Starting phenix.real_space_refine
on Wed Mar  4 01:55:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vbm_31882/03_2026/7vbm_31882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vbm_31882/03_2026/7vbm_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vbm_31882/03_2026/7vbm_31882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vbm_31882/03_2026/7vbm_31882.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vbm_31882/03_2026/7vbm_31882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vbm_31882/03_2026/7vbm_31882.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.53, per 1000 atoms: 0.24
  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: 0.88
  Conformation dependent library (CDL) restraints added in 307.4 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: 1.75
  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: 2.18

  Time building geometry restraints manager: 1.19 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:             0.720
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.530
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.130
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.011   0.001   ARG H  92 
 TYR   0.023   0.002   TYR F  88 
 PHE   0.044   0.004   PHE A  78 
 HIS   0.011   0.002   HIS H  82 

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

*********************** 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  : 0.258 
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: 0.1818
  time to fit residues: 18.6235
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  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.168285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.121821 restraints weight = 12865.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 1.04
r_work: 0.3112 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.0819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11171  Z= 0.179
  Angle     :  0.578   7.773  16169  Z= 0.344
  Chirality :  0.035   0.124   1850
  Planarity :  0.005   0.058   1168
  Dihedral  : 31.258 179.848   3477
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.32), residues: 661
  helix:  2.20 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.90 (0.41), residues: 156

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11171)
  covalent geometry    : angle       0.57801 (16169)
  hydrogen bonds       : bond        0.04659 (  686)
  hydrogen bonds       : angle       2.91954 ( 1743)

*********************** 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
  74 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.266 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8339 (tp30) cc_final: 0.8055 (tp30)
REVERT: D   59 MET cc_start: 0.8179 (tpp) cc_final: 0.7809 (tpp)
REVERT: F   39 ARG cc_start: 0.7494 (ttt90) cc_final: 0.7248 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8114 (mp10) cc_final: 0.7672 (mp10)
REVERT: H   33 ARG cc_start: 0.5814 (mtm180) cc_final: 0.5472 (mtm180)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1998
  time to fit residues: 18.1995
Evaluate side-chains
  66 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 84 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 66 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.168135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.120388 restraints weight = 12946.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.09
r_work: 0.2986 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.0903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11171  Z= 0.193
  Angle     :  0.584   7.269  16169  Z= 0.346
  Chirality :  0.035   0.129   1850
  Planarity :  0.005   0.064   1168
  Dihedral  : 31.308 179.908   3477
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  8.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.32), residues: 661
  helix:  2.23 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.95 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 116 
 TYR   0.017   0.002   TYR F  88 
 PHE   0.020   0.002   PHE G  25 
 HIS   0.005   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (11171)
  covalent geometry    : angle       0.58358 (16169)
  hydrogen bonds       : bond        0.04839 (  686)
  hydrogen bonds       : angle       2.88174 ( 1743)

*********************** 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
  65 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.267 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8421 (tp30) cc_final: 0.8171 (tp30)
REVERT: D   76 GLU cc_start: 0.8336 (tp30) cc_final: 0.8131 (tp30)
REVERT: F   39 ARG cc_start: 0.7536 (ttt90) cc_final: 0.7127 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7666 (mp10)
REVERT: H   33 ARG cc_start: 0.5532 (mtm180) cc_final: 0.5247 (mtm180)
  outliers start: 2
  outliers final: 1
  residues processed: 64
  average time/residue: 0.1642
  time to fit residues: 13.5573
Evaluate side-chains
  63 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
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 76 optimal weight:    9.9990
   chunk 69 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 84 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0870
   chunk 18 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0870
   overall best weight:    2.0340

-------------------------------------------------------------------------------
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 = 0.3888 r_free = 0.3888 target = 0.167306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.121712 restraints weight = 12921.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 1.08
r_work: 0.3065 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.0983

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= 0.198
  Angle     :  0.585   7.468  16169  Z= 0.346
  Chirality :  0.036   0.127   1850
  Planarity :  0.005   0.065   1168
  Dihedral  : 31.356 179.553   3477
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 10.18 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.32), residues: 661
  helix:  2.25 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.96 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 116 
 TYR   0.018   0.002   TYR F  88 
 PHE   0.022   0.002   PHE G  25 
 HIS   0.005   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (11171)
  covalent geometry    : angle       0.58495 (16169)
  hydrogen bonds       : bond        0.04918 (  686)
  hydrogen bonds       : angle       2.86200 ( 1743)

