Starting phenix.real_space_refine
on Fri Feb 14 08:45:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vbm_31882/02_2025/7vbm_31882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vbm_31882/02_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_31882/02_2025/7vbm_31882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vbm_31882/02_2025/7vbm_31882.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vbm_31882/02_2025/7vbm_31882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vbm_31882/02_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-5592/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: 6.52, per 1000 atoms: 0.62
  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: 2.60
  Conformation dependent library (CDL) restraints added in 677.5 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: 4.93
  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: 4.07

  Time building geometry restraints manager: 3.01 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:             0.530
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     29.890
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.100
-------------------------------------------------------------------------------
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= 0.327
  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 

*********************** 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  : 0.717 
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: 0.3838
  time to fit residues: 39.4874
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  : 0.780 
-------------------------------------------------------------------------------
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 = 12756.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.09
r_work: 0.3060 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
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= 0.262
  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 

*********************** 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  : 0.741 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8397 (tp30) cc_final: 0.8118 (tp30)
REVERT: D   59 MET cc_start: 0.8181 (tpp) cc_final: 0.7788 (tpp)
REVERT: D   76 GLU cc_start: 0.8338 (tp30) cc_final: 0.8111 (tp30)
REVERT: F   39 ARG cc_start: 0.7563 (ttt90) cc_final: 0.7251 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8129 (mp10) cc_final: 0.7649 (mp10)
REVERT: H   33 ARG cc_start: 0.5502 (mtm180) cc_final: 0.5192 (mtm180)
  outliers start: 2
  outliers final: 2
  residues processed: 73
  average time/residue: 0.3730
  time to fit residues: 34.2726
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  : 0.705 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 63 optimal weight:    0.3980
   chunk 80 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 69 optimal weight:    8.9990
   chunk 79 optimal weight:    8.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.168081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.121294 restraints weight = 12877.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.10
r_work: 0.3049 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.0956

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= 0.227
  Angle     :  0.572   7.413  16169  Z= 0.341
  Chirality :  0.035   0.127   1850
  Planarity :  0.004   0.065   1168
  Dihedral  : 31.332 179.089   3477
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  8.57 %
    Favored  : 91.25 %
  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:  2.07 (0.32), residues: 661
  helix:  2.29 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.88 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.020   0.002   PHE G  25 
 TYR   0.016   0.001   TYR F  88 
 ARG   0.004   0.000   ARG A 116 

*********************** 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
  64 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.837 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8417 (tp30) cc_final: 0.8168 (tp30)
REVERT: F   39 ARG cc_start: 0.7569 (ttt90) cc_final: 0.7131 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7655 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.3657
  time to fit residues: 29.2819
Evaluate side-chains
  61 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 16 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 57 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
C  73 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.170119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.124423 restraints weight = 12769.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.10
r_work: 0.3121 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1207

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= 0.187
  Angle     :  0.541   7.255  16169  Z= 0.325
  Chirality :  0.033   0.123   1850
  Planarity :  0.004   0.061   1168
  Dihedral  : 31.218 179.372   3477
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.36 %
    Favored  : 88.93 %
  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:  2.62 (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   0.004   0.001   HIS F  75 
 PHE   0.015   0.001   PHE G  25 
 TYR   0.014   0.001   TYR F  88 
 ARG   0.005   0.000   ARG A 116 

*********************** 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
  69 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.725 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8416 (tp30) cc_final: 0.8185 (tp30)
REVERT: E  125 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7092 (mp10)
REVERT: F   39 ARG cc_start: 0.7493 (ttt90) cc_final: 0.7134 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7730 (mp10)
  outliers start: 4
  outliers final: 2
  residues processed: 68
  average time/residue: 0.3605
  time to fit residues: 31.0696
Evaluate side-chains
  65 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 29 optimal weight:    8.9990
   chunk 55 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   chunk 84 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0870
   overall best weight:    0.8760

-------------------------------------------------------------------------------
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 = 0.4056 r_free = 0.4056 target = 0.182046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.137041 restraints weight = 12914.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 0.88
r_work: 0.3145 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1311

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= 0.173
  Angle     :  0.536   7.346  16169  Z= 0.322
  Chirality :  0.033   0.121   1850
  Planarity :  0.004   0.062   1168
  Dihedral  : 31.190 179.544   3477
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.25 %
    Favored  : 87.68 %
  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 (0.32), residues: 661
  helix:  2.79 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.73 (0.42), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.009   0.001   PHE G  25 
 TYR   0.014   0.001   TYR F  88 
 ARG   0.004   0.000   ARG A 116 

*********************** 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
  70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.745 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8385 (tp30) cc_final: 0.8181 (tp30)
REVERT: E  125 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7119 (mp10)
REVERT: F   39 ARG cc_start: 0.7534 (ttt90) cc_final: 0.7189 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7705 (mp10)
  outliers start: 6
  outliers final: 3
  residues processed: 68
  average time/residue: 0.3413
  time to fit residues: 30.0257
Evaluate side-chains
  67 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain C residue   76 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    2.1384

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.177453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.132021 restraints weight = 13198.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 0.95
r_work: 0.3102 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1282

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= 0.267
  Angle     :  0.589   7.689  16169  Z= 0.348
  Chirality :  0.036   0.130   1850
  Planarity :  0.005   0.064   1168
  Dihedral  : 31.385 179.800   3477
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.57
  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:  2.30 (0.32), residues: 661
  helix:  2.47 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.85 (0.41), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H  49 
 PHE   0.021   0.002   PHE G  25 
 TYR   0.016   0.002   TYR F  88 
 ARG   0.003   0.000   ARG F  95 

