Starting phenix.real_space_refine
on Tue Jun 10 06:30:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wlr_32591/06_2025/7wlr_32591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wlr_32591/06_2025/7wlr_32591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wlr_32591/06_2025/7wlr_32591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wlr_32591/06_2025/7wlr_32591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wlr_32591/06_2025/7wlr_32591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wlr_32591/06_2025/7wlr_32591.cif"
  }
  resolution = 3.54
  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=   1.000
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
     P     289      5.49       5
     S       6      5.16       5
     C    6588      2.51       5
     N    2222      2.21       5
     O    2817      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 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: 11922
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 794
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 666
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 802
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 740
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 794
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 813
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 714
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 8.81, per 1000 atoms: 0.74
  Number of scatterers: 11922
  At special positions: 0
  Unit cell: (118.72, 86.92, 119.78, 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)
     S       6     16.00
     P     289     15.00
     O    2817      8.00
     N    2222      7.00
     C    6588      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=0, symmetry=0
  Time building additional restraints: 3.89
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1420

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      74.5% alpha, 3.2% beta
      144 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 8.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 64 through 80
      removed outlier: 4.142A  pdb=" N   ASP A  78 " --> pdb=" O   GLU A  74 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   PHE A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 115
      removed outlier: 3.688A  pdb=" N   ALA A 115 " --> pdb=" O   CYS A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 133
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.755A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.815A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.439A  pdb=" N   VAL C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 41 through 53
      removed outlier: 3.925A  pdb=" N   LYS D  47 " --> pdb=" O   SER D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 88
      removed outlier: 3.510A  pdb=" N   ASN D  88 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 106
    Processing helix  chain 'D' and resid 107 through 129
    Processing helix  chain 'E' and resid 45 through 58
    Processing helix  chain 'E' and resid 64 through 78
      removed outlier: 3.880A  pdb=" N   ASP E  78 " --> pdb=" O   GLU E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
      removed outlier: 3.642A  pdb=" N   ALA E 115 " --> pdb=" O   CYS E 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 132
      removed outlier: 3.507A  pdb=" N   ILE E 125 " --> pdb=" O   GLN E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.999A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.426A  pdb=" N   VAL G  49 " --> pdb=" O   SER G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 41 through 53
    Processing helix  chain 'H' and resid 59 through 88
    Processing helix  chain 'H' and resid 94 through 106
    Processing helix  chain 'H' and resid 107 through 129
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 7.306A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.520A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.377A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 7.067A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.113A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    418 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      367 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 5.38

  Time building geometry restraints manager: 4.34 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1476
        1.32 -     1.44: 4699
        1.44 -     1.56: 5959
        1.56 -     1.69: 577
        1.69 -     1.81: 10
  Bond restraints: 12721
  Sorted by residual:
  bond pdb=" N   ARG B  23 "
       pdb=" CA  ARG B  23 "
