Starting phenix.real_space_refine
on Tue Aug  4 16:58:23 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7yr7_34048/08_2026/7yr7_34048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr7_34048/08_2026/7yr7_34048.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2026/7yr7_34048.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2026/7yr7_34048.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2026/7yr7_34048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2026/7yr7_34048.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2026/7yr7_34048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2026/7yr7_34048.map"
  }
  resolution = 3.8
  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=   0.004 sd=   0.054
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     118      5.49       5
     S      12      5.16       5
     C    2731      2.51       5
     N     955      2.21       5
     O    1286      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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5102
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "F"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 426
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "E"
      Number of atoms: 424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 424
          Classifications: {'peptide': 55}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 426
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "B"
      Number of atoms: 428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 428
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 2547
          Classifications: {'RNAv2': 118}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 58, 'rna3p_pyr': 36}
          Link IDs: {'rna2p': 23, 'rna3p': 94}
    Chain: "C"
      Number of atoms: 425
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 425
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 426
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
  Time building chain proxies: 1.14, per 1000 atoms: 0.22
  Number of scatterers: 5102
  At special positions: 0
  Unit cell: (95.2, 84.15, 112.2, 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      12     16.00
     P     118     15.00
     O    1286      8.00
     N     955      7.00
     C    2731      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: 0.44
  Conformation dependent library (CDL) restraints added in 95.7 milliseconds
  

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  598

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 6 sheets defined
      17.9% alpha, 16.1% beta
      26 base pairs and 49 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'F' and resid 46 through 55
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'G' and resid 46 through 55
    Processing helix  chain 'B' and resid 46 through 53
    Processing helix  chain 'C' and resid 46 through 55
    Processing helix  chain 'D' and resid 45 through 55
    Processing sheet with id=AA1, first strand: chain 'F' and resid 20 through 26
      removed outlier: 5.091A  pdb=" N   ARG F  31 " --> pdb=" O   LEU F  23 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   VAL F  25 " --> pdb=" O   GLN F  29 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   GLN F  29 " --> pdb=" O   VAL F  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 6
      removed outlier: 4.336A  pdb=" N   LEU E   4 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ILE G  32 " --> pdb=" O   LEU E   4 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 20 through 26
      removed outlier: 4.545A  pdb=" N   ARG E  31 " --> pdb=" O   LEU E  23 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   VAL E  25 " --> pdb=" O   GLN E  29 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   GLN E  29 " --> pdb=" O   VAL E  25 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ARG G   6 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   LEU G   4 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 26
      removed outlier: 5.224A  pdb=" N   ARG B  31 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   VAL B  25 " --> pdb=" O   GLN B  29 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   GLN B  29 " --> pdb=" O   VAL B  25 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE B  32 " --> pdb=" O   ILE D   3 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 26
      removed outlier: 3.602A  pdb=" N   LYS C  26 " --> pdb=" O   GLN C  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 26
      removed outlier: 5.564A  pdb=" N   VAL D  22 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLY D  33 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   GLY D  24 " --> pdb=" O   ARG D  31 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLN D  29 " --> pdb=" O   LYS D  26 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    153 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      68 hydrogen bonds
