Starting phenix.real_space_refine
on Mon Jul 28 04:19:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vbm_31882/07_2025/7vbm_31882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vbm_31882/07_2025/7vbm_31882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vbm_31882/07_2025/7vbm_31882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vbm_31882/07_2025/7vbm_31882.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vbm_31882/07_2025/7vbm_31882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vbm_31882/07_2025/7vbm_31882.cif"
  }
  resolution = 3.4
  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     251      5.49       5
     S      14      5.16       5
     C    5799      2.51       5
     N    1944      2.21       5
     O    2467      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10475
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 565
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 712
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
    Chain: "D"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 603
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "F"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 614
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "G"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 719
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 3, 'TRANS': 89}
    Chain: "H"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 2566
          Classifications: {'DNA': 126}
          Link IDs: {'rna3p': 125}
    Chain: "J"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 2597
          Classifications: {'DNA': 126}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 125}
  Time building chain proxies: 6.68, per 1000 atoms: 0.64
  Number of scatterers: 10475
  At special positions: 0
  Unit cell: (116.6, 94.34, 124.02, 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      14     16.00
     P     251     15.00
     O    2467      8.00
     N    1944      7.00
     C    5799      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: 2.74
  Conformation dependent library (CDL) restraints added in 720.9 milliseconds
  

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1258

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      76.4% alpha, 3.0% beta
      117 base pairs and 214 stacking pairs defined.
    Time for finding SS restraints: 4.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.568A  pdb=" N   CYS A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.552A  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: 3.762A  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 17 through 22
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.621A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 72
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.729A  pdb=" N   LEU C  97 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.597A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.651A  pdb=" N   VAL D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.763A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.784A  pdb=" N   THR E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.736A  pdb=" N   GLY F  28 " --> pdb=" O   ASN F  25 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.835A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.596A  pdb=" N   VAL H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.835A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.066A  pdb=" N   CYS A  83 " --> 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 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.654A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (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 101 through 102
      removed outlier: 6.926A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.105A  pdb=" N   CYS E  83 " --> 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 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.545A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (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

    380 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      306 hydrogen bonds
      612 hydrogen bond angles
      0 basepair planarities
      117 basepair parallelities
      214 stacking parallelities
  Total time for adding SS restraints: 4.29

  Time building geometry restraints manager: 3.28 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1717
        1.33 -     1.45: 3846
        1.45 -     1.57: 5084
        1.57 -     1.69: 502
        1.69 -     1.81: 22
  Bond restraints: 11171
  Sorted by residual:
  bond pdb=" CZ  ARG C  77 "
       pdb=" NH2 ARG C  77 "
    ideal  model  delta    sigma   weight residual
    1.330  1.279  0.051 1.30e-02 5.92e+03 1.55e+01
  bond pdb=" CZ  ARG F  35 "
       pdb=" NH2 ARG F  35 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.05e+00
  bond pdb=" CZ  ARG E 132 "
       pdb=" NH2 ARG E 132 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.23e+00
  bond pdb=" CZ  ARG D  92 "
       pdb=" NH2 ARG D  92 "
    ideal  model  delta    sigma   weight residual
    1.330  1.293  0.037 1.30e-02 5.92e+03 8.11e+00
  bond pdb=" CZ  ARG C  77 "
       pdb=" NH1 ARG C  77 "
    ideal  model  delta    sigma   weight residual
    1.323  1.283  0.040 1.40e-02 5.10e+03 8.08e+00
  ... (remaining 11166 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 15537
        1.79 -     3.58: 548
        3.58 -     5.37: 64
        5.37 -     7.16: 17
        7.16 -     8.96: 3
  Bond angle restraints: 16169
  Sorted by residual:
  angle pdb=" CA  CYS E  83 "
        pdb=" C   CYS E  83 "
        pdb=" N   PHE E  84 "
      ideal   model   delta    sigma   weight residual
     115.55  122.08   -6.53 1.33e+00 5.65e-01 2.41e+01
  angle pdb=" C   LEU A  61 "
        pdb=" N   ILE A  62 "
        pdb=" CA  ILE A  62 "
