Starting phenix.real_space_refine
on Fri Aug 22 15:43:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr7_34048/08_2025/7yr7_34048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr7_34048/08_2025/7yr7_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2025/7yr7_34048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2025/7yr7_34048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2025/7yr7_34048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr7_34048/08_2025/7yr7_34048.cif"
  }
  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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: 1.43, per 1000 atoms: 0.28
  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: 0.24
  Conformation dependent library (CDL) restraints added in 83.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.49
  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: 0.47

  Time building geometry restraints manager: 0.39 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 1.50e-02 4.44e+03 1.34e+01
  bond pdb=" O3'   G A  50 "
       pdb=" P     G A  51 "
    ideal  model  delta    sigma   weight residual
    1.607  1.658 -0.051 1.50e-02 4.44e+03 1.17e+01
  bond pdb=" O3'   C A  62 "
       pdb=" P     A A  63 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.50e-02 4.44e+03 1.13e+01
  bond pdb=" O3'   C A   6 "
       pdb=" P     A A   7 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.50e-02 4.44e+03 9.87e+00
  bond pdb=" O3'   A A  36 "
       pdb=" P     A A  37 "
    ideal  model  delta    sigma   weight residual
    1.607  1.654 -0.047 1.50e-02 4.44e+03 9.72e+00
  ... (remaining 5416 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 7187
        2.09 -     4.18: 619
        4.18 -     6.27: 86
        6.27 -     8.36: 14
        8.36 -    10.45: 6
  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=" O3'   C A  76 "
        pdb=" C3'   C A  76 "
        pdb=" C2'   C A  76 "
      ideal   model   delta    sigma   weight residual
     109.50   99.30   10.20 1.50e+00 4.44e-01 4.63e+01
  angle pdb=" C4'   A A  78 "
        pdb=" C3'   A A  78 "
        pdb=" O3'   A A  78 "
      ideal   model   delta    sigma   weight residual
     113.00  122.87   -9.87 1.50e+00 4.44e-01 4.33e+01
  angle pdb=" C4'   A A  75 "
        pdb=" C3'   A A  75 "
        pdb=" O3'   A A  75 "
      ideal   model   delta    sigma   weight residual
     113.00  104.18    8.82 1.50e+00 4.44e-01 3.46e+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
  ... (remaining 7907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.32: 3003
       34.32 -    68.63: 384
       68.63 -   102.95: 55
      102.95 -   137.27: 1
      137.27 -   171.58: 2
  Dihedral angle restraints: 3445
    sinusoidal: 2517
      harmonic: 928
  Sorted by residual:
  dihedral pdb=" O4'   C A  62 "
           pdb=" C1'   C A  62 "
           pdb=" N1    C A  62 "
           pdb=" C2    C A  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   60.42  171.58     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" C   THR D  19 "
           pdb=" N   THR D  19 "
           pdb=" CA  THR D  19 "
           pdb=" CB  THR D  19 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.66   13.66     0      2.50e+00 1.60e-01 2.99e+01
  dihedral pdb=" CA  LEU G   2 "
           pdb=" C   LEU G   2 "
           pdb=" N   ILE G   3 "
           pdb=" CA  ILE G   3 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.76  -27.24     0      5.00e+00 4.00e-02 2.97e+01
  ... (remaining 3442 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 791
       0.100 -    0.200: 176
       0.200 -    0.300: 42
       0.300 -    0.400: 10
       0.400 -    0.500: 1
  Chirality restraints: 1020
  Sorted by residual:
  chirality pdb=" CA  THR D  19 "
            pdb=" N   THR D  19 "
            pdb=" C   THR D  19 "
            pdb=" CB  THR D  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.03    0.50 2.00e-01 2.50e+01 6.24e+00
  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       2.41   -2.76   -0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CB  ILE E   3 "
            pdb=" CA  ILE E   3 "
            pdb=" CG1 ILE E   3 "
            pdb=" CG2 ILE E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.86e+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:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.700
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5926
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= 0.463
  Angle     :  1.253  10.451   7912  Z= 0.759
  Chirality :  0.094   0.500   1020
  Planarity :  0.008   0.065    561
  Dihedral  : 25.593 171.582   2847
  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 aren 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
  covalent geometry    : bond        0.00769 ( 5421)
  covalent geometry    : angle       1.25284 ( 7912)
  hydrogen bonds       : bond        0.22230 (  122)
  hydrogen bonds       : angle       9.10100 (  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  : 0.086 
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: 0.0963
  time to fit residues: 13.0654
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  : 0.124 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   overall best weight:    2.6388

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

Flipped N/Q/H residues before XYZ refinement:
F  28 ASN
F  29 GLN
G  35 ASN
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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.183915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.147867 restraints weight = 13775.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.151402 restraints weight = 8634.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.153747 restraints weight = 6280.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.155393 restraints weight = 5027.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.156397 restraints weight = 4286.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5421  Z= 0.210
  Angle     :  0.774   8.733   7912  Z= 0.400
  Chirality :  0.046   0.226   1020
  Planarity :  0.006   0.061    561
  Dihedral  : 26.163 177.867   2227
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.55 %
    Favored  : 81.45 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.72 %
    Favored  : 71.17 %
  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 aren not related in a simple way.