      124 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      49 stacking parallelities
  Total time for adding SS restraints: 0.57

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1154
        1.34 -     1.45: 1659
        1.45 -     1.57: 2349
        1.57 -     1.69: 235
        1.69 -     1.81: 24
  Bond restraints: 5421
  Sorted by residual:
  bond pdb=" O3'   A A  89 "
       pdb=" P     G A  90 "
    ideal  model  delta    sigma   weight residual
    1.607  1.662 -0.055 1.20e-02 6.94e+03 2.09e+01
  bond pdb=" O3'   G A  50 "
       pdb=" P     G A  51 "
    ideal  model  delta    sigma   weight residual
    1.607  1.658 -0.051 1.20e-02 6.94e+03 1.83e+01
  bond pdb=" O3'   C A  62 "
       pdb=" P     A A  63 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.20e-02 6.94e+03 1.76e+01
  bond pdb=" O3'   C A   6 "
       pdb=" P     A A   7 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.20e-02 6.94e+03 1.54e+01
  bond pdb=" O3'   A A  36 "
       pdb=" P     A A  37 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.20e-02 6.94e+03 1.52e+01
  ... (remaining 5416 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.90: 7395
        2.90 -     5.80: 487
        5.80 -     8.70: 25
        8.70 -    11.60: 4
       11.60 -    14.50: 1
  Bond angle restraints: 7912
  Sorted by residual:
  angle pdb=" N   VAL G  18 "
        pdb=" CA  VAL G  18 "
        pdb=" C   VAL G  18 "
      ideal   model   delta    sigma   weight residual
     113.71  107.11    6.60 9.50e-01 1.11e+00 4.83e+01
  angle pdb=" N   THR D  19 "
        pdb=" CA  THR D  19 "
        pdb=" C   THR D  19 "
      ideal   model   delta    sigma   weight residual
     111.02  118.12   -7.10 1.25e+00 6.40e-01 3.23e+01
  angle pdb=" C4'   A A  78 "
        pdb=" C3'   A A  78 "
        pdb=" O3'   A A  78 "
      ideal   model   delta    sigma   weight residual
     112.50  122.87  -10.37 2.00e+00 2.50e-01 2.69e+01
  angle pdb=" N   LEU E   4 "
        pdb=" CA  LEU E   4 "
        pdb=" C   LEU E   4 "
      ideal   model   delta    sigma   weight residual
     108.32  116.73   -8.41 1.64e+00 3.72e-01 2.63e+01
  angle pdb=" C   VAL B  18 "
        pdb=" N   THR B  19 "
        pdb=" CA  THR B  19 "
      ideal   model   delta    sigma   weight residual
     121.54  131.33   -9.79 1.91e+00 2.74e-01 2.63e+01
  ... (remaining 7907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.26: 2587
       34.26 -    68.53: 382
       68.53 -   102.79: 33
      102.79 -   137.05: 0
      137.05 -   171.31: 1
  Dihedral angle restraints: 3003
    sinusoidal: 2075
      harmonic: 928
  Sorted by residual:
  dihedral pdb=" C4'   G A  39 "
           pdb=" C3'   G A  39 "
           pdb=" C2'   G A  39 "
           pdb=" C1'   G A  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -40.25   76.59     1      3.10e+00 1.04e-01 7.67e+02
  dihedral pdb=" C4'   C A  76 "
           pdb=" C3'   C A  76 "
           pdb=" C2'   C A  76 "
           pdb=" C1'   C A  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.71   75.05     1      3.10e+00 1.04e-01 7.41e+02
  dihedral pdb=" C4'   C A  83 "
           pdb=" C3'   C A  83 "
           pdb=" C2'   C A  83 "
           pdb=" C1'   C A  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.01   74.36     1      3.10e+00 1.04e-01 7.30e+02
  ... (remaining 3000 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 706
       0.118 -    0.236: 186
       0.236 -    0.353: 110
       0.353 -    0.471: 5
       0.471 -    0.588: 13
  Chirality restraints: 1020
  Sorted by residual:
  chirality pdb=" P     G A  79 "
            pdb=" OP1   G A  79 "
            pdb=" OP2   G A  79 "
            pdb=" O5'   G A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.76   -0.59 2.00e-01 2.50e+01 8.65e+00
  chirality pdb=" P     G A   8 "
            pdb=" OP1   G A   8 "
            pdb=" OP2   G A   8 "
            pdb=" O5'   G A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.74   -0.56 2.00e-01 2.50e+01 7.97e+00
  chirality pdb=" P     G A  51 "
            pdb=" OP1   G A  51 "
            pdb=" OP2   G A  51 "
            pdb=" O5'   G A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.73   -0.55 2.00e-01 2.50e+01 7.65e+00
  ... (remaining 1017 not shown)

  Planarity restraints: 561
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E  47 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.95e+00
        pdb=" C   ILE E  47 "    0.046 2.00e-02 2.50e+03
        pdb=" O   ILE E  47 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TYR E  48 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A   3 "    0.009 2.00e-02 2.50e+03   1.52e-02 6.94e+00
        pdb=" N9    G A   3 "   -0.013 2.00e-02 2.50e+03
        pdb=" C8    G A   3 "   -0.011 2.00e-02 2.50e+03
        pdb=" N7    G A   3 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G A   3 "    0.009 2.00e-02 2.50e+03
        pdb=" C6    G A   3 "    0.024 2.00e-02 2.50e+03
        pdb=" O6    G A   3 "    0.003 2.00e-02 2.50e+03
