  outliers final: 4
  residues processed: 74
  average time/residue: 1.9849
  time to fit residues: 151.4163
Evaluate side-chains
  75 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  127 LYS
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   95 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   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  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.154678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.130591 restraints weight = 4270.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.18
r_work: 0.3319 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3200
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3200 r_free = 0.3200    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3200
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.164   4642  Z= 0.135
  Angle     :  0.784  17.274   6358  Z= 0.273
  Chirality :  0.041   0.193    688
  Planarity :  0.006   0.056    794
  Dihedral  : 10.138  85.797    620
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.06 %
    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:  2.52 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.96 (0.65), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.009   0.002   PHE B 118 
 TYR   0.011   0.001   TYR C 140 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  338)
  hydrogen bonds       : angle       3.82356 (  957)
  covalent geometry    : bond        0.00309 ( 4638)
  covalent geometry    : angle       0.78408 ( 6358)
  Misc. bond           : bond        0.14460 (    4)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7793 (ttmp)
REVERT: A   85 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7730 (t70)
REVERT: C   60 LYS cc_start: 0.8419 (tttm) cc_final: 0.7777 (ttmp)
REVERT: C  126 ASP cc_start: 0.8007 (t70) cc_final: 0.7663 (t70)
  outliers start: 8
  outliers final: 3
  residues processed: 73
  average time/residue: 2.3325
  time to fit residues: 175.2524
Evaluate side-chains
  74 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  127 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 45 optimal weight:    0.1980
   chunk 27 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0770
   chunk 7 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.3938

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.157591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.133840 restraints weight = 4239.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.17
r_work: 0.3357 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3239
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3239 r_free = 0.3239    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3239
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   4642  Z= 0.107
  Angle     :  0.745  16.783   6358  Z= 0.253
  Chirality :  0.038   0.185    688
  Planarity :  0.006   0.057    794
  Dihedral  :  9.885  85.104    620
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 19.38 %
    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:  3.94 (0.36), residues: 560
  helix:  2.80 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.11 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  37 
 HIS   0.003   0.001   HIS A 122 
 PHE   0.006   0.001   PHE C  98 
 TYR   0.008   0.001   TYR D 130 
 ARG   0.002   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03093 (  338)
  hydrogen bonds       : angle       3.68454 (  957)
  covalent geometry    : bond        0.00252 ( 4638)
  covalent geometry    : angle       0.74550 ( 6358)
  Misc. bond           : bond        0.09713 (    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
  79 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A   60 LYS cc_start: 0.8441 (tttm) cc_final: 0.7791 (ttmp)
REVERT: A   90 LYS cc_start: 0.8057 (mppt) cc_final: 0.7470 (tttt)
REVERT: C   60 LYS cc_start: 0.8450 (tttm) cc_final: 0.7802 (ttmp)
REVERT: C  126 ASP cc_start: 0.8023 (t70) cc_final: 0.7718 (t70)
  outliers start: 3
  outliers final: 2
  residues processed: 78
  average time/residue: 1.6093
  time to fit residues: 129.5140
Evaluate side-chains
  70 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  127 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
** A  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   9 ASN
C  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.154651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.130602 restraints weight = 4238.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.17
r_work: 0.3319 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.171   4642  Z= 0.139
  Angle     :  0.785  17.111   6358  Z= 0.277
  Chirality :  0.041   0.195    688
  Planarity :  0.006   0.055    794
  Dihedral  : 10.094  86.129    620
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 19.16 %
    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:  3.68 (0.36), residues: 560
  helix:  2.60 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop :  2.07 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A  14 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.010   0.002   PHE B 118 
 TYR   0.012   0.002   TYR C 140 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  338)
  hydrogen bonds       : angle       3.80724 (  957)
  covalent geometry    : bond        0.00320 ( 4638)
  covalent geometry    : angle       0.78498 ( 6358)
  Misc. bond           : bond        0.14568 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4699.93 seconds
wall clock time: 83 minutes 27.33 seconds (5007.33 seconds total)