Starting phenix.real_space_refine
on Thu Mar  6 06:41:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr7_34048/03_2025/7yr7_34048.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr7_34048/03_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_34048/03_2025/7yr7_34048.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr7_34048/03_2025/7yr7_34048.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr7_34048/03_2025/7yr7_34048.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr7_34048/03_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-5624/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: 4.78, per 1000 atoms: 0.94
  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: 1.20
  Conformation dependent library (CDL) restraints added in 343.4 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: 2.66
  Creating SS restraints...
    Processing helix  chain 'F' and resid 46 through 55
    Processing helix  chain 'E' and resid 46 through 55
    Processing helix  chain 'G' and resid 46 through 55
    Processing helix  chain 'B' and resid 46 through 53
    Processing helix  chain 'C' and resid 46 through 55
    Processing helix  chain 'D' and resid 45 through 55
    Processing sheet with id=AA1, first strand: chain 'F' and resid 20 through 26
      removed outlier: 5.091A  pdb=" N   ARG F  31 " --> pdb=" O   LEU F  23 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   VAL F  25 " --> pdb=" O   GLN F  29 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   GLN F  29 " --> pdb=" O   VAL F  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 6
      removed outlier: 4.336A  pdb=" N   LEU E   4 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ILE G  32 " --> pdb=" O   LEU E   4 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 20 through 26
      removed outlier: 4.545A  pdb=" N   ARG E  31 " --> pdb=" O   LEU E  23 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   VAL E  25 " --> pdb=" O   GLN E  29 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   GLN E  29 " --> pdb=" O   VAL E  25 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ARG G   6 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   LEU G   4 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 26
      removed outlier: 5.224A  pdb=" N   ARG B  31 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   VAL B  25 " --> pdb=" O   GLN B  29 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   GLN B  29 " --> pdb=" O   VAL B  25 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE B  32 " --> pdb=" O   ILE D   3 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 26
      removed outlier: 3.602A  pdb=" N   LYS C  26 " --> pdb=" O   GLN C  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 21 through 26
      removed outlier: 5.564A  pdb=" N   VAL D  22 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLY D  33 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   GLY D  24 " --> pdb=" O   ARG D  31 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLN D  29 " --> pdb=" O   LYS D  26 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    153 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      68 hydrogen bonds
      124 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      49 stacking parallelities
  Total time for adding SS restraints: 1.27

  Time building geometry restraints manager: 1.45 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:             5.710
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     19.930
  Find NCS groups from input model:        0.170
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.100
-------------------------------------------------------------------------------
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  : 0.349 
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: 0.2685
  time to fit residues: 36.0688
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  : 0.408 
-------------------------------------------------------------------------------
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 = 50)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.151406 restraints weight = 13357.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.155216 restraints weight = 8046.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.157797 restraints weight = 5747.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6281
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  : 0.422 
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: 0.7654 (mtt180) cc_final: 0.7393 (mtt180)
REVERT: E   55 LYS cc_start: 0.7752 (mttt) cc_final: 0.7262 (mttt)
REVERT: B    7 ARG cc_start: 0.6916 (ptp90) cc_final: 0.6432 (ttm170)
REVERT: B   13 MET cc_start: 0.3543 (ttt) cc_final: 0.1964 (tmm)
REVERT: B   31 ARG cc_start: 0.7661 (ttt180) cc_final: 0.6974 (mtp180)
REVERT: C   35 ASN cc_start: 0.7823 (t0) cc_final: 0.7437 (m-40)
  outliers start: 14
  outliers final: 9
  residues processed: 103
  average time/residue: 0.2272
  time to fit residues: 28.1169
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  : 0.396 
-------------------------------------------------------------------------------
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:    8.9990
   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:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   overall best weight:    1.7596

