Starting phenix.real_space_refine
on Tue Feb 11 10:11:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr7_34048/02_2025/7yr7_34048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr7_34048/02_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_34048/02_2025/7yr7_34048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr7_34048/02_2025/7yr7_34048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr7_34048/02_2025/7yr7_34048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr7_34048/02_2025/7yr7_34048.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.054
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     118      5.49       5
     S      12      5.16       5
     C    2731      2.51       5
     N     955      2.21       5
     O    1286      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.60, per 1000 atoms: 0.71
  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: 1.43
  Conformation dependent library (CDL) restraints added in 374.2 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 6 sheets defined
      17.9% alpha, 16.1% beta
      26 base pairs and 49 stacking pairs defined.
    Time for finding SS restraints: 1.77
  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: 1.24

  Time building geometry restraints manager: 1.29 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.840
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.870
-------------------------------------------------------------------------------
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= 0.474
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.006   0.002   HIS E  43 
 TYR   0.023   0.003   TYR E  48 
 ARG   0.006   0.001   ARG E   6 

*********************** 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  : 0.352 
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: 0.2449
  time to fit residues: 32.9697
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  : 0.330 
-------------------------------------------------------------------------------
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 34 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0970
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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
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 = 0.4536 r_free = 0.4536 target = 0.188289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.151405 restraints weight = 13357.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.155243 restraints weight = 8044.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.157796 restraints weight = 5736.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6277
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5421  Z= 0.180
  Angle     :  0.688   7.438   7912  Z= 0.357
  Chirality :  0.043   0.215   1020
  Planarity :  0.005   0.044    561
  Dihedral  : 25.766 168.863   2227
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.98 %
    Favored  : 83.02 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 21.53 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.52 (0.39), residues: 318
  helix: -2.94 (0.52), residues: 55
  sheet: -3.90 (0.78), residues: 20
  loop : -3.22 (0.35), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS F  43 
 TYR   0.010   0.002   TYR E  48 
 ARG   0.004   0.001   ARG E  44 

*********************** 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
  108 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   31 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7384 (mtt180)
REVERT: E   55 LYS cc_start: 0.7744 (mttt) cc_final: 0.7255 (mttt)
REVERT: B    7 ARG cc_start: 0.6918 (ptp90) cc_final: 0.6427 (ttm170)
REVERT: B   13 MET cc_start: 0.3539 (ttt) cc_final: 0.1959 (tmm)
REVERT: B   31 ARG cc_start: 0.7658 (ttt180) cc_final: 0.6965 (mtp180)
REVERT: C   35 ASN cc_start: 0.7835 (t0) cc_final: 0.7438 (m-40)
  outliers start: 14
  outliers final: 9
  residues processed: 103
  average time/residue: 0.2276
  time to fit residues: 28.0988
Evaluate side-chains
  95 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
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   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   54 GLU
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 22 optimal weight:    9.9990
   chunk 4 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0040
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   overall best weight:    1.5996

-------------------------------------------------------------------------------
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 = 0.4504 r_free = 0.4504 target = 0.185481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.149100 restraints weight = 13344.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.152888 restraints weight = 8128.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.155423 restraints weight = 5831.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6333
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5421  Z= 0.181
  Angle     :  0.637   7.678   7912  Z= 0.330
  Chirality :  0.041   0.194   1020
  Planarity :  0.004   0.036    561
  Dihedral  : 25.648 171.671   2222
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.04 %
    Favored  : 83.96 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 24.45 %
    Favored  : 69.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.43), residues: 318
  helix: -1.79 (0.59), residues: 55
  sheet: -4.04 (0.84), residues: 20
  loop : -2.78 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.003   HIS B  43 
 TYR   0.013   0.001   TYR E  48 
 ARG   0.010   0.001   ARG E   6 