    ideal  model  delta    sigma   weight residual
    1.457  1.511 -0.054 1.29e-02 6.01e+03 1.75e+01
  bond pdb=" C   ARG B  35 "
       pdb=" O   ARG B  35 "
    ideal  model  delta    sigma   weight residual
    1.237  1.197  0.040 1.19e-02 7.06e+03 1.14e+01
  bond pdb=" CZ  ARG C  32 "
       pdb=" NH2 ARG C  32 "
    ideal  model  delta    sigma   weight residual
    1.330  1.287  0.043 1.30e-02 5.92e+03 1.07e+01
  bond pdb=" CZ  ARG F  35 "
       pdb=" NH2 ARG F  35 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG A 135 "
       pdb=" NH2 ARG A 135 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  ... (remaining 12716 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 16892
        1.55 -     3.10: 1297
        3.10 -     4.65: 178
        4.65 -     6.20: 44
        6.20 -     7.74: 13
  Bond angle restraints: 18424
  Sorted by residual:
  angle pdb=" C   THR A  59 "
        pdb=" N   GLU A  60 "
        pdb=" CA  GLU A  60 "
      ideal   model   delta    sigma   weight residual
     120.82  127.74   -6.92 1.47e+00 4.63e-01 2.22e+01
  angle pdb=" C   SER G  14 "
        pdb=" N   THR G  15 "
        pdb=" CA  THR G  15 "
      ideal   model   delta    sigma   weight residual
     120.90  127.52   -6.62 1.41e+00 5.03e-01 2.21e+01
  angle pdb=" N   ARG F  23 "
        pdb=" CA  ARG F  23 "
        pdb=" C   ARG F  23 "
      ideal   model   delta    sigma   weight residual
     111.34  118.15   -6.81 1.49e+00 4.50e-01 2.09e+01
  angle pdb=" N   GLU G  91 "
        pdb=" CA  GLU G  91 "
        pdb=" C   GLU G  91 "
      ideal   model   delta    sigma   weight residual
     111.28  115.95   -4.67 1.09e+00 8.42e-01 1.84e+01
  angle pdb=" O   GLY D 108 "
        pdb=" C   GLY D 108 "
        pdb=" N   GLU D 109 "
      ideal   model   delta    sigma   weight residual
     122.13  118.01    4.12 9.90e-01 1.02e+00 1.74e+01
  ... (remaining 18419 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.23: 4488
       21.23 -    42.46: 1286
       42.46 -    63.69: 1085
       63.69 -    84.92: 46
       84.92 -   106.15: 8
  Dihedral angle restraints: 6913
    sinusoidal: 4719
      harmonic: 2194
  Sorted by residual:
  dihedral pdb=" CA  GLY E  45 "
           pdb=" C   GLY E  45 "
           pdb=" N   THR E  46 "
           pdb=" CA  THR E  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.28  -25.72     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  GLY A  45 "
           pdb=" C   GLY A  45 "
           pdb=" N   THR A  46 "
           pdb=" CA  THR A  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.53  -25.47     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  ARG B  23 "
           pdb=" C   ARG B  23 "
           pdb=" N   ASP B  24 "
           pdb=" CA  ASP B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.82  -23.18     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 6910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1787
       0.062 -    0.124: 281
       0.124 -    0.187: 25
       0.187 -    0.249: 10
       0.249 -    0.311: 4
  Chirality restraints: 2107
  Sorted by residual:
  chirality pdb=" CA  ARG F  23 "
            pdb=" N   ARG F  23 "
            pdb=" C   ARG F  23 "
            pdb=" CB  ARG F  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  LYS G 118 "
            pdb=" N   LYS G 118 "
            pdb=" C   LYS G 118 "
            pdb=" CB  LYS G 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  THR A  46 "
            pdb=" N   THR A  46 "
            pdb=" C   THR A  46 "
            pdb=" CB  THR A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.95e+00
  ... (remaining 2104 not shown)

  Planarity restraints: 1323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  44 "    0.045 2.00e-02 2.50e+03   3.82e-02 2.92e+01
        pdb=" CG  TYR D  44 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  44 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  44 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  44 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  44 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  44 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR D  44 "    0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 101 "   -0.020 2.00e-02 2.50e+03   4.02e-02 1.62e+01
        pdb=" C   GLY B 101 "    0.070 2.00e-02 2.50e+03
        pdb=" O   GLY B 101 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLY B 102 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS H  53 "    0.014 2.00e-02 2.50e+03   3.24e-02 1.57e+01
        pdb=" CG  HIS H  53 "   -0.005 2.00e-02 2.50e+03