      ideal   model   delta    sigma   weight residual
     123.14  129.14   -6.00 1.31e+00 5.83e-01 2.10e+01
  angle pdb=" C   THR B  30 "
        pdb=" N   LYS B  31 "
        pdb=" CA  LYS B  31 "
      ideal   model   delta    sigma   weight residual
     120.58  126.32   -5.74 1.32e+00 5.74e-01 1.89e+01
  angle pdb=" C   ASN C  73 "
        pdb=" N   LYS C  74 "
        pdb=" CA  LYS C  74 "
      ideal   model   delta    sigma   weight residual
     122.07  128.08   -6.01 1.43e+00 4.89e-01 1.76e+01
  angle pdb=" C   ARG A 116 "
        pdb=" N   VAL A 117 "
        pdb=" CA  VAL A 117 "
      ideal   model   delta    sigma   weight residual
     121.84  126.31   -4.47 1.13e+00 7.83e-01 1.56e+01
  ... (remaining 16164 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.82: 4839
       35.82 -    71.65: 1170
       71.65 -   107.47: 9
      107.47 -   143.29: 3
      143.29 -   179.12: 3
  Dihedral angle restraints: 6024
    sinusoidal: 4069
      harmonic: 1955
  Sorted by residual:
  dihedral pdb=" CA  LEU A  82 "
           pdb=" C   LEU A  82 "
           pdb=" N   CYS A  83 "
           pdb=" CA  CYS A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.10   23.90     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" N   GLN E  76 "
           pdb=" C   GLN E  76 "
           pdb=" CA  GLN E  76 "
           pdb=" CB  GLN E  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.49  -10.69     0      2.50e+00 1.60e-01 1.83e+01
  dihedral pdb=" CA  THR A  80 "
           pdb=" C   THR A  80 "
           pdb=" N   ASP A  81 "
           pdb=" CA  ASP A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.06  -20.94     0      5.00e+00 4.00e-02 1.75e+01
  ... (remaining 6021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1755
       0.082 -    0.164: 85
       0.164 -    0.245: 6
       0.245 -    0.327: 2
       0.327 -    0.409: 2
  Chirality restraints: 1850
  Sorted by residual:
  chirality pdb=" CA  GLN E  76 "
            pdb=" N   GLN E  76 "
            pdb=" C   GLN E  76 "
            pdb=" CB  GLN E  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.18e+00
  chirality pdb=" CA  LYS E 122 "
            pdb=" N   LYS E 122 "
            pdb=" C   LYS E 122 "
            pdb=" CB  LYS E 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" CA  ARG H  33 "
            pdb=" N   ARG H  33 "
            pdb=" C   ARG H  33 "
            pdb=" CB  ARG H  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.63e+00
  ... (remaining 1847 not shown)

  Planarity restraints: 1168
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  78 "    0.044 2.00e-02 2.50e+03   2.81e-02 1.38e+01
        pdb=" CG  PHE A  78 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  78 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  78 "   -0.035 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  78 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  78 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  78 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 100 "   -0.018 2.00e-02 2.50e+03   3.64e-02 1.32e+01
        pdb=" C   PHE B 100 "    0.063 2.00e-02 2.50e+03
        pdb=" O   PHE B 100 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLY B 101 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  92 "   -0.281 9.50e-02 1.11e+02   1.26e-01 1.02e+01
        pdb=" NE  ARG H  92 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  92 "    0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  92 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  92 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1165 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1387
        2.76 -     3.29: 9078
        3.29 -     3.83: 20471
        3.83 -     4.36: 23963
        4.36 -     4.90: 34740
  Nonbonded interactions: 89639
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  68 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" NH1 ARG G  32 "
            pdb=" OP1  DG J -44 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" NH1 ARG C  88 "
            pdb=" OD1 ASN C  94 "
     model   vdw
     2.417 3.120
  ... (remaining 89634 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' and resid 61 through 132)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 16 through 106)
  selection = (chain 'G' and resid 16 through 106)
}
ncs_group {
  reference = chain 'D'
  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=1.00 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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     30.220
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
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      :  0.005   0.075  11171  Z= 0.276
  Angle     :  0.748   8.955  16169  Z= 0.463
  Chirality :  0.044   0.409   1850
  Planarity :  0.008   0.126   1168
  Dihedral  : 28.389 179.118   4766
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.54 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.16 %
  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:  1.47 (0.32), residues: 661
  helix:  1.84 (0.23), residues: 500
  sheet:  None (None), residues: 0
  loop : -1.89 (0.40), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS H  82 
 PHE   0.044   0.004   PHE A  78 
 TYR   0.023   0.002   TYR F  88 
 ARG   0.011   0.001   ARG H  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10167 (  686)
  hydrogen bonds       : angle       3.92453 ( 1743)
  covalent geometry    : bond        0.00549 (11171)
  covalent geometry    : angle       0.74835 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.847 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8119 (tp30) cc_final: 0.7777 (tp30)
REVERT: E   79 LYS cc_start: 0.7036 (tppt) cc_final: 0.6548 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 82
  average time/residue: 0.3722
  time to fit residues: 38.4621