*********************** 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
  114 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.301 
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: 0.7617 (mttt) cc_final: 0.7096 (mttt)
REVERT: G   31 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6803 (mtp180)
REVERT: B    7 ARG cc_start: 0.6888 (ptp90) cc_final: 0.6403 (ttm170)
REVERT: B   13 MET cc_start: 0.3568 (ttt) cc_final: 0.2078 (tmm)
REVERT: B   31 ARG cc_start: 0.7574 (ttt180) cc_final: 0.7076 (mtp180)
REVERT: B   49 GLN cc_start: 0.7723 (tp40) cc_final: 0.7439 (tp40)
REVERT: C   35 ASN cc_start: 0.7822 (t0) cc_final: 0.7451 (m-40)
  outliers start: 16
  outliers final: 10
  residues processed: 108
  average time/residue: 0.2276
  time to fit residues: 29.3386
Evaluate side-chains
  98 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   19 THR
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 C residue   18 VAL
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 32 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 30 optimal weight:    9.9990
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
F  29 GLN
B  35 ASN
B  43 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.186057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.151239 restraints weight = 13956.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.154825 restraints weight = 8491.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.157307 restraints weight = 6090.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5421  Z= 0.182
  Angle     :  0.627   8.351   7912  Z= 0.321
  Chirality :  0.040   0.162   1020
  Planarity :  0.004   0.033    561
  Dihedral  : 25.630 174.394   2221
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.98 %
    Favored  : 83.02 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 29.56 %
    Favored  : 64.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.45), residues: 318
  helix: -1.40 (0.61), residues: 55
  sheet: -2.75 (1.08), residues: 20
  loop : -2.56 (0.40), residues: 243

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

*********************** 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
  107 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    4 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7731 (pp)
REVERT: E   55 LYS cc_start: 0.7475 (mttt) cc_final: 0.6960 (mttt)
REVERT: G   31 ARG cc_start: 0.7320 (mtp180) cc_final: 0.6884 (mtp180)
REVERT: B    7 ARG cc_start: 0.6878 (ptp90) cc_final: 0.6336 (ttm-80)
REVERT: B   13 MET cc_start: 0.3607 (ttt) cc_final: 0.2176 (tmm)
REVERT: B   31 ARG cc_start: 0.7603 (ttt180) cc_final: 0.7290 (mtp180)
REVERT: B   49 GLN cc_start: 0.7830 (tp40) cc_final: 0.7527 (tp40)
REVERT: C    1 MET cc_start: 0.6648 (ptm) cc_final: 0.5978 (ptp)
REVERT: C   35 ASN cc_start: 0.7982 (t0) cc_final: 0.7595 (m-40)
  outliers start: 16
  outliers final: 10
  residues processed: 103
  average time/residue: 0.2376
  time to fit residues: 29.3643
Evaluate side-chains
  96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue    4 LEU
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain G residue   46 GLU
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   42 VAL
Chi-restraints excluded: chain C residue   54 GLU
Chi-restraints excluded: chain D residue   14 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    2.9786

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.178673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.144191 restraints weight = 13760.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.147252 restraints weight = 9299.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.148553 restraints weight = 6640.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6546
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   5421  Z= 0.282
  Angle     :  0.761   9.744   7912  Z= 0.387
  Chirality :  0.044   0.175   1020
  Planarity :  0.005   0.048    561
  Dihedral  : 26.044 167.086   2217
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 18.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.70 %
    Favored  : 78.30 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 28.47 %
    Favored  : 63.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.46), residues: 318
  helix: -1.87 (0.62), residues: 55
  sheet: -3.43 (1.12), residues: 20
  loop : -2.63 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.003   HIS C  43 
 TYR   0.020   0.002   TYR E  48 
 ARG   0.004   0.001   ARG D   6 