        pdb=" ND1 HIS H  53 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 HIS H  53 "   -0.040 2.00e-02 2.50e+03
        pdb=" CE1 HIS H  53 "   -0.035 2.00e-02 2.50e+03
        pdb=" NE2 HIS H  53 "    0.055 2.00e-02 2.50e+03
  ... (remaining 1320 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1741
        2.77 -     3.30: 10480
        3.30 -     3.83: 23372
        3.83 -     4.37: 27505
        4.37 -     4.90: 39362
  Nonbonded interactions: 102460
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  50 "
            pdb=" N2   DG J  96 "
     model   vdw
     2.232 2.496
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  72 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG  SER H  94 "
            pdb=" OE1 GLU H  97 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   PHE C  25 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   PHE G  25 "
     model   vdw
     2.383 3.040
  ... (remaining 102455 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 15 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 38 through 129)
  selection = chain 'H'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             13.320
  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:          0.480
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     40.530
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.070
  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:3.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
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      :  0.006   0.060  12721  Z= 0.351
  Angle     :  0.884   7.744  18424  Z= 0.569
  Chirality :  0.049   0.311   2107
  Planarity :  0.010   0.124   1323
  Dihedral  : 29.271 106.152   5493
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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:  1.65 (0.29), residues: 738
  helix:  1.78 (0.21), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.77 (0.40), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.047   0.003   HIS H  53 
 PHE   0.008   0.001   PHE D  74 
 TYR   0.068   0.004   TYR D  44 
 ARG   0.012   0.001   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11505 (  785)
  hydrogen bonds       : angle       3.72291 ( 1963)
  covalent geometry    : bond        0.00598 (12721)
  covalent geometry    : angle       0.88408 (18424)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.917 
Fit side-chains
REVERT: B   91 LYS cc_start: 0.7799 (tttp) cc_final: 0.7208 (ttmm)
REVERT: C   41 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7399 (mt0)
REVERT: C   95 LYS cc_start: 0.7478 (ttmt) cc_final: 0.7248 (tttm)
REVERT: D   38 LYS cc_start: 0.7201 (tptm) cc_final: 0.6779 (tppt)
REVERT: D   89 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7467 (mttm)
REVERT: E  111 CYS cc_start: 0.6645 (p) cc_final: 0.6433 (p)
REVERT: G   36 ARG cc_start: 0.6975 (tpp80) cc_final: 0.6569 (mmt90)
REVERT: G  107 VAL cc_start: 0.8850 (p) cc_final: 0.8620 (m)
REVERT: H   75 GLU cc_start: 0.6979 (tp30) cc_final: 0.6624 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.4313
  time to fit residues: 58.8820
Evaluate side-chains
  62 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  53 HIS
D  88 ASN
E  77 GLN
E  94 GLN
F  25 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.165257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.112380 restraints weight = 14670.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.111129 restraints weight = 19054.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.111951 restraints weight = 18619.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12721  Z= 0.162
  Angle     :  0.561   6.643  18424  Z= 0.342
  Chirality :  0.034   0.129   2107
  Planarity :  0.004   0.042   1323
  Dihedral  : 31.192  93.918   4005
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  5.96 %
    Favored  : 93.57 %
  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:  2.74 (0.30), residues: 738
  helix:  2.57 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.54 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.002   PHE H  74 
 TYR   0.012   0.001   TYR G  57 
 ARG   0.004   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04610 (  785)
  hydrogen bonds       : angle       2.75778 ( 1963)
  covalent geometry    : bond        0.00353 (12721)
  covalent geometry    : angle       0.56118 (18424)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 1.927 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7735 (tm-30)
REVERT: B   91 LYS cc_start: 0.8352 (tttp) cc_final: 0.7985 (ttmm)
REVERT: D   46 TYR cc_start: 0.8200 (t80) cc_final: 0.7372 (t80)