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.184578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.147921 restraints weight = 13277.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.151705 restraints weight = 8069.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.154237 restraints weight = 5796.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6352
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5421  Z= 0.192
  Angle     :  0.651   7.585   7912  Z= 0.337
  Chirality :  0.041   0.192   1020
  Planarity :  0.005   0.036    561
  Dihedral  : 25.694 172.235   2222
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.98 %
    Favored  : 83.02 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 25.18 %
    Favored  : 69.34 %
  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: -3.81 (0.43), residues: 318
  helix: -1.85 (0.59), residues: 55
  sheet: -4.05 (0.84), residues: 20
  loop : -2.79 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.014   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
  113 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.362 
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: 0.7628 (mttt) cc_final: 0.7115 (mttt)
REVERT: G   31 ARG cc_start: 0.7235 (mtp180) cc_final: 0.6813 (mtp180)
REVERT: B    7 ARG cc_start: 0.6897 (ptp90) cc_final: 0.6405 (ttm170)
REVERT: B   13 MET cc_start: 0.3576 (ttt) cc_final: 0.2092 (tmm)
REVERT: B   31 ARG cc_start: 0.7575 (ttt180) cc_final: 0.7093 (mtp180)
REVERT: B   49 GLN cc_start: 0.7725 (tp40) cc_final: 0.7421 (tp40)
REVERT: C   35 ASN cc_start: 0.7847 (t0) cc_final: 0.7465 (m-40)
  outliers start: 15
  outliers final: 9
  residues processed: 107
  average time/residue: 0.2224
  time to fit residues: 28.5849
Evaluate side-chains
  96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 27 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 30 optimal weight:    9.9990
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
F  29 GLN
** E  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  35 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.185891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.149863 restraints weight = 13727.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.153660 restraints weight = 8237.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.156089 restraints weight = 5881.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6322
moved from start:          0.3639

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= 0.163
  Angle     :  0.608   8.221   7912  Z= 0.310
  Chirality :  0.040   0.159   1020
  Planarity :  0.004   0.033    561
  Dihedral  : 25.574 175.519   2221
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.72 %
    Favored  : 84.28 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 28.83 %
    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: -3.27 (0.46), residues: 318
  helix: -1.33 (0.62), residues: 55
  sheet: -2.84 (1.04), residues: 20
  loop : -2.53 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  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
  103 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.368 
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: 0.7527 (mttt) cc_final: 0.7004 (mttt)
REVERT: G   31 ARG cc_start: 0.7312 (mtp180) cc_final: 0.6879 (mtp180)
REVERT: B    7 ARG cc_start: 0.6903 (ptp90) cc_final: 0.6324 (ttm-80)
REVERT: B   13 MET cc_start: 0.3518 (ttt) cc_final: 0.2123 (tmm)
REVERT: B   31 ARG cc_start: 0.7599 (ttt180) cc_final: 0.7368 (mtp180)
REVERT: B   49 GLN cc_start: 0.7808 (tp40) cc_final: 0.7463 (tp40)
REVERT: C    1 MET cc_start: 0.6730 (ptm) cc_final: 0.5896 (ptp)
REVERT: C   35 ASN cc_start: 0.7963 (t0) cc_final: 0.7581 (m-40)
  outliers start: 15
  outliers final: 9
  residues processed: 100
  average time/residue: 0.3200
  time to fit residues: 37.7689
Evaluate side-chains
  92 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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   47 ILE
Chi-restraints excluded: chain C residue   18 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:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 1 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0170
   chunk 4 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0970
   chunk 39 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.3220

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.185349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.150049 restraints weight = 13712.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.153826 restraints weight = 8260.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.156413 restraints weight = 5884.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5421  Z= 0.170
  Angle     :  0.602   7.894   7912  Z= 0.306
  Chirality :  0.039   0.174   1020
  Planarity :  0.004   0.029    561
  Dihedral  : 25.531 173.977   2217
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.98 %
    Favored  : 83.02 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 29.93 %
    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: -3.03 (0.47), residues: 318
  helix: -1.18 (0.63), residues: 55
  sheet: -2.55 (1.54), residues: 10
  loop : -2.40 (0.41), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.003   HIS C  43 
 TYR   0.012   0.001   TYR E  48 
 ARG   0.001   0.000   ARG C  31 