*********************** 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
  69 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.752 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8366 (tp30) cc_final: 0.8153 (tp30)
REVERT: D   59 MET cc_start: 0.8101 (tpp) cc_final: 0.7801 (tpp)
REVERT: E  125 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7137 (mp10)
REVERT: F   39 ARG cc_start: 0.7618 (ttt90) cc_final: 0.7210 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7770 (mp10)
  outliers start: 8
  outliers final: 5
  residues processed: 65
  average time/residue: 0.3291
  time to fit residues: 27.6807
Evaluate side-chains
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   74 GLU
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:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3940 r_free = 0.3940 target = 0.171688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.125410 restraints weight = 12989.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 1.13
r_work: 0.3163 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1578

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= 0.169
  Angle     :  0.525   7.304  16169  Z= 0.317
  Chirality :  0.032   0.122   1850
  Planarity :  0.004   0.062   1168
  Dihedral  : 31.140 178.841   3477
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.50 %
    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:  2.85 (0.32), residues: 661
  helix:  2.89 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.76 (0.41), 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   0.015   0.001   TYR F  88 
 ARG   0.003   0.000   ARG A 116 

*********************** 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
  75 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.788 
Fit side-chains
REVERT: E  125 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7134 (mp10)
REVERT: F   39 ARG cc_start: 0.7574 (ttt90) cc_final: 0.7198 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7704 (mp10)
  outliers start: 10
  outliers final: 6
  residues processed: 71
  average time/residue: 0.3441
  time to fit residues: 31.2999
Evaluate side-chains
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   80 THR
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   74 GLU
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:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 84 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.166627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.120822 restraints weight = 12920.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.11
r_work: 0.3069 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  11171  Z= 0.309
  Angle     :  0.612   8.102  16169  Z= 0.358
  Chirality :  0.037   0.131   1850
  Planarity :  0.005   0.065   1168
  Dihedral  : 31.479 178.979   3477
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.32 %
    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:  2.17 (0.32), residues: 661
  helix:  2.40 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.96 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS H  49 
 PHE   0.020   0.002   PHE G  25 
 TYR   0.013   0.002   TYR F  88 
 ARG   0.003   0.000   ARG F  95 

*********************** 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
  71 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.761 
Fit side-chains
REVERT: E  125 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7129 (mp10)
REVERT: F   39 ARG cc_start: 0.7716 (ttt90) cc_final: 0.7207 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7710 (mp10)
  outliers start: 10
  outliers final: 6
  residues processed: 67
  average time/residue: 0.3608
  time to fit residues: 30.8938
Evaluate side-chains
  70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   80 THR
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   74 GLU
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:    0.0370
   chunk 70 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7664

-------------------------------------------------------------------------------
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 = 0.3935 r_free = 0.3935 target = 0.171328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.126137 restraints weight = 12995.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.07
r_work: 0.3119 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1678

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= 0.170
  Angle     :  0.528   7.225  16169  Z= 0.318
  Chirality :  0.033   0.124   1850
  Planarity :  0.004   0.066   1168
  Dihedral  : 31.187 177.721   3477
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.50 %
    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:  2.80 (0.32), residues: 661
  helix:  2.85 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.76 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.009   0.001   PHE G  25 
 TYR   0.015   0.001   TYR F  88 
 ARG   0.002   0.000   ARG A 116 

*********************** 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
  71 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.995 
Fit side-chains
REVERT: E  125 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7094 (mp10)
REVERT: F   39 ARG cc_start: 0.7533 (ttt90) cc_final: 0.7152 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7771 (mp10)
  outliers start: 8
  outliers final: 6
  residues processed: 67
  average time/residue: 0.3667
  time to fit residues: 31.8122
Evaluate side-chains
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   80 THR
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   74 GLU
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:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 82 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.168569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.122501 restraints weight = 12949.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.05
r_work: 0.3076 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11171  Z= 0.240
  Angle     :  0.566   7.538  16169  Z= 0.335
  Chirality :  0.035   0.134   1850
  Planarity :  0.004   0.067   1168
  Dihedral  : 31.266 179.281   3477
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.50 %
    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:  2.55 (0.32), residues: 661
  helix:  2.66 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.81 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.016   0.002   PHE G  25 
 TYR   0.015   0.001   TYR F  88 
 ARG   0.003   0.000   ARG H  72 

********************** 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
  67 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.828 
Fit side-chains
REVERT: E  125 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7112 (mp10)
REVERT: F   39 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7198 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7707 (mp10)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 0.3309
  time to fit residues: 27.1470
Evaluate side-chains
  67 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   80 THR
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   74 GLU
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:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.169762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.123378 restraints weight = 12831.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.07
r_work: 0.3113 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11171  Z= 0.186
  Angle     :  0.549   7.618  16169  Z= 0.327
  Chirality :  0.034   0.158   1850
  Planarity :  0.004   0.067   1168
  Dihedral  : 31.268 178.650   3477
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.50 %
    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:  2.65 (0.32), residues: 661
  helix:  2.74 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.80 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.012   0.001   PHE G  25 
 TYR   0.015   0.001   TYR F  88 
 ARG   0.002   0.000   ARG A 116 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3929.81 seconds
wall clock time: 70 minutes 43.21 seconds (4243.21 seconds total)