  whole: -4.66 (0.40), residues: 318
  helix: -2.83 (0.53), residues: 55
  sheet: -4.48 (0.60), residues: 30
  loop : -3.22 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E   6 
 TYR   0.014   0.002   TYR E  48 
 HIS   0.008   0.002   HIS F  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 5421)
  covalent geometry    : angle       0.77360 ( 7912)
  hydrogen bonds       : bond        0.07982 (  122)
  hydrogen bonds       : angle       5.32830 (  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  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 LYS cc_start: 0.7789 (mttt) cc_final: 0.7273 (mttt)
REVERT: B    7 ARG cc_start: 0.6891 (ptp90) cc_final: 0.6497 (ttm170)
REVERT: B   13 MET cc_start: 0.3658 (ttt) cc_final: 0.2237 (tmm)
REVERT: B   31 ARG cc_start: 0.7648 (ttt180) cc_final: 0.6950 (mtp180)
REVERT: B   49 GLN cc_start: 0.7603 (tp40) cc_final: 0.7130 (tp40)
REVERT: C   35 ASN cc_start: 0.7905 (t0) cc_final: 0.7543 (m-40)
  outliers start: 14
  outliers final: 10
  residues processed: 106
  average time/residue: 0.0931
  time to fit residues: 11.9598
Evaluate side-chains
  96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.0030
   chunk 33 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 9 optimal weight:    8.9990
   chunk 23 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 21 optimal weight:    9.9990
   overall best weight:    1.2192

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

Flipped N/Q/H residues before XYZ refinement:
F  29 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.185856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.149673 restraints weight = 13553.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.153472 restraints weight = 8311.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.156089 restraints weight = 5960.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.157915 restraints weight = 4705.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.159213 restraints weight = 3955.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6253
moved from start:          0.3269

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= 0.131
  Angle     :  0.634   7.525   7912  Z= 0.325
  Chirality :  0.041   0.173   1020
  Planarity :  0.004   0.036    561
  Dihedral  : 25.685 178.325   2223
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.61 %
    Favored  : 82.39 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 25.91 %
    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 aren not related in a simple way.
  whole: -3.73 (0.43), residues: 318
  helix: -1.88 (0.58), residues: 55
  sheet: -3.30 (1.36), residues: 10
  loop : -2.85 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E   6 
 TYR   0.009   0.001   TYR E  48 
 HIS   0.005   0.002   HIS B  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 5421)
  covalent geometry    : angle       0.63392 ( 7912)
  hydrogen bonds       : bond        0.06215 (  122)
  hydrogen bonds       : angle       4.59204 (  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
  111 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.095 
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: 0.8738 (mt0) cc_final: 0.8509 (mt0)
REVERT: E   55 LYS cc_start: 0.7655 (mttt) cc_final: 0.7111 (mttt)
REVERT: B    7 ARG cc_start: 0.6892 (ptp90) cc_final: 0.6356 (ttt180)
REVERT: B   31 ARG cc_start: 0.7531 (ttt180) cc_final: 0.7263 (mtp180)
REVERT: B   49 GLN cc_start: 0.7671 (tp40) cc_final: 0.7283 (tp40)
REVERT: C    1 MET cc_start: 0.8310 (pmm) cc_final: 0.7414 (pmm)
REVERT: C   35 ASN cc_start: 0.7793 (t0) cc_final: 0.7442 (m-40)
  outliers start: 16
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0866
  time to fit residues: 10.7809
Evaluate side-chains
  99 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   54 GLU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   44 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 27 optimal weight:    9.9990
   chunk 33 optimal weight:    0.2980
   chunk 4 optimal weight:    5.9990
   chunk 26 optimal weight:    6.9990
   chunk 30 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   chunk 18 optimal weight:    5.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
** E  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  35 ASN
C  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.179409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.144629 restraints weight = 13901.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.148106 restraints weight = 8679.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.150468 restraints weight = 6287.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.152069 restraints weight = 5012.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.153274 restraints weight = 4270.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6427
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5421  Z= 0.220
  Angle     :  0.753  10.122   7912  Z= 0.385
  Chirality :  0.045   0.160   1020
  Planarity :  0.005   0.032    561
  Dihedral  : 26.175 171.277   2221
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.70 %
    Favored  : 78.30 %
  Rotamer:
    Outliers :  8.03 %
    Allowed  : 27.74 %
    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 aren not related in a simple way.