*********************** 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
  98 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   55 LYS cc_start: 0.7403 (mttt) cc_final: 0.6925 (mttt)
REVERT: G   31 ARG cc_start: 0.7328 (mtp180) cc_final: 0.6918 (mtp180)
REVERT: B    7 ARG cc_start: 0.6934 (ptp90) cc_final: 0.6371 (ttm-80)
REVERT: B   13 MET cc_start: 0.3608 (ttt) cc_final: 0.2188 (tmm)
REVERT: B   31 ARG cc_start: 0.7569 (ttt180) cc_final: 0.7318 (mtp180)
REVERT: B   49 GLN cc_start: 0.7807 (tp40) cc_final: 0.7606 (tp40)
REVERT: C    1 MET cc_start: 0.6552 (ptm) cc_final: 0.5984 (ptp)
REVERT: C   35 ASN cc_start: 0.7925 (t0) cc_final: 0.7587 (m-40)
  outliers start: 12
  outliers final: 10
  residues processed: 95
  average time/residue: 0.2929
  time to fit residues: 33.7148
Evaluate side-chains
  93 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   19 THR
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   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   54 GLU
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:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0770
   chunk 31 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   overall best weight:    1.7742

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.183207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.147167 restraints weight = 13720.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.151053 restraints weight = 8304.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.153569 restraints weight = 5896.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
moved from start:          0.4227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5421  Z= 0.204
  Angle     :  0.654   8.736   7912  Z= 0.328
  Chirality :  0.040   0.155   1020
  Planarity :  0.004   0.028    561
  Dihedral  : 25.609 171.936   2217
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.92 %
    Favored  : 82.08 %
  Rotamer:
    Outliers :  7.30 %
    Allowed  : 26.28 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.12 (0.47), residues: 318
  helix: -1.50 (0.62), residues: 55
  sheet: -2.34 (1.15), residues: 20
  loop : -2.39 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS C  43 
 TYR   0.012   0.001   TYR E  48 
 ARG   0.010   0.000   ARG E   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
  102 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.6360 (ttm) cc_final: 0.5697 (ttm)
REVERT: E   55 LYS cc_start: 0.7449 (mttt) cc_final: 0.6971 (mttt)
REVERT: G   31 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6929 (mtp180)
REVERT: B    1 MET cc_start: 0.7658 (ttt) cc_final: 0.7198 (ttt)
REVERT: B    7 ARG cc_start: 0.7002 (ptp90) cc_final: 0.6363 (ttm170)
REVERT: B   13 MET cc_start: 0.3692 (ttt) cc_final: 0.2467 (ttt)
REVERT: B   49 GLN cc_start: 0.7891 (tp40) cc_final: 0.7614 (tp40)
REVERT: C    1 MET cc_start: 0.6580 (ptm) cc_final: 0.6030 (ptp)
REVERT: C   35 ASN cc_start: 0.8013 (t0) cc_final: 0.7632 (m-40)
  outliers start: 20
  outliers final: 13
  residues processed: 97
  average time/residue: 0.2243
  time to fit residues: 26.9892
Evaluate side-chains
  93 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  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   40 VAL
Chi-restraints excluded: chain G 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   47 ILE
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   30 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:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    2.1788