REVERT: D   66 MET cc_start: 0.8625 (mmm) cc_final: 0.8384 (mmm)
REVERT: D   89 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7897 (mttm)
REVERT: G   36 ARG cc_start: 0.6910 (tpp80) cc_final: 0.6614 (mmt90)
  outliers start: 3
  outliers final: 1
  residues processed: 78
  average time/residue: 0.3620
  time to fit residues: 40.0310
Evaluate side-chains
  64 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 71 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
E  77 GLN
F  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.161058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.107743 restraints weight = 14798.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.105700 restraints weight = 23068.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.106706 restraints weight = 22284.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12721  Z= 0.184
  Angle     :  0.565   6.462  18424  Z= 0.342
  Chirality :  0.035   0.143   2107
  Planarity :  0.004   0.037   1323
  Dihedral  : 31.176  97.390   4005
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  9.56 %
    Favored  : 89.66 %
  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:  2.71 (0.30), residues: 738
  helix:  2.60 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.72 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE G  25 
 TYR   0.012   0.001   TYR G  57 
 ARG   0.008   0.001   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05119 (  785)
  hydrogen bonds       : angle       2.73702 ( 1963)
  covalent geometry    : bond        0.00424 (12721)
  covalent geometry    : angle       0.56453 (18424)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7688 (tm-30)
REVERT: B   91 LYS cc_start: 0.8506 (tttp) cc_final: 0.8125 (ttmm)
REVERT: C   45 SER cc_start: 0.8925 (m) cc_final: 0.8702 (p)
REVERT: D   46 TYR cc_start: 0.8256 (t80) cc_final: 0.7404 (t80)
REVERT: D   63 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8708 (tpp)
REVERT: D   89 LYS cc_start: 0.8362 (mmmt) cc_final: 0.7891 (mttm)
REVERT: G   36 ARG cc_start: 0.6899 (tpp80) cc_final: 0.6443 (mmt90)
REVERT: H   38 LYS cc_start: 0.7777 (tppt) cc_final: 0.7197 (mtpt)
  outliers start: 5
  outliers final: 2
  residues processed: 75
  average time/residue: 0.3284
  time to fit residues: 33.5256
Evaluate side-chains
  69 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   63 MET
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  77 GLN
F  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.162835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.109755 restraints weight = 14595.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.107703 restraints weight = 22866.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.108681 restraints weight = 21989.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12721  Z= 0.150
  Angle     :  0.523   5.768  18424  Z= 0.322
  Chirality :  0.033   0.136   2107
  Planarity :  0.004   0.036   1323
  Dihedral  : 30.728  95.788   4005
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 10.66 %
    Favored  : 88.56 %
  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:  3.00 (0.30), residues: 738
  helix:  2.82 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.64 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.006   0.001   PHE H  74 
 TYR   0.010   0.001   TYR G  57 
 ARG   0.003   0.000   ARG H 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04379 (  785)
  hydrogen bonds       : angle       2.60088 ( 1963)
  covalent geometry    : bond        0.00325 (12721)
  covalent geometry    : angle       0.52341 (18424)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.806 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7587 (tm-30)
REVERT: B   91 LYS cc_start: 0.8424 (tttp) cc_final: 0.7990 (ttmm)
REVERT: C   45 SER cc_start: 0.8926 (m) cc_final: 0.8672 (p)
REVERT: D   46 TYR cc_start: 0.8201 (t80) cc_final: 0.7363 (t80)
REVERT: D   63 MET cc_start: 0.8940 (tpp) cc_final: 0.8650 (tpp)
REVERT: D   66 MET cc_start: 0.8682 (mmm) cc_final: 0.8455 (mmm)
REVERT: D   89 LYS cc_start: 0.8452 (mmmt) cc_final: 0.7871 (mttm)
REVERT: G   36 ARG cc_start: 0.6936 (tpp80) cc_final: 0.6519 (mmt90)
REVERT: H   38 LYS cc_start: 0.7736 (tppt) cc_final: 0.7187 (mtpt)
  outliers start: 5
  outliers final: 1
  residues processed: 75
  average time/residue: 0.2742
  time to fit residues: 28.8171
Evaluate side-chains
  72 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:   20.0000
   chunk 15 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 79 optimal weight:   10.0000
   chunk 14 optimal weight:    0.5980
   chunk 81 optimal weight:   10.0000