Evaluate side-chains
  70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    8.9990
   chunk 67 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.167850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.121219 restraints weight = 12756.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.09
r_work: 0.3061 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.0818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  11171  Z= 0.199
  Angle     :  0.601   7.989  16169  Z= 0.355
  Chirality :  0.036   0.126   1850
  Planarity :  0.005   0.059   1168
  Dihedral  : 31.365 179.508   3477
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  6.43 %
    Favored  : 93.21 %
  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:  1.75 (0.32), residues: 661
  helix:  2.05 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.97 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H  49 
 PHE   0.023   0.002   PHE G  25 
 TYR   0.016   0.002   TYR F  88 
 ARG   0.003   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05021 (  686)
  hydrogen bonds       : angle       2.98445 ( 1743)
  covalent geometry    : bond        0.00454 (11171)
  covalent geometry    : angle       0.60070 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.731 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8390 (tp30) cc_final: 0.8107 (tp30)
REVERT: D   59 MET cc_start: 0.8161 (tpp) cc_final: 0.7766 (tpp)
REVERT: D   76 GLU cc_start: 0.8338 (tp30) cc_final: 0.8110 (tp30)
REVERT: F   39 ARG cc_start: 0.7570 (ttt90) cc_final: 0.7251 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8124 (mp10) cc_final: 0.7646 (mp10)
REVERT: H   33 ARG cc_start: 0.5518 (mtm180) cc_final: 0.5209 (mtm180)
  outliers start: 2
  outliers final: 2
  residues processed: 73
  average time/residue: 0.3730
  time to fit residues: 34.3046
Evaluate side-chains
  65 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain E residue  117 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 63 optimal weight:    0.2980
   chunk 80 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0980
   chunk 69 optimal weight:    8.9990
   chunk 79 optimal weight:    8.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.170314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.123325 restraints weight = 12906.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.15
r_work: 0.3137 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11171  Z= 0.155
  Angle     :  0.543   7.057  16169  Z= 0.327
  Chirality :  0.033   0.123   1850
  Planarity :  0.004   0.062   1168
  Dihedral  : 31.199 179.051   3477
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  8.39 %
    Favored  : 91.43 %
  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:  2.41 (0.32), residues: 661
  helix:  2.54 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.75 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.013   0.001   PHE G  25 
 TYR   0.013   0.001   TYR F  88 
 ARG   0.004   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  686)
  hydrogen bonds       : angle       2.73004 ( 1743)
  covalent geometry    : bond        0.00336 (11171)
  covalent geometry    : angle       0.54293 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.789 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8432 (tp30) cc_final: 0.8188 (tp30)
REVERT: D   59 MET cc_start: 0.8097 (tpp) cc_final: 0.7753 (tpp)
REVERT: F   39 ARG cc_start: 0.7560 (ttt90) cc_final: 0.7113 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7607 (mp10)
REVERT: H   33 ARG cc_start: 0.5764 (mtm180) cc_final: 0.5142 (mtm110)
  outliers start: 1
  outliers final: 0
  residues processed: 66
  average time/residue: 0.3826
  time to fit residues: 31.8122
Evaluate side-chains
  63 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   93 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 71 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 76 optimal weight:    9.9990
   chunk 16 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 42 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.169000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.123769 restraints weight = 12743.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.11
r_work: 0.3013 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.1140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11171  Z= 0.172
  Angle     :  0.558   7.235  16169  Z= 0.333
  Chirality :  0.034   0.125   1850
  Planarity :  0.004   0.062   1168
  Dihedral  : 31.245 179.279   3477
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.00 %
    Favored  : 89.29 %
  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:  2.38 (0.32), residues: 661
  helix:  2.52 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.79 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.017   0.002   PHE G  25 
 TYR   0.015   0.001   TYR F  88 
 ARG   0.003   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04419 (  686)
  hydrogen bonds       : angle       2.73846 ( 1743)
  covalent geometry    : bond        0.00383 (11171)
  covalent geometry    : angle       0.55778 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.777 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8438 (tp30) cc_final: 0.8204 (tp30)
REVERT: E  125 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7056 (mp10)
REVERT: F   39 ARG cc_start: 0.7509 (ttt90) cc_final: 0.7143 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7640 (mp10)
  outliers start: 4
  outliers final: 1
  residues processed: 67
  average time/residue: 0.3451
  time to fit residues: 30.0258
Evaluate side-chains
  65 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 75 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9980
   chunk 84 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.168223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.116614 restraints weight = 12913.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 0.98