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.181260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.146088 restraints weight = 13634.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.149692 restraints weight = 8456.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.152153 restraints weight = 6124.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.4615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5421  Z= 0.220
  Angle     :  0.695   9.458   7912  Z= 0.345
  Chirality :  0.041   0.193   1020
  Planarity :  0.004   0.026    561
  Dihedral  : 25.759 170.154   2217
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.81 %
    Favored  : 80.19 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 28.47 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.31 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.44 (0.46), residues: 318
  helix: -1.69 (0.61), residues: 55
  sheet: -3.22 (0.75), residues: 40
  loop : -2.41 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C  43 
 TYR   0.014   0.002   TYR E  48 
 ARG   0.009   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
  103 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.6430 (ttm) cc_final: 0.5782 (ttm)
REVERT: E    6 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.8034 (tpp-160)
REVERT: E   55 LYS cc_start: 0.7470 (mttt) cc_final: 0.6970 (mttt)
REVERT: G   31 ARG cc_start: 0.7343 (mtp180) cc_final: 0.6855 (mtp180)
REVERT: B    1 MET cc_start: 0.7621 (ttt) cc_final: 0.7376 (ttt)
REVERT: B    7 ARG cc_start: 0.6989 (ptp90) cc_final: 0.6482 (ttm170)
REVERT: B   13 MET cc_start: 0.4037 (ttt) cc_final: 0.2790 (ttt)
REVERT: B   49 GLN cc_start: 0.7912 (tp40) cc_final: 0.7592 (tp40)
REVERT: C    1 MET cc_start: 0.6289 (ptm) cc_final: 0.5964 (ptp)
REVERT: C   35 ASN cc_start: 0.7991 (t0) cc_final: 0.7645 (m-40)
  outliers start: 14
  outliers final: 11
  residues processed: 99
  average time/residue: 0.2262
  time to fit residues: 27.6913
Evaluate side-chains
  97 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
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   40 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 C residue   30 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:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0050
   overall best weight:    0.7798

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.186613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.152190 restraints weight = 13555.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.156197 restraints weight = 8009.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.158973 restraints weight = 5592.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
moved from start:          0.4873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   5421  Z= 0.157
  Angle     :  0.618   8.408   7912  Z= 0.305
  Chirality :  0.038   0.167   1020
  Planarity :  0.004   0.032    561
  Dihedral  : 25.405 176.400   2217
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.84 %
    Favored  : 86.16 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 31.02 %
    Favored  : 65.33 %
  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: -3.00 (0.46), residues: 318
  helix: -1.49 (0.60), residues: 55
  sheet: -2.42 (0.94), residues: 30
  loop : -2.22 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C  43 
 TYR   0.007   0.001   TYR E  48 
 ARG   0.005   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
  91 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.6252 (ttm) cc_final: 0.5166 (ttm)
REVERT: E   55 LYS cc_start: 0.7289 (mttt) cc_final: 0.6790 (mttt)
REVERT: G   31 ARG cc_start: 0.7372 (mtp180) cc_final: 0.6937 (mtp180)
REVERT: B    1 MET cc_start: 0.7948 (ttt) cc_final: 0.7491 (ttt)
REVERT: B    7 ARG cc_start: 0.6927 (ptp90) cc_final: 0.6320 (ttm170)
REVERT: B   10 GLU cc_start: 0.5468 (mm-30) cc_final: 0.5240 (mm-30)
REVERT: B   13 MET cc_start: 0.3874 (ttt) cc_final: 0.2647 (ttt)
REVERT: C    1 MET cc_start: 0.5865 (ptm) cc_final: 0.5447 (ptp)
REVERT: C   35 ASN cc_start: 0.7952 (t0) cc_final: 0.7670 (m-40)
REVERT: D   50 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7577 (mtt180)
  outliers start: 10
  outliers final: 8
  residues processed: 90
  average time/residue: 0.1921
  time to fit residues: 21.2424
Evaluate side-chains
  86 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
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   40 VAL
Chi-restraints excluded: chain B residue   25 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:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.0182