  whole: -3.72 (0.45), residues: 318
  helix: -2.10 (0.57), residues: 55
  sheet: -3.70 (1.10), residues: 20
  loop : -2.68 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D   6 
 TYR   0.017   0.002   TYR E  48 
 HIS   0.005   0.002   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 5421)
  covalent geometry    : angle       0.75264 ( 7912)
  hydrogen bonds       : bond        0.07814 (  122)
  hydrogen bonds       : angle       5.04945 (  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  : 0.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.7142 (ttm) cc_final: 0.6553 (ttm)
REVERT: E   55 LYS cc_start: 0.7656 (mttt) cc_final: 0.7127 (mttt)
REVERT: G   35 ASN cc_start: 0.4212 (OUTLIER) cc_final: 0.3587 (m110)
REVERT: B    7 ARG cc_start: 0.6960 (ptp90) cc_final: 0.6318 (ttt90)
REVERT: B   31 ARG cc_start: 0.7570 (ttt180) cc_final: 0.7337 (mtp180)
REVERT: B   49 GLN cc_start: 0.7772 (tp40) cc_final: 0.7508 (tp40)
REVERT: C   35 ASN cc_start: 0.7989 (t0) cc_final: 0.7680 (m-40)
  outliers start: 22
  outliers final: 16
  residues processed: 109
  average time/residue: 0.0825
  time to fit residues: 10.8891
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  : 0.077 
-------------------------------------------------------------------------------
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   42 VAL
Chi-restraints excluded: chain G residue   35 ASN
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   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain D residue   14 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:    3.9990
   chunk 28 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 32 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
G  35 ASN
C  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.184159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.148509 restraints weight = 13941.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.152375 restraints weight = 8354.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.155030 restraints weight = 5898.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.156876 restraints weight = 4618.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.158173 restraints weight = 3871.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6282
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5421  Z= 0.129
  Angle     :  0.643   8.332   7912  Z= 0.322
  Chirality :  0.040   0.171   1020
  Planarity :  0.004   0.043    561
  Dihedral  : 25.769 175.955   2221
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.98 %
    Favored  : 83.02 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 30.29 %
    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 aren not related in a simple way.
  whole: -3.37 (0.45), residues: 318
  helix: -1.69 (0.60), residues: 55
  sheet: -2.42 (1.62), residues: 10
  loop : -2.60 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E   6 
 TYR   0.009   0.001   TYR E  48 
 HIS   0.003   0.001   HIS E  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5421)
  covalent geometry    : angle       0.64309 ( 7912)
  hydrogen bonds       : bond        0.06120 (  122)
  hydrogen bonds       : angle       4.50608 (  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
  105 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8746 (mt0) cc_final: 0.8440 (mt0)
REVERT: E    1 MET cc_start: 0.6748 (ttm) cc_final: 0.5769 (ttm)
REVERT: E   55 LYS cc_start: 0.7378 (mttt) cc_final: 0.6883 (mttt)
REVERT: G   31 ARG cc_start: 0.7351 (mtp180) cc_final: 0.6885 (mtp180)
REVERT: G   35 ASN cc_start: 0.4459 (OUTLIER) cc_final: 0.3797 (m-40)
REVERT: G   46 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6741 (mp0)
REVERT: B    7 ARG cc_start: 0.6893 (ptp90) cc_final: 0.6317 (ttm-80)
REVERT: B   31 ARG cc_start: 0.7479 (ttt180) cc_final: 0.7173 (mtp180)
REVERT: B   49 GLN cc_start: 0.7709 (tp40) cc_final: 0.7459 (tp40)
REVERT: C    1 MET cc_start: 0.8408 (pmm) cc_final: 0.6989 (pmm)
REVERT: C   35 ASN cc_start: 0.7957 (t0) cc_final: 0.7641 (m-40)
  outliers start: 18
  outliers final: 12
  residues processed: 102
  average time/residue: 0.0963
  time to fit residues: 11.8223
Evaluate side-chains
  96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   35 ASN
Chi-restraints excluded: chain G residue   46 GLU
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   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain D residue   14 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:    7.9990
   chunk 12 optimal weight:    0.0870
   chunk 39 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
C  52 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.186144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.151446 restraints weight = 13981.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.155368 restraints weight = 8239.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.157952 restraints weight = 5775.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.159838 restraints weight = 4514.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.161167 restraints weight = 3771.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6211
moved from start:          0.4489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5421  Z= 0.113
  Angle     :  0.615   8.201   7912  Z= 0.304
  Chirality :  0.039   0.147   1020
  Planarity :  0.005   0.066    561
  Dihedral  : 25.512 176.079   2221
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.35 %
    Favored  : 83.65 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 29.93 %
    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 aren not related in a simple way.