r_work: 0.2986 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
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   0.038  11171  Z= 0.216
  Angle     :  0.602   7.574  16169  Z= 0.355
  Chirality :  0.037   0.129   1850
  Planarity :  0.005   0.067   1168
  Dihedral  : 31.466 179.874   3477
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.61 %
    Favored  : 87.32 %
  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:  2.04 (0.32), residues: 661
  helix:  2.27 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.92 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H  49 
 PHE   0.022   0.002   PHE G  25 
 TYR   0.015   0.002   TYR F  88 
 ARG   0.003   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05203 (  686)
  hydrogen bonds       : angle       2.89321 ( 1743)
  covalent geometry    : bond        0.00496 (11171)
  covalent geometry    : angle       0.60226 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.692 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8401 (tp30) cc_final: 0.8161 (tp30)
REVERT: E  125 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7026 (mp10)
REVERT: F   39 ARG cc_start: 0.7563 (ttt90) cc_final: 0.7092 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7681 (mp10)
  outliers start: 6
  outliers final: 4
  residues processed: 64
  average time/residue: 0.3233
  time to fit residues: 26.9830
Evaluate side-chains
  66 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 68 optimal weight:    7.9990
   chunk 57 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
D  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.169833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.119542 restraints weight = 13149.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.05
r_work: 0.3067 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11171  Z= 0.191
  Angle     :  0.583   7.595  16169  Z= 0.345
  Chirality :  0.035   0.126   1850
  Planarity :  0.005   0.067   1168
  Dihedral  : 31.425 179.855   3477
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.14 %
    Favored  : 86.43 %
  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:  2.13 (0.32), residues: 661
  helix:  2.35 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.93 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H  49 
 PHE   0.019   0.002   PHE G  25 
 TYR   0.019   0.002   TYR F  88 
 ARG   0.002   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04858 (  686)
  hydrogen bonds       : angle       2.83790 ( 1743)
  covalent geometry    : bond        0.00432 (11171)
  covalent geometry    : angle       0.58285 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.835 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8468 (tp30) cc_final: 0.8242 (tp30)
REVERT: E  125 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7069 (mp10)
REVERT: F   39 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7167 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7700 (mp10)
  outliers start: 8
  outliers final: 6
  residues processed: 62
  average time/residue: 0.3229
  time to fit residues: 26.2513
Evaluate side-chains
  65 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 23 optimal weight:    0.1980
   chunk 50 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 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 = 0.4057 r_free = 0.4057 target = 0.182033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.136804 restraints weight = 13182.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 0.94
r_work: 0.3121 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11171  Z= 0.149
  Angle     :  0.535   7.234  16169  Z= 0.322
  Chirality :  0.033   0.133   1850
  Planarity :  0.004   0.065   1168
  Dihedral  : 31.216 179.059   3477
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 12.68 %
    Favored  : 86.07 %
  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:  2.69 (0.33), residues: 661
  helix:  2.77 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.78 (0.42), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.010   0.001   PHE G  25 
 TYR   0.014   0.001   TYR F  88 
 ARG   0.002   0.000   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  686)
  hydrogen bonds       : angle       2.65889 ( 1743)
  covalent geometry    : bond        0.00321 (11171)
  covalent geometry    : angle       0.53493 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.732 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7897 (ttp80)
REVERT: C   61 GLU cc_start: 0.8392 (tp30) cc_final: 0.8189 (tp30)
REVERT: E  125 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7125 (mp10)
REVERT: F   39 ARG cc_start: 0.7540 (ttt90) cc_final: 0.7223 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7697 (mp10)
  outliers start: 7
  outliers final: 3
  residues processed: 68
  average time/residue: 0.3590
  time to fit residues: 31.1559
Evaluate side-chains
  65 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 81 optimal weight:    8.9990
   chunk 84 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 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 = 0.3905 r_free = 0.3905 target = 0.168204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.121632 restraints weight = 12849.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.11
r_work: 0.3009 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11171  Z= 0.182
  Angle     :  0.566   7.481  16169  Z= 0.336
  Chirality :  0.035   0.127   1850
  Planarity :  0.004   0.065   1168
  Dihedral  : 31.303 179.206   3477
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.68 %
    Favored  : 85.54 %
  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:  2.47 (0.32), residues: 661
  helix:  2.61 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.86 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H  49 