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.185914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.151310 restraints weight = 13465.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.155220 restraints weight = 8086.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.157923 restraints weight = 5693.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6317
moved from start:          0.4978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5421  Z= 0.157
  Angle     :  0.618   8.428   7912  Z= 0.304
  Chirality :  0.038   0.153   1020
  Planarity :  0.004   0.041    561
  Dihedral  : 25.376 173.686   2217
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.04 %
    Favored  : 83.96 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 32.12 %
    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: -2.84 (0.46), residues: 318
  helix: -1.49 (0.59), residues: 55
  sheet: -1.70 (1.22), residues: 20
  loop : -2.17 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C  43 
 TYR   0.010   0.001   TYR E  48 
 ARG   0.009   0.000   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
  96 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E    1 MET cc_start: 0.6264 (ttm) cc_final: 0.5498 (ttm)
REVERT: E    6 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.7971 (mpt180)
REVERT: E   55 LYS cc_start: 0.7374 (mttt) cc_final: 0.6868 (mttt)
REVERT: G   31 ARG cc_start: 0.7371 (mtp180) cc_final: 0.6938 (mtp180)
REVERT: B    1 MET cc_start: 0.7902 (ttt) cc_final: 0.7482 (ttt)
REVERT: B    7 ARG cc_start: 0.6980 (ptp90) cc_final: 0.6379 (ttm170)
REVERT: B   10 GLU cc_start: 0.5462 (mm-30) cc_final: 0.5182 (mm-30)
REVERT: B   13 MET cc_start: 0.3987 (ttt) cc_final: 0.2722 (ttt)
REVERT: C    1 MET cc_start: 0.5853 (ptm) cc_final: 0.5609 (ptp)
REVERT: C   13 MET cc_start: 0.1273 (mpp) cc_final: -0.0065 (mtm)
REVERT: C   35 ASN cc_start: 0.7951 (t0) cc_final: 0.7686 (m-40)
  outliers start: 14
  outliers final: 13
  residues processed: 94
  average time/residue: 0.2008
  time to fit residues: 23.3807
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  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    2 LEU
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   40 VAL
Chi-restraints excluded: chain G 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   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:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 7 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    7.9990
   chunk 15 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   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**
** B  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  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 = 0.4418 r_free = 0.4418 target = 0.176446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.141943 restraints weight = 14094.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.145460 restraints weight = 8548.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.147875 restraints weight = 6083.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6551
moved from start:          0.5452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   5421  Z= 0.362
  Angle     :  0.879  11.931   7912  Z= 0.437
  Chirality :  0.048   0.202   1020
  Planarity :  0.006   0.036    561
  Dihedral  : 26.124 165.167   2217
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 22.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 22.96 %
    Favored  : 77.04 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 33.21 %
    Favored  : 62.41 %
  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: -3.53 (0.44), residues: 318
  helix: -2.31 (0.55), residues: 55
  sheet: -3.29 (1.04), residues: 20
  loop : -2.47 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C  43 
 TYR   0.021   0.002   TYR E  48 
 ARG   0.008   0.001   ARG E   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
  100 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   31 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7293 (mtt180)
REVERT: E    1 MET cc_start: 0.6116 (ttm) cc_final: 0.5415 (ttm)
REVERT: E   55 LYS cc_start: 0.7703 (mttt) cc_final: 0.7219 (mttt)
REVERT: G   31 ARG cc_start: 0.7332 (mtp180) cc_final: 0.6922 (mtp180)
REVERT: B    7 ARG cc_start: 0.7148 (ptp90) cc_final: 0.6432 (ttm170)
REVERT: B   49 GLN cc_start: 0.7969 (tp40) cc_final: 0.7714 (tp40)
REVERT: C   35 ASN cc_start: 0.8104 (t0) cc_final: 0.7819 (m-40)
  outliers start: 12
  outliers final: 10
  residues processed: 98
  average time/residue: 0.1924
  time to fit residues: 23.3976
Evaluate side-chains
  95 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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    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:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 11 optimal weight:    0.6980
   chunk 14 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  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 = 0.4445 r_free = 0.4445 target = 0.179340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.143664 restraints weight = 13879.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.147684 restraints weight = 8030.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.150427 restraints weight = 5569.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6435
moved from start:          0.5492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5421  Z= 0.221
  Angle     :  0.714   9.468   7912  Z= 0.353
  Chirality :  0.042   0.178   1020
  Planarity :  0.005   0.031    561
  Dihedral  : 25.836 171.057   2217
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.92 %
    Favored  : 82.08 %
  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: -3.06 (0.45), residues: 318
  helix: -2.11 (0.58), residues: 55
  sheet: -1.43 (1.77), residues: 10
  loop : -2.24 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS E  43 
 TYR   0.013   0.002   TYR E  48 
 ARG   0.006   0.000   ARG E   6 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2203.46 seconds
wall clock time: 40 minutes 5.32 seconds (2405.32 seconds total)