   overall best weight:    5.7188

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C 104 GLN
E  77 GLN
E  94 GLN
H  88 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.154285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.102812 restraints weight = 14507.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.101404 restraints weight = 22965.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.102377 restraints weight = 20378.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.063  12721  Z= 0.368
  Angle     :  0.716   9.453  18424  Z= 0.415
  Chirality :  0.043   0.161   2107
  Planarity :  0.005   0.042   1323
  Dihedral  : 31.621 106.230   4005
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.44 %
    Favored  : 86.99 %
  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:  1.93 (0.30), residues: 738
  helix:  2.12 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -1.33 (0.38), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS H  53 
 PHE   0.014   0.002   PHE H  69 
 TYR   0.017   0.002   TYR B  51 
 ARG   0.005   0.001   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07008 (  785)
  hydrogen bonds       : angle       3.08725 ( 1963)
  covalent geometry    : bond        0.00897 (12721)
  covalent geometry    : angle       0.71603 (18424)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 1.075 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7701 (tm-30)
REVERT: B   91 LYS cc_start: 0.8616 (tttp) cc_final: 0.8139 (ttmm)
REVERT: D   46 TYR cc_start: 0.8452 (t80) cc_final: 0.7716 (t80)
REVERT: D   63 MET cc_start: 0.9027 (tpp) cc_final: 0.8757 (mmm)
REVERT: D   89 LYS cc_start: 0.8466 (mmmt) cc_final: 0.7952 (mtmm)
REVERT: G   36 ARG cc_start: 0.7241 (tpp80) cc_final: 0.6731 (mmt90)
REVERT: H   75 GLU cc_start: 0.7759 (tp30) cc_final: 0.7486 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 78
  average time/residue: 0.3300
  time to fit residues: 34.6500
Evaluate side-chains
  70 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain H residue   86 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    0.0030
   chunk 54 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.160988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.109097 restraints weight = 14569.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.107375 restraints weight = 21245.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.108308 restraints weight = 21856.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12721  Z= 0.147
  Angle     :  0.533   6.216  18424  Z= 0.327
  Chirality :  0.033   0.134   2107
  Planarity :  0.004   0.042   1323
  Dihedral  : 30.782 101.867   4005
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 11.44 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.30), residues: 738
  helix:  2.78 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.11 (0.38), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.010   0.001   PHE A  68 
 TYR   0.010   0.001   TYR G  57 
 ARG   0.003   0.000   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  785)
  hydrogen bonds       : angle       2.61003 ( 1963)
  covalent geometry    : bond        0.00310 (12721)
  covalent geometry    : angle       0.53288 (18424)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: B   91 LYS cc_start: 0.8464 (tttp) cc_final: 0.8077 (ttmm)
REVERT: D   46 TYR cc_start: 0.8199 (t80) cc_final: 0.7353 (t80)
REVERT: D   63 MET cc_start: 0.8939 (tpp) cc_final: 0.8571 (mmm)
REVERT: D   89 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7887 (mttm)
REVERT: G   36 ARG cc_start: 0.7167 (tpp80) cc_final: 0.6735 (mmt90)
REVERT: H   38 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7495 (mtpt)
  outliers start: 6
  outliers final: 4
  residues processed: 78
  average time/residue: 0.3053
  time to fit residues: 32.7601
Evaluate side-chains
  74 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain H residue   38 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 95 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 86 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.154889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.102904 restraints weight = 14621.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.101551 restraints weight = 21660.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.102488 restraints weight = 20873.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  12721  Z= 0.307
  Angle     :  0.662   9.793  18424  Z= 0.387
  Chirality :  0.040   0.149   2107
  Planarity :  0.005   0.042   1323
  Dihedral  : 31.405 108.088   4005