*********************** 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: 8
    poor density    : 60
  time to evaluate  : 0.246 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8418 (tp30) cc_final: 0.8185 (tp30)
REVERT: D   76 GLU cc_start: 0.8322 (tp30) cc_final: 0.8077 (tp30)
REVERT: E  125 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7082 (mp10)
REVERT: F   39 ARG cc_start: 0.7524 (ttt90) cc_final: 0.7128 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7697 (mp10)
  outliers start: 8
  outliers final: 4
  residues processed: 65
  average time/residue: 0.1556
  time to fit residues: 13.0282
Evaluate side-chains
  67 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
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   93 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 80 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.167820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.119951 restraints weight = 12834.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.08
r_work: 0.3057 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1066

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= 0.184
  Angle     :  0.574   7.369  16169  Z= 0.341
  Chirality :  0.035   0.124   1850
  Planarity :  0.004   0.068   1168
  Dihedral  : 31.348 178.946   3477
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.96 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.32), residues: 661
  helix:  2.35 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.93 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  23 
 TYR   0.017   0.001   TYR F  88 
 PHE   0.019   0.002   PHE G  25 
 HIS   0.005   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (11171)
  covalent geometry    : angle       0.57422 (16169)
  hydrogen bonds       : bond        0.04726 (  686)
  hydrogen bonds       : angle       2.81401 ( 1743)

*********************** 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
  68 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.261 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8524 (tp30) cc_final: 0.8316 (tp30)
REVERT: E  125 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7058 (mp10)
REVERT: F   39 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7169 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7673 (mp10)
  outliers start: 7
  outliers final: 5
  residues processed: 66
  average time/residue: 0.1576
  time to fit residues: 13.4646
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  : 0.269 
-------------------------------------------------------------------------------
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   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 2 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 64 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
D  95 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.168571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.117052 restraints weight = 13112.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 0.98
r_work: 0.3046 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.1139

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= 0.207
  Angle     :  0.596   7.477  16169  Z= 0.352
  Chirality :  0.036   0.130   1850
  Planarity :  0.005   0.068   1168
  Dihedral  : 31.426 179.876   3477
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.14 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.32), residues: 661
  helix:  2.25 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -2.01 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  23 
 TYR   0.021   0.002   TYR F  88 
 PHE   0.023   0.002   PHE G  25 
 HIS   0.006   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (11171)
  covalent geometry    : angle       0.59632 (16169)
  hydrogen bonds       : bond        0.05095 (  686)
  hydrogen bonds       : angle       2.88691 ( 1743)

*********************** 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
  73 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.328 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8489 (tp30) cc_final: 0.8274 (tp30)
REVERT: D   46 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8014 (mmtm)
REVERT: D   47 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8431 (tt0)
REVERT: E  125 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7026 (mp10)
REVERT: F   39 ARG cc_start: 0.7633 (ttt90) cc_final: 0.7153 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7672 (mp10)
  outliers start: 11
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1558
  time to fit residues: 13.8067
Evaluate side-chains
  72 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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   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  117 VAL
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 31 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 51 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4043 r_free = 0.4043 target = 0.180848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.135423 restraints weight = 12975.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 0.85
r_work: 0.3111 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1281

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= 0.158
  Angle     :  0.547   7.401  16169  Z= 0.328
  Chirality :  0.034   0.124   1850
  Planarity :  0.004   0.067   1168
  Dihedral  : 31.262 179.835   3477
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.39 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.32), residues: 661
  helix:  2.61 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.89 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  72 
 TYR   0.017   0.001   TYR F  88 
 PHE   0.012   0.001   PHE G  25 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (11171)
  covalent geometry    : angle       0.54740 (16169)
  hydrogen bonds       : bond        0.04256 (  686)
  hydrogen bonds       : angle       2.71428 ( 1743)

*********************** 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
  73 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.257 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7931 (mmtm)
REVERT: E  125 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7032 (mp10)
REVERT: F   39 ARG cc_start: 0.7539 (ttt90) cc_final: 0.7211 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7658 (mp10)
  outliers start: 9
  outliers final: 5
  residues processed: 70
  average time/residue: 0.1688
  time to fit residues: 14.9110
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  : 0.281 
-------------------------------------------------------------------------------
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 D residue   46 LYS
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 73 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   chunk 50 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   overall best weight:    3.7786

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.165426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.113922 restraints weight = 13074.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.01
r_work: 0.3004 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  11171  Z= 0.298
  Angle     :  0.685   8.060  16169  Z= 0.394
  Chirality :  0.041   0.136   1850
  Planarity :  0.005   0.069   1168
  Dihedral  : 31.807 179.652   3477
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.39 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.32), residues: 661
  helix:  1.84 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -2.13 (0.39), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  72 
 TYR   0.020   0.002   TYR F  88 
 PHE   0.026   0.003   PHE G  25 
 HIS   0.007   0.002   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00699 (11171)
  covalent geometry    : angle       0.68465 (16169)
  hydrogen bonds       : bond        0.06329 (  686)
  hydrogen bonds       : angle       3.11418 ( 1743)