  whole: -3.15 (0.47), residues: 318
  helix: -1.42 (0.61), residues: 55
  sheet: -2.76 (1.15), residues: 20
  loop : -2.39 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E   6 
 TYR   0.008   0.001   TYR E  48 
 HIS   0.002   0.001   HIS E  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 5421)
  covalent geometry    : angle       0.61481 ( 7912)
  hydrogen bonds       : bond        0.05759 (  122)
  hydrogen bonds       : angle       4.22369 (  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
  103 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8698 (mt0) cc_final: 0.8386 (mt0)
REVERT: E    1 MET cc_start: 0.5929 (ttm) cc_final: 0.5594 (ttm)
REVERT: E   55 LYS cc_start: 0.7286 (mttt) cc_final: 0.6801 (mttt)
REVERT: G   31 ARG cc_start: 0.7240 (mtp180) cc_final: 0.6851 (mtp180)
REVERT: G   45 GLU cc_start: 0.8019 (tp30) cc_final: 0.7472 (tm-30)
REVERT: B    1 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6999 (ttt)
REVERT: B    7 ARG cc_start: 0.6907 (ptp90) cc_final: 0.6379 (ttt180)
REVERT: B   44 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.5229 (ttp-110)
REVERT: B   49 GLN cc_start: 0.7723 (tp40) cc_final: 0.7447 (tp40)
REVERT: C    1 MET cc_start: 0.8338 (pmm) cc_final: 0.6891 (pmm)
REVERT: C   35 ASN cc_start: 0.7914 (t0) cc_final: 0.7616 (m-40)
  outliers start: 18
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0818
  time to fit residues: 9.8273
Evaluate side-chains
  95 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 G residue   42 VAL
Chi-restraints excluded: chain B residue    1 MET
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  52 GLN
** E  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  35 ASN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  28 ASN
C  52 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.172784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.139350 restraints weight = 14033.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.141841 restraints weight = 9113.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.143024 restraints weight = 6543.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.143939 restraints weight = 5872.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.144365 restraints weight = 5568.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6626
moved from start:          0.5324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.078   5421  Z= 0.368
  Angle     :  1.022  12.923   7912  Z= 0.512
  Chirality :  0.053   0.237   1020
  Planarity :  0.008   0.073    561
  Dihedral  : 26.493 163.696   2217
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 27.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.10 %
    Favored  : 73.90 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 30.66 %
    Favored  : 61.68 %
  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 aren not related in a simple way.