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.76 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.30), residues: 738
  helix:  2.27 (0.21), residues: 551
  sheet:  None (None), residues: 0
  loop : -1.35 (0.39), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H  53 
 PHE   0.011   0.002   PHE H  69 
 TYR   0.014   0.002   TYR B  51 
 ARG   0.004   0.001   ARG D 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06497 (  785)
  hydrogen bonds       : angle       2.99653 ( 1963)
  covalent geometry    : bond        0.00737 (12721)
  covalent geometry    : angle       0.66173 (18424)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: B   91 LYS cc_start: 0.8585 (tttp) cc_final: 0.8112 (ttmm)
REVERT: D   46 TYR cc_start: 0.8375 (t80) cc_final: 0.7588 (t80)
REVERT: D   63 MET cc_start: 0.9034 (tpp) cc_final: 0.8698 (mmm)
REVERT: D   89 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7908 (mtmm)
REVERT: E   66 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8501 (mm)
REVERT: G   36 ARG cc_start: 0.7251 (tpp80) cc_final: 0.6806 (mmt90)
REVERT: G   83 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8706 (mt)
REVERT: H   38 LYS cc_start: 0.8147 (tptt) cc_final: 0.7508 (mtpt)
REVERT: H   75 GLU cc_start: 0.7740 (tp30) cc_final: 0.7428 (mt-10)
  outliers start: 11
  outliers final: 8
  residues processed: 74
  average time/residue: 0.2759
  time to fit residues: 28.4431
Evaluate side-chains
  73 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain G residue   83 LEU
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 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 = 0.3825 r_free = 0.3825 target = 0.160295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.108648 restraints weight = 14611.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.107444 restraints weight = 20993.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.108332 restraints weight = 20185.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12721  Z= 0.151
  Angle     :  0.531   5.978  18424  Z= 0.325
  Chirality :  0.033   0.138   2107
  Planarity :  0.004   0.042   1323
  Dihedral  : 30.753 103.078   4005
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.91 %
    Favored  : 86.36 %
  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:  2.81 (0.30), residues: 738
  helix:  2.84 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.25 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.010   0.001   PHE A  68 
 TYR   0.010   0.001   TYR G  57 
 ARG   0.003   0.000   ARG G  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04375 (  785)
  hydrogen bonds       : angle       2.61696 ( 1963)
  covalent geometry    : bond        0.00326 (12721)
  covalent geometry    : angle       0.53090 (18424)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.807 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7536 (tm-30)
REVERT: B   91 LYS cc_start: 0.8539 (tttp) cc_final: 0.8130 (ttmm)
REVERT: D   46 TYR cc_start: 0.8270 (t80) cc_final: 0.7386 (t80)
REVERT: D   63 MET cc_start: 0.8955 (tpp) cc_final: 0.8541 (tpp)
REVERT: D   89 LYS cc_start: 0.8432 (mmmt) cc_final: 0.7969 (mttm)
REVERT: E   66 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8163 (mp)
REVERT: G   36 ARG cc_start: 0.7136 (tpp80) cc_final: 0.6758 (mmt90)
REVERT: G   83 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8695 (mt)
REVERT: H   38 LYS cc_start: 0.8157 (tptt) cc_final: 0.7626 (mtpt)
  outliers start: 11
  outliers final: 8
  residues processed: 78
  average time/residue: 0.2738
  time to fit residues: 30.3955
Evaluate side-chains
  79 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   83 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 78 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 85 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 68 optimal weight:    0.0670
   chunk 35 optimal weight:    0.8980
   chunk 98 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.160406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.108917 restraints weight = 14489.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.107570 restraints weight = 21229.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.108400 restraints weight = 20225.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12721  Z= 0.147
  Angle     :  0.528   6.210  18424  Z= 0.324
  Chirality :  0.033   0.131   2107
  Planarity :  0.004   0.039   1323
  Dihedral  : 30.774 103.075   4005
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.91 %
    Favored  : 86.83 %
  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:  3.01 (0.30), residues: 738