        pdb=" N1    G A   3 "   -0.039 2.00e-02 2.50e+03
        pdb=" C2    G A   3 "    0.013 2.00e-02 2.50e+03
        pdb=" N2    G A   3 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G A   3 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G A   3 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F  36 "    0.043 5.00e-02 4.00e+02   6.48e-02 6.72e+00
        pdb=" N   PRO F  37 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO F  37 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO F  37 "    0.036 5.00e-02 4.00e+02
  ... (remaining 558 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1653
        2.89 -     3.39: 4213
        3.39 -     3.89: 9409
        3.89 -     4.40: 9604
        4.40 -     4.90: 13814
  Nonbonded interactions: 38693
  Sorted by model distance:
  nonbonded pdb=" OG1 THR G  21 "
            pdb=" O   GLY G  33 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" O5'   A A  49 "
            pdb=" O4'   A A  49 "
     model   vdw
     2.438 2.432
  nonbonded pdb=" O   THR E   5 "
            pdb=" OG1 THR E   5 "
     model   vdw
     2.445 3.040
  nonbonded pdb=" O5'   C A   6 "
            pdb=" O4'   C A   6 "
     model   vdw
     2.447 2.432
  nonbonded pdb=" N2    G A  40 "
            pdb=" O   ALA D  36 "
     model   vdw
     2.448 3.120
  ... (remaining 38688 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 'B' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ 
e N or name CA or name C or name O )) or resid 25 or (resid 26 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 27 through 55))
  selection = (chain 'C' and (resid 1 through 22 or (resid 23 through 24 and (name N or name C \ 
A or name C or name O )) or resid 25 or (resid 26 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 27 through 55))
  selection = (chain 'D' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ 
e N or name CA or name C or name O )) or resid 25 through 55))
  selection = (chain 'E' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 25 or (resid 26 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 27 through 55))
  selection = (chain 'F' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ 
e N or name CA or name C or name O )) or resid 25 through 55))
  selection = (chain 'G' and (resid 1 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 22 or (resid 23 through 24 and (nam \ 
e N or name CA or name C or name O )) or resid 25 through 55))
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.770
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6024
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      :  0.008   0.055   5421  Z= 0.474
  Angle     :  1.406  14.504   7912  Z= 0.703
  Chirality :  0.144   0.588   1020
  Planarity :  0.008   0.065    561
  Dihedral  : 24.752 171.314   2405
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 12.77 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -5.36 (0.35), residues: 318
  helix: -4.63 (0.31), residues: 54
  sheet: -4.54 (0.75), residues: 20
  loop : -3.53 (0.33), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E   6 
 TYR   0.023   0.003   TYR E  48 
 HIS   0.006   0.002   HIS E  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00777 /  0.47 ( 5421)
  covalent geometry    : angle       1.40571 /  0.70 ( 7912)
  hydrogen bonds       : bond        0.22230 / 14.83 (  122)
  hydrogen bonds       : angle       9.10100 /  6.24 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   31 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7741 (mtt180)
REVERT: E   55 LYS cc_start: 0.7684 (mttt) cc_final: 0.7199 (mttt)
REVERT: B    7 ARG cc_start: 0.6979 (ptp90) cc_final: 0.6373 (ttm170)
REVERT: B   31 ARG cc_start: 0.7764 (ttt180) cc_final: 0.7312 (mmm-85)
REVERT: C   13 MET cc_start: 0.1168 (mtm) cc_final: 0.0761 (mpp)
REVERT: C   42 VAL cc_start: 0.8757 (t) cc_final: 0.8528 (m)
REVERT: D   10 GLU cc_start: 0.6359 (mm-30) cc_final: 0.5930 (mm-30)
  outliers start: 13
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1053
  time to fit residues: 14.4130
Evaluate side-chains
  91 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.8388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  28 ASN
F  29 GLN
B  35 ASN
B  43 HIS
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D  52 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.185183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.149578 restraints weight = 13738.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.152995 restraints weight = 8747.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.155326 restraints weight = 6438.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.156933 restraints weight = 5183.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.158101 restraints weight = 4438.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5421  Z= 0.255
  Angle     :  1.317  13.764   7912  Z= 0.546
  Chirality :  0.099   0.569   1020
