Starting phenix.real_space_refine
on Tue Jul 29 16:21:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wz9_21971/07_2025/6wz9_21971.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wz9_21971/07_2025/6wz9_21971.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wz9_21971/07_2025/6wz9_21971.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wz9_21971/07_2025/6wz9_21971.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wz9_21971/07_2025/6wz9_21971.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wz9_21971/07_2025/6wz9_21971.cif"
  }
  resolution = 2.8
  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=   0.000 sd=   0.002
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     296      5.49       5
     S      12      5.16       5
     C    6569      2.51       5
     N    2233      2.21       5
     O    2816      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11926
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 784
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 786
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "D"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 784
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 818
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 3050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 3050
          Classifications: {'DNA': 148}
          Link IDs: {'rna3p': 147}
    Chain: "J"
      Number of atoms: 3018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 3018
          Classifications: {'DNA': 148}
          Link IDs: {'rna3p': 147}
  Time building chain proxies: 8.91, per 1000 atoms: 0.75
  Number of scatterers: 11926
  At special positions: 0
  Unit cell: (124.02, 95.4, 116.6, 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     296     15.00
     O    2816      8.00
     N    2233      7.00
     C    6569      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: 2.67
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1384

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      74.8% alpha, 3.3% beta
      148 base pairs and 269 stacking pairs defined.
    Time for finding SS restraints: 6.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.189A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.738A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 45 through 72
      removed outlier: 4.265A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.920A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.580A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.764A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.331A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 120
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.875A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.540A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.297A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.757A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.195A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    411 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      380 hydrogen bonds
      760 hydrogen bond angles
      0 basepair planarities
      148 basepair parallelities
      269 stacking parallelities
  Total time for adding SS restraints: 4.77

  Time building geometry restraints manager: 3.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2091
        1.33 -     1.45: 4337
        1.45 -     1.57: 5701
        1.57 -     1.69: 590
        1.69 -     1.81: 22
  Bond restraints: 12741
  Sorted by residual:
  bond pdb=" C   LEU D  98 "
       pdb=" N   LEU D  99 "
    ideal  model  delta    sigma   weight residual
    1.339  1.263  0.076 5.57e-02 3.22e+02 1.87e+00
  bond pdb=" C3'  DG I -37 "
       pdb=" O3'  DG I -37 "
    ideal  model  delta    sigma   weight residual
    1.422  1.383  0.039 3.00e-02 1.11e+03 1.66e+00
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.58e+00
  bond pdb=" C3'  DG I  -6 "
       pdb=" O3'  DG I  -6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.386  0.036 3.00e-02 1.11e+03 1.46e+00
  bond pdb=" CG  LEU H  42 "
       pdb=" CD2 LEU H  42 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.46e+00
  ... (remaining 12736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 18186
        2.23 -     4.47: 283
        4.47 -     6.70: 11
        6.70 -     8.93: 2
        8.93 -    11.17: 2
  Bond angle restraints: 18484
  Sorted by residual:
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  121.17   -8.47 3.00e+00 1.11e-01 7.98e+00
  angle pdb=" N   PRO D 100 "
        pdb=" CA  PRO D 100 "
        pdb=" C   PRO D 100 "
      ideal   model   delta    sigma   weight residual
     110.21  114.73   -4.52 1.64e+00 3.72e-01 7.60e+00
  angle pdb=" N   LYS A  64 "
        pdb=" CA  LYS A  64 "
        pdb=" C   LYS A  64 "
      ideal   model   delta    sigma   weight residual
     111.07  113.91   -2.84 1.07e+00 8.73e-01 7.03e+00
  angle pdb=" CA  LEU G  85 "
        pdb=" CB  LEU G  85 "
        pdb=" CG  LEU G  85 "
      ideal   model   delta    sigma   weight residual
     116.30  125.38   -9.08 3.50e+00 8.16e-02 6.73e+00
  angle pdb=" CA  ILE H  51 "
        pdb=" CB  ILE H  51 "
        pdb=" CG1 ILE H  51 "
      ideal   model   delta    sigma   weight residual
     110.40  114.80   -4.40 1.70e+00 3.46e-01 6.70e+00
  ... (remaining 18479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.12: 5262
       33.12 -    66.24: 1589
       66.24 -    99.36: 31
       99.36 -   132.48: 0
      132.48 -   165.60: 2
  Dihedral angle restraints: 6884
    sinusoidal: 4740
      harmonic: 2144
  Sorted by residual:
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.40  165.60     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   80.53  139.47     1      3.50e+01 8.16e-04 1.38e+01
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.47   17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 6881 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1287
       0.034 -    0.069: 594
       0.069 -    0.103: 178