  helix:  2.99 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.19 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.007   0.001   PHE E  68 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.003   0.000   ARG H 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04242 (  785)
  hydrogen bonds       : angle       2.60071 ( 1963)
  covalent geometry    : bond        0.00317 (12721)
  covalent geometry    : angle       0.52755 (18424)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7575 (tm-30)
REVERT: B   91 LYS cc_start: 0.8511 (tttp) cc_final: 0.8110 (ttmm)
REVERT: D   46 TYR cc_start: 0.8257 (t80) cc_final: 0.7375 (t80)
REVERT: D   63 MET cc_start: 0.8952 (tpp) cc_final: 0.8541 (tpp)
REVERT: D   89 LYS cc_start: 0.8443 (mmmt) cc_final: 0.7970 (mttm)
REVERT: E   66 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8244 (mp)
REVERT: G   36 ARG cc_start: 0.7116 (tpp80) cc_final: 0.6743 (mmt90)
REVERT: G   83 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8700 (mt)
REVERT: H   38 LYS cc_start: 0.8167 (tptt) cc_final: 0.7636 (mtpt)
  outliers start: 8
  outliers final: 6
  residues processed: 74
  average time/residue: 0.2748
  time to fit residues: 28.5670
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   83 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 78 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.159868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.108353 restraints weight = 14411.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.106878 restraints weight = 20933.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.107674 restraints weight = 20741.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.4032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12721  Z= 0.156
  Angle     :  0.534   9.859  18424  Z= 0.325
  Chirality :  0.033   0.135   2107
  Planarity :  0.004   0.041   1323
  Dihedral  : 30.779 102.781   4005
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.91 %
    Favored  : 86.83 %
  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:  3.01 (0.30), residues: 738
  helix:  2.99 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.18 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.007   0.001   PHE E  68 
 TYR   0.008   0.001   TYR G  57 
 ARG   0.003   0.000   ARG H 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04389 (  785)
  hydrogen bonds       : angle       2.60336 ( 1963)
  covalent geometry    : bond        0.00345 (12721)
  covalent geometry    : angle       0.53370 (18424)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7548 (tm-30)
REVERT: B   91 LYS cc_start: 0.8466 (tttp) cc_final: 0.8022 (ttmm)
REVERT: D   46 TYR cc_start: 0.8257 (t80) cc_final: 0.7365 (t80)
REVERT: D   63 MET cc_start: 0.8956 (tpp) cc_final: 0.8583 (tpp)
REVERT: D   89 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7927 (mttm)
REVERT: E   66 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8253 (mp)
REVERT: G   36 ARG cc_start: 0.7177 (tpp80) cc_final: 0.6790 (mmt90)
REVERT: G   83 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8636 (mt)
REVERT: H   38 LYS cc_start: 0.8155 (tptt) cc_final: 0.7581 (mtpt)
  outliers start: 8
  outliers final: 6
  residues processed: 74
  average time/residue: 0.2838
  time to fit residues: 29.7648
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   83 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 77 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.160180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.108532 restraints weight = 14467.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.107095 restraints weight = 21041.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.107917 restraints weight = 20602.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12721  Z= 0.156
  Angle     :  0.533   7.325  18424  Z= 0.325
  Chirality :  0.033   0.135   2107
  Planarity :  0.004   0.043   1323
  Dihedral  : 30.784 102.763   4005
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.44 %
    Favored  : 86.83 %
  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:  3.02 (0.30), residues: 738
  helix:  3.00 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.18 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.007   0.001   PHE E  68 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.003   0.000   ARG H 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04399 (  785)
  hydrogen bonds       : angle       2.60863 ( 1963)
  covalent geometry    : bond        0.00346 (12721)
  covalent geometry    : angle       0.53261 (18424)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3571.44 seconds
wall clock time: 64 minutes 35.39 seconds (3875.39 seconds total)