  Planarity :  0.006   0.054    561
  Dihedral  : 21.457 165.252   1785
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.81 %
    Favored  : 80.19 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 22.63 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

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: -4.70 (0.39), residues: 318
  helix: -2.88 (0.53), residues: 55
  sheet: -4.36 (0.62), residues: 30
  loop : -3.27 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D   6 
 TYR   0.014   0.002   TYR E  48 
 HIS   0.008   0.002   HIS F  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00530 /  0.26 ( 5421)
  covalent geometry    : angle       1.31719 /  0.55 ( 7912)
  hydrogen bonds       : bond        0.08307 /  5.36 (  122)
  hydrogen bonds       : angle       5.43995 /  3.65 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 LYS cc_start: 0.7766 (mttt) cc_final: 0.7254 (mttt)
REVERT: B    7 ARG cc_start: 0.6892 (ptp90) cc_final: 0.6490 (ttm170)
REVERT: B   13 MET cc_start: 0.3713 (ttt) cc_final: 0.2254 (tmm)
REVERT: B   31 ARG cc_start: 0.7683 (ttt180) cc_final: 0.7068 (mtp180)
REVERT: B   49 GLN cc_start: 0.7653 (tp40) cc_final: 0.7147 (tp40)
REVERT: C   35 ASN cc_start: 0.7926 (t0) cc_final: 0.7589 (m-40)
  outliers start: 14
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0944
  time to fit residues: 11.7376
Evaluate side-chains
  98 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   21 THR
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   43 HIS
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain D residue   14 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  29 GLN
** E  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.187902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.151545 restraints weight = 13270.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.155508 restraints weight = 8027.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.158128 restraints weight = 5739.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.159973 restraints weight = 4536.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.161252 restraints weight = 3829.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6332
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5421  Z= 0.168
  Angle     :  1.023  12.640   7912  Z= 0.426
  Chirality :  0.078   0.487   1020
  Planarity :  0.005   0.040    561
  Dihedral  : 20.819 167.616   1777
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 24.09 %
    Favored  : 68.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.90 (0.42), residues: 318
  helix: -1.95 (0.57), residues: 55
  sheet: -2.96 (1.43), residues: 10
  loop : -3.01 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  44 
 TYR   0.009   0.001   TYR E  48 
 HIS   0.021   0.003   HIS B  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.17 ( 5421)
  covalent geometry    : angle       1.02278 /  0.43 ( 7912)
  hydrogen bonds       : bond        0.06381 /  4.02 (  122)
  hydrogen bonds       : angle       4.59995 /  3.04 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8736 (mt0) cc_final: 0.8464 (mt0)
REVERT: E   55 LYS cc_start: 0.7706 (mttt) cc_final: 0.7153 (mttt)
REVERT: B    1 MET cc_start: 0.7270 (ptm) cc_final: 0.6843 (ptm)
REVERT: B    7 ARG cc_start: 0.6891 (ptp90) cc_final: 0.6311 (ttt90)
REVERT: B   13 MET cc_start: 0.3528 (ttt) cc_final: 0.2045 (tmm)
REVERT: B   31 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7266 (mtp180)
REVERT: B   49 GLN cc_start: 0.7694 (tp40) cc_final: 0.7301 (tp40)
REVERT: C    2 LEU cc_start: 0.8775 (tt) cc_final: 0.8416 (tt)
REVERT: C   35 ASN cc_start: 0.7799 (t0) cc_final: 0.7341 (m-40)
  outliers start: 21
  outliers final: 12
  residues processed: 108
  average time/residue: 0.0865
  time to fit residues: 11.3626
Evaluate side-chains
  99 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   43 HIS
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain D residue   14 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  52 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.184842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.151787 restraints weight = 13675.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.156966 restraints weight = 10085.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.158279 restraints weight = 6157.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.158398 restraints weight = 5284.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.158912 restraints weight = 5322.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6420
moved from start:          0.4848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5421  Z= 0.207
  Angle     :  1.078  15.269   7912  Z= 0.448
  Chirality :  0.081   0.721   1020
  Planarity :  0.005   0.032    561
  Dihedral  : 20.866 164.782   1775
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.07 %
    Favored  : 78.93 %
  Rotamer:
    Outliers :  8.03 %