*********************** 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
  70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.276 
Fit side-chains
REVERT: B   92 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7907 (ttp80)
REVERT: D   46 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7987 (mmtm)
REVERT: D   47 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8451 (tt0)
REVERT: D   59 MET cc_start: 0.8197 (tpp) cc_final: 0.7802 (tpp)
REVERT: E  125 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7080 (mp10)
REVERT: F   39 ARG cc_start: 0.7658 (ttt90) cc_final: 0.7211 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7740 (mp10)
  outliers start: 11
  outliers final: 6
  residues processed: 65
  average time/residue: 0.1699
  time to fit residues: 14.0223
Evaluate side-chains
  70 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   80 THR
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  117 VAL
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 57 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 60 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4055 r_free = 0.4055 target = 0.181812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.137040 restraints weight = 13029.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 0.87
r_work: 0.3145 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1592

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     :  0.536   7.073  16169  Z= 0.324
  Chirality :  0.033   0.125   1850
  Planarity :  0.004   0.066   1168
  Dihedral  : 31.241 177.986   3477
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.57 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.32), residues: 661
  helix:  2.65 (0.23), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.84 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 116 
 TYR   0.019   0.001   TYR F  88 
 PHE   0.009   0.001   PHE G  25 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (11171)
  covalent geometry    : angle       0.53559 (16169)
  hydrogen bonds       : bond        0.03881 (  686)
  hydrogen bonds       : angle       2.65191 ( 1743)

*********************** 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
  73 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.291 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7993 (mmtm)
REVERT: D   47 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8355 (tt0)
REVERT: D   90 THR cc_start: 0.8596 (p) cc_final: 0.8317 (m)
REVERT: E  125 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7048 (mp10)
REVERT: F   39 ARG cc_start: 0.7487 (ttt90) cc_final: 0.7203 (mtp-110)
REVERT: F   84 MET cc_start: 0.8577 (mmm) cc_final: 0.8363 (tpt)
REVERT: F   93 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7685 (mp10)
  outliers start: 9
  outliers final: 4
  residues processed: 69
  average time/residue: 0.1667
  time to fit residues: 14.7456
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  : 0.262 
-------------------------------------------------------------------------------
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 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   93 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 85 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4054 r_free = 0.4054 target = 0.181789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.136461 restraints weight = 12910.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 0.85
r_work: 0.3155 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1616

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= 0.150
  Angle     :  0.537   7.292  16169  Z= 0.323
  Chirality :  0.033   0.122   1850
  Planarity :  0.004   0.066   1168
  Dihedral  : 31.237 178.073   3477
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.11 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.32), residues: 661
  helix:  2.80 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.79 (0.40), residues: 156

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (11171)
  covalent geometry    : angle       0.53746 (16169)
  hydrogen bonds       : bond        0.03867 (  686)
  hydrogen bonds       : angle       2.64689 ( 1743)

********************** 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  : 0.283 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8050 (mmtm)
REVERT: D   59 MET cc_start: 0.8030 (tpp) cc_final: 0.7707 (tpp)
REVERT: E  125 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7009 (mp10)
REVERT: F   39 ARG cc_start: 0.7496 (ttt90) cc_final: 0.7205 (mtp-110)
REVERT: F   93 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7669 (mp10)
  outliers start: 8
  outliers final: 5
  residues processed: 64
  average time/residue: 0.1643
  time to fit residues: 13.5934
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  : 0.281 
-------------------------------------------------------------------------------
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 D residue   46 LYS
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 27 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 3 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 85 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.177650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.132231 restraints weight = 13117.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 0.91
r_work: 0.3105 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1533

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= 0.180
  Angle     :  0.569   7.601  16169  Z= 0.337
  Chirality :  0.035   0.127   1850
  Planarity :  0.004   0.067   1168
  Dihedral  : 31.317 179.655   3477
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.57 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.32), residues: 661
  helix:  2.65 (0.22), residues: 505
  sheet:  None (None), residues: 0
  loop : -1.86 (0.40), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 116 
 TYR   0.023   0.002   TYR F  88 
 PHE   0.015   0.002   PHE G  25 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 (11171)
  covalent geometry    : angle       0.56871 (16169)
  hydrogen bonds       : bond        0.04512 (  686)
  hydrogen bonds       : angle       2.74718 ( 1743)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2047.40 seconds
wall clock time: 35 minutes 47.59 seconds (2147.59 seconds total)