  whole: -3.83 (0.46), residues: 318
  helix: -2.00 (0.62), residues: 53
  sheet: -4.12 (1.07), residues: 20
  loop : -2.77 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G   6 
 TYR   0.025   0.002   TYR E  48 
 HIS   0.007   0.002   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00759 ( 5421)
  covalent geometry    : angle       1.02173 ( 7912)
  hydrogen bonds       : bond        0.09847 (  122)
  hydrogen bonds       : angle       5.84829 (  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
  112 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   31 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7550 (mtt180)
REVERT: E    1 MET cc_start: 0.6522 (ttm) cc_final: 0.6092 (ttm)
REVERT: E   55 LYS cc_start: 0.7719 (mttt) cc_final: 0.7237 (mttt)
REVERT: G   35 ASN cc_start: 0.4788 (OUTLIER) cc_final: 0.4325 (m110)
REVERT: B    7 ARG cc_start: 0.7031 (ptp90) cc_final: 0.6390 (ttm170)
REVERT: B   31 ARG cc_start: 0.7822 (ttt180) cc_final: 0.7620 (mtp180)
REVERT: B   44 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6227 (ttp-110)
REVERT: B   49 GLN cc_start: 0.7966 (tp40) cc_final: 0.7629 (tp40)
REVERT: C    1 MET cc_start: 0.8377 (pmm) cc_final: 0.7456 (pmm)
REVERT: C   35 ASN cc_start: 0.8087 (t0) cc_final: 0.7710 (m-40)
  outliers start: 21
  outliers final: 16
  residues processed: 106
  average time/residue: 0.0693
  time to fit residues: 9.2160
Evaluate side-chains
  104 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
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 E residue   20 VAL
Chi-restraints excluded: chain E residue   21 THR
Chi-restraints excluded: chain E residue   22 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain G residue   35 ASN
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain B residue   21 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue   25 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   17 ASP
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:    0.6980
   chunk 29 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0980
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.182036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.147204 restraints weight = 13883.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.151028 restraints weight = 8275.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.153633 restraints weight = 5849.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.155394 restraints weight = 4566.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.156755 restraints weight = 3837.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6368
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5421  Z= 0.137
  Angle     :  0.708   9.110   7912  Z= 0.354
  Chirality :  0.041   0.156   1020
  Planarity :  0.006   0.086    561
  Dihedral  : 25.866 176.862   2217
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.35 %
    Favored  : 83.65 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 36.86 %
    Favored  : 58.39 %
  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 aren not related in a simple way.
  whole: -3.27 (0.46), residues: 318
  helix: -1.77 (0.61), residues: 55
  sheet:  None (None), residues: 0
  loop : -2.52 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G   6 
 TYR   0.010   0.001   TYR E  48 
 HIS   0.003   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5421)
  covalent geometry    : angle       0.70765 ( 7912)
  hydrogen bonds       : bond        0.06613 (  122)
  hydrogen bonds       : angle       4.90692 (  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
  96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.5967 (ttm) cc_final: 0.5282 (ttm)
REVERT: E   55 LYS cc_start: 0.7361 (mttt) cc_final: 0.6879 (mttt)
REVERT: G   35 ASN cc_start: 0.4518 (OUTLIER) cc_final: 0.4171 (m-40)
REVERT: B    1 MET cc_start: 0.7536 (ttt) cc_final: 0.6755 (ttt)
REVERT: B    7 ARG cc_start: 0.6950 (ptp90) cc_final: 0.6371 (ttm170)
REVERT: B   31 ARG cc_start: 0.7539 (ttt180) cc_final: 0.7334 (mtp180)
REVERT: B   44 ARG cc_start: 0.6400 (OUTLIER) cc_final: 0.5503 (ttp-110)
REVERT: C    1 MET cc_start: 0.8073 (pmm) cc_final: 0.7174 (pmm)
  outliers start: 13
  outliers final: 9
  residues processed: 96
  average time/residue: 0.0757
  time to fit residues: 8.9350
Evaluate side-chains
  94 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   21 THR
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   35 ASN
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain D residue   14 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 24 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0470
   chunk 19 optimal weight:    0.0570
   chunk 12 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.1980
   overall best weight:    1.8600

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.180046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.144497 restraints weight = 13600.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.148266 restraints weight = 8226.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.150792 restraints weight = 5882.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.152608 restraints weight = 4655.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.153901 restraints weight = 3909.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6411
moved from start:          0.5294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5421  Z= 0.160
  Angle     :  0.706   9.360   7912  Z= 0.353
  Chirality :  0.041   0.208   1020
  Planarity :  0.006   0.109    561
  Dihedral  : 25.893 171.702   2217
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.07 %
    Favored  : 78.93 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 35.77 %
    Favored  : 59.49 %
  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 aren not related in a simple way.