    Allowed  : 25.55 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.94 (0.44), residues: 318
  helix: -1.89 (0.57), residues: 55
  sheet: -3.69 (0.83), residues: 30
  loop : -2.87 (0.40), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D   6 
 TYR   0.015   0.002   TYR E  48 
 HIS   0.005   0.002   HIS E  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.21 ( 5421)
  covalent geometry    : angle       1.07802 /  0.45 ( 7912)
  hydrogen bonds       : bond        0.07432 /  4.80 (  122)
  hydrogen bonds       : angle       4.77266 /  3.19 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8605 (mt0) cc_final: 0.8382 (mt0)
REVERT: F   31 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7522 (mtt180)
REVERT: E   55 LYS cc_start: 0.7642 (mttt) cc_final: 0.7122 (mttt)
REVERT: B    1 MET cc_start: 0.7417 (ptm) cc_final: 0.6640 (ptm)
REVERT: B    7 ARG cc_start: 0.6914 (ptp90) cc_final: 0.6316 (ttm170)
REVERT: B   13 MET cc_start: 0.3833 (ttt) cc_final: 0.2358 (tmm)
REVERT: B   31 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7370 (mtp180)
REVERT: B   49 GLN cc_start: 0.7774 (tp40) cc_final: 0.7500 (tp40)
REVERT: C    2 LEU cc_start: 0.8800 (tt) cc_final: 0.8591 (tt)
REVERT: C   35 ASN cc_start: 0.7758 (t0) cc_final: 0.7229 (m-40)
  outliers start: 22
  outliers final: 19
  residues processed: 108
  average time/residue: 0.0957
  time to fit residues: 12.5199
Evaluate side-chains
  106 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 28 optimal weight:    9.9990
   chunk 21 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 HIS ** 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 = 0.4530 r_free = 0.4530 target = 0.187509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.151168 restraints weight = 13663.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.155227 restraints weight = 8205.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.157952 restraints weight = 5803.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.159827 restraints weight = 4545.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.161138 restraints weight = 3826.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.4208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.5209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5421  Z= 0.148
  Angle     :  0.957  14.267   7912  Z= 0.398
  Chirality :  0.073   0.690   1020
  Planarity :  0.004   0.038    561
  Dihedral  : 20.501 166.008   1775
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.98 %
    Favored  : 83.02 %
  Rotamer:
    Outliers :  8.39 %
    Allowed  : 27.01 %
    Favored  : 64.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.53 (0.45), residues: 318
  helix: -1.76 (0.58), residues: 55
  sheet: -2.83 (1.63), residues: 10
  loop : -2.71 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G   6 
 TYR   0.010   0.002   TYR E  48 
 HIS   0.010   0.002   HIS C  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 ( 5421)
  covalent geometry    : angle       0.95741 /  0.40 ( 7912)
  hydrogen bonds       : bond        0.06249 /  3.99 (  122)
  hydrogen bonds       : angle       4.38042 /  2.90 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8714 (mt0) cc_final: 0.8468 (mt0)
REVERT: E   55 LYS cc_start: 0.7478 (mttt) cc_final: 0.6963 (mttt)
REVERT: B    7 ARG cc_start: 0.6913 (ptp90) cc_final: 0.6279 (ttm170)
REVERT: B   13 MET cc_start: 0.3684 (ttt) cc_final: 0.2274 (tmm)
REVERT: B   31 ARG cc_start: 0.7618 (ttt180) cc_final: 0.7382 (mmm-85)
REVERT: B   46 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7054 (pt0)
REVERT: B   49 GLN cc_start: 0.7768 (tp40) cc_final: 0.7546 (tp40)
REVERT: C    1 MET cc_start: 0.7668 (pmm) cc_final: 0.7366 (pmm)
REVERT: C    2 LEU cc_start: 0.8826 (tt) cc_final: 0.8566 (tt)
  outliers start: 23
  outliers final: 17
  residues processed: 102
  average time/residue: 0.0854
  time to fit residues: 10.6944
Evaluate side-chains
  98 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue    3 ILE
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   14 VAL
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.189438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.153303 restraints weight = 13683.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.157388 restraints weight = 8122.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.160167 restraints weight = 5726.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.162103 restraints weight = 4476.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.163461 restraints weight = 3740.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6279
moved from start:          0.5544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5421  Z= 0.135
  Angle     :  0.930  14.780   7912  Z= 0.385
  Chirality :  0.071   0.738   1020
  Planarity :  0.004   0.032    561
  Dihedral  : 20.356 166.099   1775
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 28.47 %
    Favored  : 64.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.34 (0.45), residues: 318