       0.103 -    0.138: 43
       0.138 -    0.172: 8
  Chirality restraints: 2110
  Sorted by residual:
  chirality pdb=" CA  LYS B  79 "
            pdb=" N   LYS B  79 "
            pdb=" C   LYS B  79 "
            pdb=" CB  LYS B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.42e-01
  chirality pdb=" CA  ILE D  86 "
            pdb=" N   ILE D  86 "
            pdb=" C   ILE D  86 "
            pdb=" CB  ILE D  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.85e-01
  chirality pdb=" CA  ILE H  86 "
            pdb=" N   ILE H  86 "
            pdb=" C   ILE H  86 "
            pdb=" CB  ILE H  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 2107 not shown)

  Planarity restraints: 1312
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  42 "   -0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO A  43 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  47 "   -0.029 2.00e-02 2.50e+03   1.22e-02 4.09e+00
        pdb=" N9   DA I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DA I  47 "    0.008 2.00e-02 2.50e+03
        pdb=" N7   DA I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  47 "   -0.011 2.00e-02 2.50e+03
        pdb=" N1   DA I  47 "    0.000 2.00e-02 2.50e+03
        pdb=" C2   DA I  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DA I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I  47 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E  42 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.69e+00
        pdb=" N   PRO E  43 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO E  43 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  43 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1309 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 71
        2.59 -     3.17: 9062
        3.17 -     3.75: 22466
        3.75 -     4.32: 31511
        4.32 -     4.90: 43549
  Nonbonded interactions: 106659
  Sorted by model distance:
  nonbonded pdb=" OG1 THR H  29 "
            pdb=" OP1  DT J  30 "
     model   vdw
     2.015 3.040
  nonbonded pdb=" NZ  LYS F  59 "
            pdb=" OE2 GLU F  63 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" NH2 ARG C  20 "
            pdb=" OP1  DG I -42 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OE1 GLU A 105 "
            pdb=" NH2 ARG E 129 "
     model   vdw
     2.298 3.120
  ... (remaining 106654 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 16 through 116)
  selection = (chain 'G' and resid 16 through 116)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.010
  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:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     35.450
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  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:13.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   56.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
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      :  0.006   0.076  12741  Z= 0.270
  Angle     :  0.743  11.165  18484  Z= 0.457
  Chirality :  0.043   0.172   2110
  Planarity :  0.005   0.052   1312
  Dihedral  : 28.895 165.603   5500
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  4.55 %
    Favored  : 93.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  0.07 (0.28), residues: 722
  helix:  0.56 (0.20), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.33 (0.38), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.003   HIS E 113 
 PHE   0.020   0.003   PHE H  67 
 TYR   0.019   0.002   TYR H  37 
 ARG   0.008   0.001   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08981 (  791)
  hydrogen bonds       : angle       3.57803 ( 1969)
  covalent geometry    : bond        0.00606 (12741)
  covalent geometry    : angle       0.74300 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.5531 (mmm) cc_final: 0.5156 (mmm)
REVERT: B   91 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7648 (ttmt)
REVERT: C  108 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7236 (mt)
REVERT: D   31 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6879 (tppt)
REVERT: F   68 ASP cc_start: 0.7377 (m-30) cc_final: 0.6858 (m-30)
REVERT: H   68 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7425 (mt-10)
  outliers start: 14
  outliers final: 3
  residues processed: 161
  average time/residue: 1.7597
  time to fit residues: 299.8910
Evaluate side-chains
  105 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 57 optimal weight:    0.2980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
C  31 HIS
D  81 ASN
E  39 HIS
E 108 ASN
E 125 GLN
F  93 GLN
G  31 HIS
G  89 ASN
G 110 ASN
H  44 GLN
H  64 ASN
H  81 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.129417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.113813 restraints weight = 23740.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 0.98
r_work: 0.3842 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3750 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12741  Z= 0.174
  Angle     :  0.588   8.338  18484  Z= 0.352
  Chirality :  0.035   0.133   2110
  Planarity :  0.005   0.049   1312
  Dihedral  : 31.325 165.610   4063
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 13.80 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.73 (0.29), residues: 722
  helix:  1.82 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.94 (0.38), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C  82 
 PHE   0.019   0.002   PHE A  67 
 TYR   0.010   0.001   TYR H 118 
 ARG   0.007   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04196 (  791)
  hydrogen bonds       : angle       2.95509 ( 1969)
  covalent geometry    : bond        0.00383 (12741)
  covalent geometry    : angle       0.58803 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.6125 (mmm) cc_final: 0.5550 (ttm)
REVERT: A  125 GLN cc_start: 0.7625 (mt0) cc_final: 0.7185 (mp10)
REVERT: B   92 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6166 (ptm160)
REVERT: D   31 LYS cc_start: 0.6968 (mmtt) cc_final: 0.6681 (tppt)