*********************** 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
  114 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.7551 (ttm) cc_final: 0.7023 (ttm)
REVERT: E   55 LYS cc_start: 0.7702 (mttt) cc_final: 0.7196 (mttt)
REVERT: G   31 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7089 (mtp180)
REVERT: G   35 ASN cc_start: 0.4173 (OUTLIER) cc_final: 0.3681 (m110)
REVERT: B    7 ARG cc_start: 0.6939 (ptp90) cc_final: 0.6380 (ttm170)
REVERT: B   31 ARG cc_start: 0.7641 (ttt180) cc_final: 0.7431 (mtp180)
REVERT: B   49 GLN cc_start: 0.7958 (tp40) cc_final: 0.7694 (tp40)
REVERT: C   35 ASN cc_start: 0.8001 (t0) cc_final: 0.7695 (m-40)
  outliers start: 21
  outliers final: 16
  residues processed: 108
  average time/residue: 0.2351
  time to fit residues: 30.9864
Evaluate side-chains
  108 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain E residue    4 LEU
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   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   25 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain D residue   14 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 38 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    1.2382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.184206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.148638 restraints weight = 13845.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.152757 restraints weight = 8083.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.155444 restraints weight = 5612.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5421  Z= 0.172
  Angle     :  0.660   8.895   7912  Z= 0.327
  Chirality :  0.040   0.158   1020
  Planarity :  0.004   0.039    561
  Dihedral  : 25.697 173.835   2217
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.04 %
    Favored  : 83.96 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 30.29 %
    Favored  : 64.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.23 (0.45), residues: 318
  helix: -1.63 (0.60), residues: 55
  sheet: -2.18 (1.19), residues: 20
  loop : -2.48 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C  43 
 TYR   0.010   0.001   TYR E  48 
 ARG   0.006   0.001   ARG G   6 

*********************** 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
  98 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8574 (mt0) cc_final: 0.8308 (mt0)
REVERT: E    1 MET cc_start: 0.7236 (ttm) cc_final: 0.6360 (ttm)
REVERT: E   55 LYS cc_start: 0.7333 (mttt) cc_final: 0.6861 (mttt)
REVERT: G   31 ARG cc_start: 0.7332 (mtp180) cc_final: 0.6920 (mtp180)
REVERT: G   35 ASN cc_start: 0.4414 (OUTLIER) cc_final: 0.3926 (m-40)
REVERT: G   46 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6846 (mp0)
REVERT: B    7 ARG cc_start: 0.7014 (ptp90) cc_final: 0.6286 (ttm170)
REVERT: B   13 MET cc_start: 0.3718 (ttt) cc_final: 0.2384 (ttt)
REVERT: B   31 ARG cc_start: 0.7504 (ttt180) cc_final: 0.7185 (mtp180)
REVERT: C    1 MET cc_start: 0.6385 (ptp) cc_final: 0.5933 (ptp)
REVERT: C   35 ASN cc_start: 0.7966 (t0) cc_final: 0.7695 (m-40)
  outliers start: 13
  outliers final: 9
  residues processed: 95
  average time/residue: 0.2347
  time to fit residues: 26.9269
Evaluate side-chains
  93 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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    3 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:    6.9990
   chunk 1 optimal weight:    0.0570
   chunk 8 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7298

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

Flipped N/Q/H residues before XYZ refinement:
E  28 ASN
** C  43 HIS ** 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 = 0.4531 r_free = 0.4531 target = 0.187696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.153194 restraints weight = 13827.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.157278 restraints weight = 8046.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.159998 restraints weight = 5597.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.4194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6229
moved from start:          0.4772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   5421  Z= 0.142
  Angle     :  0.601   8.345   7912  Z= 0.299
  Chirality :  0.038   0.167   1020
  Planarity :  0.004   0.027    561
  Dihedral  : 25.415 174.448   2217
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.72 %
    Favored  : 84.28 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 29.56 %
    Favored  : 65.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.46), residues: 318
  helix: -1.26 (0.63), residues: 55
  sheet: -2.29 (0.94), residues: 30
  loop : -2.26 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C  43 
 TYR   0.008   0.001   TYR E  48 
 ARG   0.005   0.001   ARG G   6 