  helix: -1.58 (0.59), residues: 55
  sheet: -2.74 (1.68), residues: 10
  loop : -2.59 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  31 
 TYR   0.009   0.001   TYR E  48 
 HIS   0.004   0.001   HIS E  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.14 ( 5421)
  covalent geometry    : angle       0.93001 /  0.39 ( 7912)
  hydrogen bonds       : bond        0.06256 /  4.06 (  122)
  hydrogen bonds       : angle       4.07795 /  2.71 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8742 (mt0) cc_final: 0.8486 (mt0)
REVERT: E   55 LYS cc_start: 0.7401 (mttt) cc_final: 0.6893 (mttt)
REVERT: G   31 ARG cc_start: 0.7299 (mtp180) cc_final: 0.6977 (mtp180)
REVERT: G   45 GLU cc_start: 0.8141 (tp30) cc_final: 0.7245 (tm-30)
REVERT: B    2 LEU cc_start: 0.8215 (tp) cc_final: 0.7895 (tt)
REVERT: B    7 ARG cc_start: 0.6887 (ptp90) cc_final: 0.6310 (ttm-80)
REVERT: B   13 MET cc_start: 0.3636 (ttt) cc_final: 0.2286 (tmm)
REVERT: B   31 ARG cc_start: 0.7592 (ttt180) cc_final: 0.7356 (mmm-85)
REVERT: B   46 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.7008 (pt0)
REVERT: B   49 GLN cc_start: 0.7791 (tp40) cc_final: 0.7526 (tp40)
REVERT: C    1 MET cc_start: 0.7722 (pmm) cc_final: 0.7470 (pmm)
REVERT: C    2 LEU cc_start: 0.8841 (tt) cc_final: 0.8554 (tt)
REVERT: C   31 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6860 (mmt90)
REVERT: C   35 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7078 (m-40)
  outliers start: 19
  outliers final: 15
  residues processed: 101
  average time/residue: 0.0860
  time to fit residues: 10.6320
Evaluate side-chains
  100 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue    3 ILE
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   35 ASN
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0570
   chunk 25 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:    0.2980
   chunk 26 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 3 optimal weight:    0.0170
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.8740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  35 ASN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.188271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.154343 restraints weight = 13911.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.159188 restraints weight = 9913.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.161324 restraints weight = 6212.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.161394 restraints weight = 5416.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.161811 restraints weight = 5141.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6346
moved from start:          0.5630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5421  Z= 0.169
  Angle     :  0.972  15.871   7912  Z= 0.402
  Chirality :  0.074   0.842   1020
  Planarity :  0.004   0.030    561
  Dihedral  : 20.440 166.242   1775
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.50 %
    Favored  : 80.50 %
  Rotamer:
    Outliers :  8.76 %
    Allowed  : 27.74 %
    Favored  : 63.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.27 (0.45), residues: 318
  helix: -1.62 (0.60), residues: 55
  sheet: -2.54 (1.19), residues: 20
  loop : -2.48 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  44 
 TYR   0.013   0.001   TYR E  48 
 HIS   0.006   0.001   HIS C  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.17 ( 5421)
  covalent geometry    : angle       0.97219 /  0.40 ( 7912)
  hydrogen bonds       : bond        0.06812 /  4.46 (  122)
  hydrogen bonds       : angle       4.24584 /  2.85 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8625 (mt0) cc_final: 0.8420 (mt0)
REVERT: E   55 LYS cc_start: 0.7582 (mttt) cc_final: 0.7065 (mttt)
REVERT: G   31 ARG cc_start: 0.7592 (mtp180) cc_final: 0.7146 (mtp180)
REVERT: G   45 GLU cc_start: 0.8097 (tp30) cc_final: 0.7163 (tm-30)
REVERT: B    1 MET cc_start: 0.6956 (ptm) cc_final: 0.6710 (ttp)
REVERT: B    7 ARG cc_start: 0.7044 (ptp90) cc_final: 0.6444 (ttm-80)
REVERT: B   13 MET cc_start: 0.3918 (ttt) cc_final: 0.2637 (ttt)
REVERT: B   31 ARG cc_start: 0.7640 (ttt180) cc_final: 0.7428 (mtp180)
REVERT: B   44 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.5458 (ttp-110)
REVERT: B   49 GLN cc_start: 0.7854 (tp40) cc_final: 0.7537 (tp40)
REVERT: C    1 MET cc_start: 0.7867 (pmm) cc_final: 0.7584 (pmm)
REVERT: C    2 LEU cc_start: 0.8813 (tt) cc_final: 0.8479 (tt)
REVERT: D    1 MET cc_start: 0.4730 (tpt) cc_final: 0.4467 (tpt)
  outliers start: 24
  outliers final: 20
  residues processed: 103
  average time/residue: 0.0697
  time to fit residues: 8.7396
Evaluate side-chains
  106 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    2 LEU
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   22 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 17 optimal weight:    0.4980