 PHE   0.015   0.002   PHE G  25 
 TYR   0.017   0.001   TYR F  88 
 ARG   0.002   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04592 (  686)
  hydrogen bonds       : angle       2.76579 ( 1743)
  covalent geometry    : bond        0.00410 (11171)
  covalent geometry    : angle       0.56646 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.802 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7899 (ttp80)
REVERT: C   61 GLU cc_start: 0.8409 (tp30) cc_final: 0.8192 (tp30)
REVERT: D   46 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8004 (mmtm)
REVERT: D   47 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8347 (tt0)
REVERT: E  125 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7062 (mp10)
REVERT: F   39 ARG cc_start: 0.7619 (ttt90) cc_final: 0.7162 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7756 (mp10)
  outliers start: 10
  outliers final: 4
  residues processed: 66
  average time/residue: 0.3522
  time to fit residues: 29.9936
Evaluate side-chains
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.168440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.122615 restraints weight = 13010.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.15
r_work: 0.3070 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11171  Z= 0.173
  Angle     :  0.563   7.573  16169  Z= 0.335
  Chirality :  0.034   0.126   1850
  Planarity :  0.004   0.065   1168
  Dihedral  : 31.302 179.007   3477
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.68 %
    Favored  : 85.71 %
  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:  2.50 (0.32), residues: 661
  helix:  2.63 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.85 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.014   0.002   PHE G  25 
 TYR   0.017   0.001   TYR F  88 
 ARG   0.002   0.000   ARG F  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  686)
  hydrogen bonds       : angle       2.76106 ( 1743)
  covalent geometry    : bond        0.00388 (11171)
  covalent geometry    : angle       0.56290 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.724 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7891 (ttp80)
REVERT: C   61 GLU cc_start: 0.8445 (tp30) cc_final: 0.8227 (tp30)
REVERT: D   46 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8017 (mmtm)
REVERT: D   47 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8335 (tt0)
REVERT: E  125 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7041 (mp10)
REVERT: F   39 ARG cc_start: 0.7647 (ttt90) cc_final: 0.7173 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7758 (mp10)
  outliers start: 9
  outliers final: 4
  residues processed: 65
  average time/residue: 0.3375
  time to fit residues: 28.1516
Evaluate side-chains
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.171105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.121493 restraints weight = 12987.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 1.09
r_work: 0.3038 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11171  Z= 0.156
  Angle     :  0.554   7.701  16169  Z= 0.331
  Chirality :  0.034   0.128   1850
  Planarity :  0.004   0.065   1168
  Dihedral  : 31.296 178.613   3477
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.68 %
    Favored  : 85.71 %
  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:  2.62 (0.32), residues: 661
  helix:  2.73 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.83 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.011   0.001   PHE G  25 
 TYR   0.018   0.001   TYR F  88 
 ARG   0.002   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04353 (  686)
  hydrogen bonds       : angle       2.74292 ( 1743)
  covalent geometry    : bond        0.00338 (11171)
  covalent geometry    : angle       0.55384 (16169)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 1.511 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7915 (ttp80)
REVERT: D   46 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7985 (mmtm)
REVERT: D   47 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8381 (tt0)
REVERT: E  125 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7061 (mp10)
REVERT: F   39 ARG cc_start: 0.7707 (ttt90) cc_final: 0.7192 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7779 (mp10)
  outliers start: 9
  outliers final: 3
  residues processed: 65
  average time/residue: 0.6243
  time to fit residues: 51.6093
Evaluate side-chains
  66 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 1.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   93 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 23 optimal weight:    0.1980
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.180688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.134889 restraints weight = 12890.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 0.91
r_work: 0.3143 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11171  Z= 0.145
  Angle     :  0.538   7.852  16169  Z= 0.323
  Chirality :  0.033   0.127   1850
  Planarity :  0.004   0.064   1168
  Dihedral  : 31.232 177.946   3477
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.04 %
    Favored  : 85.89 %
  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:  2.85 (0.32), residues: 661
  helix:  2.89 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.77 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.010   0.001   PHE D  65 
 TYR   0.017   0.001   TYR F  88 
 ARG   0.002   0.000   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  686)
  hydrogen bonds       : angle       2.67323 ( 1743)
  covalent geometry    : bond        0.00307 (11171)
  covalent geometry    : angle       0.53829 (16169)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4635.87 seconds
wall clock time: 82 minutes 11.35 seconds (4931.35 seconds total)