*********************** 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
  94 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8601 (mt0) cc_final: 0.8252 (mt0)
REVERT: E    1 MET cc_start: 0.6340 (ttm) cc_final: 0.5077 (ttm)
REVERT: E   55 LYS cc_start: 0.7127 (mttt) cc_final: 0.6652 (mttt)
REVERT: G   31 ARG cc_start: 0.7238 (mtp180) cc_final: 0.6818 (mtp180)
REVERT: G   46 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6756 (mp0)
REVERT: B    1 MET cc_start: 0.6963 (ptm) cc_final: 0.6732 (ttt)
REVERT: B    7 ARG cc_start: 0.6936 (ptp90) cc_final: 0.6302 (ttm-80)
REVERT: B   13 MET cc_start: 0.3803 (ttt) cc_final: 0.2543 (ttt)
REVERT: C   35 ASN cc_start: 0.7958 (t0) cc_final: 0.7673 (m-40)
  outliers start: 13
  outliers final: 8
  residues processed: 93
  average time/residue: 0.2051
  time to fit residues: 23.2868
Evaluate side-chains
  88 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain G residue   46 GLU
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    3 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain D residue   14 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.3988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.185134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.150206 restraints weight = 13700.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.154110 restraints weight = 8217.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.156724 restraints weight = 5796.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6358
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5421  Z= 0.175
  Angle     :  0.637   9.078   7912  Z= 0.313
  Chirality :  0.039   0.164   1020
  Planarity :  0.004   0.028    561
  Dihedral  : 25.505 171.690   2217
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.35 %
    Favored  : 83.65 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 31.75 %
    Favored  : 62.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.46), residues: 318
  helix: -1.33 (0.62), residues: 55
  sheet: -1.72 (1.21), residues: 20
  loop : -2.19 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS E  43 
 TYR   0.012   0.001   TYR E  48 
 ARG   0.006   0.001   ARG C  44 

*********************** 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
  98 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8496 (mt0) cc_final: 0.8259 (mt0)
REVERT: E    1 MET cc_start: 0.6516 (ttm) cc_final: 0.5945 (ttm)
REVERT: E   55 LYS cc_start: 0.7430 (mttt) cc_final: 0.6939 (mttt)
REVERT: G   31 ARG cc_start: 0.7360 (mtp180) cc_final: 0.6927 (mtp180)
REVERT: G   46 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6781 (mp0)
REVERT: B    1 MET cc_start: 0.7100 (ptm) cc_final: 0.6686 (ptm)
REVERT: B    7 ARG cc_start: 0.6956 (ptp90) cc_final: 0.6388 (ttm170)
REVERT: B   10 GLU cc_start: 0.5626 (mm-30) cc_final: 0.5237 (mm-30)
REVERT: B   13 MET cc_start: 0.4068 (ttt) cc_final: 0.2841 (ttt)
  outliers start: 15
  outliers final: 12
  residues processed: 97
  average time/residue: 0.2026
  time to fit residues: 24.2335
Evaluate side-chains
  95 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   19 THR
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 GLU
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    3 ILE
Chi-restraints excluded: chain C residue   18 VAL
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 35 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** E  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  49 GLN ** 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 = 0.4432 r_free = 0.4432 target = 0.175983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.140566 restraints weight = 13667.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.144091 restraints weight = 8433.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.146454 restraints weight = 6052.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6589
moved from start:          0.5534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   5421  Z= 0.356
  Angle     :  0.886  11.199   7912  Z= 0.438
  Chirality :  0.048   0.219   1020
  Planarity :  0.008   0.121    561
  Dihedral  : 26.166 163.007   2217
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 23.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.96 %
    Favored  : 77.04 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 34.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.44), residues: 318
  helix: -2.05 (0.58), residues: 55
  sheet: -3.14 (1.09), residues: 20
  loop : -2.59 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS D  43 
 TYR   0.022   0.002   TYR E  48 
 ARG   0.012   0.001   ARG G   6 