   chunk 29 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 8 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.4782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 HIS ** 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 = 0.4555 r_free = 0.4555 target = 0.189048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.154900 restraints weight = 13876.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.159201 restraints weight = 9492.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.162116 restraints weight = 5960.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.161993 restraints weight = 5236.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.162807 restraints weight = 4774.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6340
moved from start:          0.5825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5421  Z= 0.151
  Angle     :  0.955  16.758   7912  Z= 0.394
  Chirality :  0.074   0.918   1020
  Planarity :  0.004   0.030    561
  Dihedral  : 20.357 165.647   1775
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.04 %
    Favored  : 83.96 %
  Rotamer:
    Outliers :  8.39 %
    Allowed  : 27.37 %
    Favored  : 64.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.23 (0.45), residues: 318
  helix: -1.71 (0.59), residues: 55
  sheet: -2.70 (1.62), residues: 10
  loop : -2.44 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  44 
 TYR   0.011   0.001   TYR E  48 
 HIS   0.004   0.001   HIS C  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.15 ( 5421)
  covalent geometry    : angle       0.95480 /  0.39 ( 7912)
  hydrogen bonds       : bond        0.06616 /  4.36 (  122)
  hydrogen bonds       : angle       4.23760 /  2.87 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8663 (mt0) cc_final: 0.8442 (mt0)
REVERT: E   55 LYS cc_start: 0.7450 (mttt) cc_final: 0.6964 (mttt)
REVERT: G   31 ARG cc_start: 0.7537 (mtp180) cc_final: 0.7101 (mtp180)
REVERT: G   45 GLU cc_start: 0.8139 (tp30) cc_final: 0.7126 (tm-30)
REVERT: B    1 MET cc_start: 0.6983 (ptm) cc_final: 0.6691 (ttp)
REVERT: B    7 ARG cc_start: 0.7066 (ptp90) cc_final: 0.6427 (ttm-80)
REVERT: B   13 MET cc_start: 0.3998 (ttt) cc_final: 0.2767 (ttt)
REVERT: B   44 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5283 (ttp-110)
REVERT: B   49 GLN cc_start: 0.7809 (tp40) cc_final: 0.7590 (tp40)
REVERT: C    1 MET cc_start: 0.7981 (pmm) cc_final: 0.7708 (pmm)
REVERT: C    2 LEU cc_start: 0.8767 (tt) cc_final: 0.8413 (tt)
REVERT: D    1 MET cc_start: 0.4663 (tpt) cc_final: 0.4418 (tpt)
  outliers start: 23
  outliers final: 21
  residues processed: 104
  average time/residue: 0.0852
  time to fit residues: 10.7435
Evaluate side-chains
  107 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    2 LEU
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   22 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain G residue   46 GLU
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.4980
   chunk 16 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 HIS ** 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 = 0.4541 r_free = 0.4541 target = 0.187817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.153822 restraints weight = 13993.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.158157 restraints weight = 9630.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.161115 restraints weight = 5942.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.161136 restraints weight = 5100.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.161890 restraints weight = 4719.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.6106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5421  Z= 0.166
  Angle     :  0.990  17.397   7912  Z= 0.410
  Chirality :  0.077   1.022   1020
  Planarity :  0.004   0.024    561
  Dihedral  : 20.396 165.375   1775
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.24 %
    Favored  : 81.76 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 28.47 %
    Favored  : 63.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.30 (0.45), residues: 318
  helix: -1.72 (0.60), residues: 55
  sheet: -2.88 (1.61), residues: 10
  loop : -2.50 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G   6 
 TYR   0.016   0.002   TYR E  48 
 HIS   0.006   0.002   HIS C  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.17 ( 5421)
  covalent geometry    : angle       0.99011 /  0.41 ( 7912)
  hydrogen bonds       : bond        0.06705 /  4.42 (  122)
  hydrogen bonds       : angle       4.20155 /  2.84 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 LYS cc_start: 0.7613 (mttt) cc_final: 0.7113 (mttt)
REVERT: G   31 ARG cc_start: 0.7484 (mtp180) cc_final: 0.7017 (mtp180)
REVERT: B    1 MET cc_start: 0.7027 (ptm) cc_final: 0.6720 (ttp)
REVERT: B    7 ARG cc_start: 0.7075 (ptp90) cc_final: 0.6371 (ttm-80)
REVERT: B   13 MET cc_start: 0.4089 (ttt) cc_final: 0.2809 (ttt)
REVERT: B   44 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.5500 (ttp-170)
REVERT: C    1 MET cc_start: 0.8121 (pmm) cc_final: 0.7738 (pmm)