  whole: -3.37 (0.46), residues: 318
  helix: -1.68 (0.63), residues: 55
  sheet: -4.86 (0.97), residues: 10
  loop : -2.48 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E   6 
 TYR   0.015   0.001   TYR E  48 
 HIS   0.004   0.001   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5421)
  covalent geometry    : angle       0.70644 ( 7912)
  hydrogen bonds       : bond        0.06831 (  122)
  hydrogen bonds       : angle       4.98721 (  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
  97 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   31 ARG cc_start: 0.7635 (mtt180) cc_final: 0.6900 (mtp85)
REVERT: E    1 MET cc_start: 0.6122 (ttm) cc_final: 0.5646 (ttm)
REVERT: E   55 LYS cc_start: 0.7577 (mttt) cc_final: 0.7053 (mttt)
REVERT: G   35 ASN cc_start: 0.4020 (OUTLIER) cc_final: 0.3746 (m-40)
REVERT: B    1 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6925 (ttt)
REVERT: B    7 ARG cc_start: 0.6943 (ptp90) cc_final: 0.6290 (ttm-80)
REVERT: B   44 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.5689 (ttp-110)
REVERT: B   49 GLN cc_start: 0.7781 (tp40) cc_final: 0.7479 (tp40)
  outliers start: 13
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0700
  time to fit residues: 8.1708
Evaluate side-chains
  96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   21 THR
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   35 ASN
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   44 ARG
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain D residue   14 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 27 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  35 ASN
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.176464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.142115 restraints weight = 14043.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.145513 restraints weight = 8417.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.147971 restraints weight = 5987.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.149664 restraints weight = 4692.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.150746 restraints weight = 3942.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
moved from start:          0.5649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   5421  Z= 0.237
  Angle     :  0.833  11.348   7912  Z= 0.417
  Chirality :  0.046   0.226   1020
  Planarity :  0.007   0.116    561
  Dihedral  : 26.185 168.453   2217
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 20.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.33 %
    Favored  : 77.67 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 33.58 %
    Favored  : 60.22 %
  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 aren not related in a simple way.
  whole: -3.66 (0.45), residues: 318
  helix: -1.99 (0.62), residues: 55
  sheet: -5.17 (0.82), residues: 10
  loop : -2.66 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E   6 
 TYR   0.021   0.002   TYR E  48 
 HIS   0.006   0.002   HIS D  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 5421)
  covalent geometry    : angle       0.83339 ( 7912)
  hydrogen bonds       : bond        0.07870 (  122)
  hydrogen bonds       : angle       5.56804 (  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
  104 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   31 ARG cc_start: 0.7680 (mtt180) cc_final: 0.6894 (mtp85)
REVERT: E    1 MET cc_start: 0.5938 (ttm) cc_final: 0.5570 (ttm)
REVERT: E   55 LYS cc_start: 0.7614 (mttt) cc_final: 0.7116 (mttt)
REVERT: G   31 ARG cc_start: 0.7266 (mtp180) cc_final: 0.6703 (mtp180)
REVERT: G   35 ASN cc_start: 0.4247 (OUTLIER) cc_final: 0.3878 (m-40)
REVERT: B    1 MET cc_start: 0.7466 (ttt) cc_final: 0.7077 (tpt)
REVERT: B    7 ARG cc_start: 0.7015 (ptp90) cc_final: 0.6281 (ttm-80)
REVERT: B   44 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.5931 (ttp-110)
REVERT: B   49 GLN cc_start: 0.7930 (tp40) cc_final: 0.7642 (tp40)
  outliers start: 17
  outliers final: 14
  residues processed: 102
  average time/residue: 0.0747
  time to fit residues: 9.4325
Evaluate side-chains
  100 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   21 THR
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain F residue   43 HIS
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   35 ASN
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    3 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 3 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 24 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 GLN ** 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 = 0.4423 r_free = 0.4423 target = 0.176866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.141444 restraints weight = 13948.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.145108 restraints weight = 8315.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.147650 restraints weight = 5885.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.149396 restraints weight = 4616.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.150645 restraints weight = 3878.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6436
moved from start:          0.5731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5421  Z= 0.194
  Angle     :  0.764  10.365   7912  Z= 0.381
  Chirality :  0.044   0.212   1020
  Planarity :  0.006   0.079    561
  Dihedral  : 26.067 171.526   2217
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 16.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.07 %
    Favored  : 78.93 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 35.04 %
    Favored  : 59.49 %
  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 aren not related in a simple way.
  whole: -3.62 (0.44), residues: 318
  helix: -1.84 (0.63), residues: 55
  sheet: -4.93 (0.95), residues: 10
  loop : -2.67 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E   6 
 TYR   0.017   0.002   TYR E  48 
 HIS   0.005   0.001   HIS E  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 5421)
  covalent geometry    : angle       0.76403 ( 7912)
  hydrogen bonds       : bond        0.07258 (  122)
  hydrogen bonds       : angle       5.29514 (  277)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 994.00 seconds
wall clock time: 17 minutes 43.86 seconds (1063.86 seconds total)