*********************** 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
  103 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.5990 (ttm) cc_final: 0.5421 (ttm)
REVERT: E   55 LYS cc_start: 0.7701 (mttt) cc_final: 0.7211 (mttt)
REVERT: G   31 ARG cc_start: 0.7438 (mtp180) cc_final: 0.6926 (mtp180)
REVERT: G   46 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6917 (mp0)
REVERT: B    7 ARG cc_start: 0.7124 (ptp90) cc_final: 0.6499 (ttm170)
REVERT: B   31 ARG cc_start: 0.7727 (ttt180) cc_final: 0.7491 (mtp180)
REVERT: B   49 GLN cc_start: 0.7965 (tp40) cc_final: 0.7664 (tp40)
  outliers start: 14
  outliers final: 13
  residues processed: 100
  average time/residue: 0.2114
  time to fit residues: 25.7364
Evaluate side-chains
  100 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
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   42 VAL
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 GLU
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    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 4 optimal weight:    0.9980
   chunk 30 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
E  28 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 = 0.4463 r_free = 0.4463 target = 0.179698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.144805 restraints weight = 13706.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.148553 restraints weight = 8256.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.151132 restraints weight = 5835.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6463
moved from start:          0.5554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5421  Z= 0.236
  Angle     :  0.752  10.864   7912  Z= 0.368
  Chirality :  0.043   0.175   1020
  Planarity :  0.006   0.102    561
  Dihedral  : 25.902 169.721   2217
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 35.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.45), residues: 318
  helix: -1.95 (0.58), residues: 55
  sheet: -1.26 (1.89), residues: 10
  loop : -2.30 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS E  43 
 TYR   0.013   0.001   TYR E  48 
 ARG   0.011   0.001   ARG G   6 

********************** 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
  93 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   29 GLN cc_start: 0.8523 (mt0) cc_final: 0.8240 (mt0)
REVERT: E    1 MET cc_start: 0.5846 (ttm) cc_final: 0.5078 (ttm)
REVERT: E    6 ARG cc_start: 0.6731 (mmt-90) cc_final: 0.6417 (mmt-90)
REVERT: E   55 LYS cc_start: 0.7522 (mttt) cc_final: 0.7062 (mttt)
REVERT: G   31 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6840 (mtp180)
REVERT: G   46 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6919 (mp0)
REVERT: B    7 ARG cc_start: 0.7071 (ptp90) cc_final: 0.6391 (ttm170)
REVERT: B   13 MET cc_start: 0.4148 (ttt) cc_final: 0.2783 (ttt)
REVERT: C   31 ARG cc_start: 0.7293 (mmt-90) cc_final: 0.7089 (mmt-90)
  outliers start: 11
  outliers final: 9
  residues processed: 91
  average time/residue: 0.2314
  time to fit residues: 25.2510
Evaluate side-chains
  91 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   23 LEU
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain G residue   46 GLU
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    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 20 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0070
   chunk 14 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.9602

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

Flipped N/Q/H residues before XYZ refinement:
D  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.184404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.150458 restraints weight = 14087.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.154356 restraints weight = 8406.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.157023 restraints weight = 5844.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.4180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          0.5726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5421  Z= 0.170
  Angle     :  0.665  10.205   7912  Z= 0.322
  Chirality :  0.039   0.164   1020
  Planarity :  0.004   0.024    561
  Dihedral  : 25.569 174.340   2217
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 35.77 %
    Favored  : 60.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.46), residues: 318
  helix: -1.81 (0.58), residues: 55
  sheet: -1.32 (1.29), residues: 20
  loop : -2.31 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C  43 
 TYR   0.008   0.001   TYR E  48 
 ARG   0.003   0.000   ARG C  44 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1964.85 seconds
wall clock time: 35 minutes 43.62 seconds (2143.62 seconds total)