REVERT: C    2 LEU cc_start: 0.8770 (tt) cc_final: 0.8409 (tt)
REVERT: C   31 ARG cc_start: 0.7472 (mmt180) cc_final: 0.7132 (mmt-90)
  outliers start: 21
  outliers final: 16
  residues processed: 101
  average time/residue: 0.0727
  time to fit residues: 8.9676
Evaluate side-chains
  98 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    2 LEU
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   22 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   42 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  29 GLN
** F  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.178264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.142754 restraints weight = 13439.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.146050 restraints weight = 8611.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.148354 restraints weight = 6356.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.149996 restraints weight = 5117.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.151077 restraints weight = 4376.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6542
moved from start:          0.6451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5421  Z= 0.269
  Angle     :  1.206  17.999   7912  Z= 0.505
  Chirality :  0.091   1.221   1020
  Planarity :  0.006   0.037    561
  Dihedral  : 20.819 161.909   1775
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 21.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.58 %
    Favored  : 76.42 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 29.20 %
    Favored  : 64.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.77 (0.43), residues: 318
  helix: -2.34 (0.56), residues: 55
  sheet: -4.24 (1.45), residues: 10
  loop : -2.72 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  44 
 TYR   0.021   0.002   TYR E  48 
 HIS   0.005   0.002   HIS C  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00562 /  0.27 ( 5421)
  covalent geometry    : angle       1.20584 /  0.51 ( 7912)
  hydrogen bonds       : bond        0.08148 /  5.33 (  122)
  hydrogen bonds       : angle       5.02806 /  3.47 (  277)

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

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

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  636 Ramachandran restraints generated.
    318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8649 (mt0) cc_final: 0.8350 (mt0)
REVERT: E   55 LYS cc_start: 0.7664 (mttt) cc_final: 0.7177 (mttt)
REVERT: G   31 ARG cc_start: 0.7368 (mtp180) cc_final: 0.6923 (mtp180)
REVERT: B    7 ARG cc_start: 0.7083 (ptp90) cc_final: 0.6347 (ttm170)
REVERT: B   44 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.5887 (ttp-170)
REVERT: B   49 GLN cc_start: 0.7994 (tp40) cc_final: 0.7711 (tp40)
REVERT: C    1 MET cc_start: 0.8108 (pmm) cc_final: 0.7535 (pmm)
REVERT: C    2 LEU cc_start: 0.8723 (tt) cc_final: 0.8495 (tt)
REVERT: C   31 ARG cc_start: 0.7646 (mmt180) cc_final: 0.7328 (mmt-90)
REVERT: D    1 MET cc_start: 0.4643 (tpt) cc_final: 0.4386 (tpt)
  outliers start: 17
  outliers final: 16
  residues processed: 101
  average time/residue: 0.0772
  time to fit residues: 9.7488
Evaluate side-chains
  104 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   22 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   51 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.186413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.152020 restraints weight = 13721.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.155804 restraints weight = 8329.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.158431 restraints weight = 5931.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.160291 restraints weight = 4637.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.161585 restraints weight = 3870.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.4222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6334
moved from start:          0.6571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5421  Z= 0.149
  Angle     :  0.991  17.682   7912  Z= 0.411
  Chirality :  0.077   1.056   1020
  Planarity :  0.004   0.029    561
  Dihedral  : 20.338 166.926   1775
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 31.02 %
    Favored  : 63.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    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: -3.34 (0.44), residues: 318
  helix: -1.89 (0.59), residues: 55
  sheet: -2.95 (1.58), residues: 10
  loop : -2.49 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F   6 
 TYR   0.010   0.001   TYR E  48 
 HIS   0.004   0.001   HIS C  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.15 ( 5421)
  covalent geometry    : angle       0.99145 /  0.41 ( 7912)
  hydrogen bonds       : bond        0.06492 /  4.18 (  122)
  hydrogen bonds       : angle       4.27611 /  2.88 (  277)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1071.46 seconds
wall clock time: 19 minutes 7.19 seconds (1147.19 seconds total)