REVERT: F   68 ASP cc_start: 0.7802 (m-30) cc_final: 0.7366 (m-30)
REVERT: H   68 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7340 (mp0)
REVERT: H   83 ARG cc_start: 0.8171 (mpt-90) cc_final: 0.7954 (mmt90)
REVERT: H   90 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7270 (mp0)
REVERT: H  113 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6991 (tmtt)
  outliers start: 24
  outliers final: 6
  residues processed: 130
  average time/residue: 2.2067
  time to fit residues: 304.6720
Evaluate side-chains
  105 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
B  75 HIS
D  81 ASN
E 125 GLN
H  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.127483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.111791 restraints weight = 24028.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 0.99
r_work: 0.3804 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3710 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12741  Z= 0.204
  Angle     :  0.611   8.586  18484  Z= 0.363
  Chirality :  0.036   0.142   2110
  Planarity :  0.005   0.047   1312
  Dihedral  : 31.361 163.696   4060
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 17.05 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.00 (0.30), residues: 722
  helix:  1.96 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.69 (0.41), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.002   HIS G  82 
 PHE   0.023   0.002   PHE A  67 
 TYR   0.011   0.002   TYR B  88 
 ARG   0.005   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04691 (  791)
  hydrogen bonds       : angle       3.00762 ( 1969)
  covalent geometry    : bond        0.00458 (12741)
  covalent geometry    : angle       0.61139 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.6155 (mmm) cc_final: 0.5718 (tmm)
REVERT: A  105 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6247 (tm-30)
REVERT: A  125 GLN cc_start: 0.7716 (mt0) cc_final: 0.7251 (mp10)
REVERT: B   78 ARG cc_start: 0.7150 (mtm180) cc_final: 0.6893 (mtp85)
REVERT: C   41 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8255 (mp0)
REVERT: E  120 MET cc_start: 0.7920 (mtm) cc_final: 0.7685 (mtm)
REVERT: F   68 ASP cc_start: 0.7863 (m-30) cc_final: 0.7419 (m-30)
REVERT: H   68 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7352 (mp0)
REVERT: H   90 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7257 (mp0)
REVERT: H  113 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6991 (tmtt)
  outliers start: 29
  outliers final: 14
  residues processed: 128
  average time/residue: 1.6155
  time to fit residues: 220.1026
Evaluate side-chains
  116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B  27 GLN
D  44 GLN
E 125 GLN
H  44 GLN
H  46 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.125841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.110113 restraints weight = 24058.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 1.00
r_work: 0.3776 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7168
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  12741  Z= 0.254
  Angle     :  0.659   9.174  18484  Z= 0.387
  Chirality :  0.039   0.150   2110
  Planarity :  0.005   0.049   1312
  Dihedral  : 31.597 162.353   4060
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  7.47 %
    Allowed  : 15.75 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.52 (0.29), residues: 722
  helix:  1.63 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.97 (0.41), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.002   HIS G  82 
 PHE   0.022   0.003   PHE A  67 
 TYR   0.012   0.002   TYR H  37 
 ARG   0.005   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05528 (  791)
  hydrogen bonds       : angle       3.23822 ( 1969)
  covalent geometry    : bond        0.00578 (12741)
  covalent geometry    : angle       0.65863 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 104
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7608 (mmt180) cc_final: 0.7281 (mmt180)
REVERT: A   80 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7545 (t)
REVERT: A  131 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7894 (mtt180)
REVERT: B   95 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7617 (mtp85)
REVERT: F   68 ASP cc_start: 0.7835 (m-30) cc_final: 0.7390 (m-30)
REVERT: F   74 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7628 (tp30)
REVERT: H   68 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7512 (mp0)
REVERT: H   90 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7384 (mp0)
REVERT: H  113 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7170 (tmtt)
  outliers start: 46
  outliers final: 19
  residues processed: 128
  average time/residue: 1.7160
  time to fit residues: 233.2715
Evaluate side-chains
  122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   24 ASP
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B  27 GLN
C  38 ASN
E 125 GLN
G  38 ASN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.128475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.112834 restraints weight = 23972.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 0.98
r_work: 0.3826 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12741  Z= 0.172
  Angle     :  0.582   8.014  18484  Z= 0.347
  Chirality :  0.034   0.138   2110
  Planarity :  0.004   0.045   1312
  Dihedral  : 31.238 163.635   4060
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 20.94 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.09 (0.30), residues: 722
  helix:  2.10 (0.21), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.82 (0.40), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS G  82 
 PHE   0.025   0.002   PHE A  67 
 TYR   0.011   0.001   TYR G  50 
 ARG   0.005   0.000   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04130 (  791)
  hydrogen bonds       : angle       2.92955 ( 1969)
  covalent geometry    : bond        0.00377 (12741)
  covalent geometry    : angle       0.58161 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7595 (t)
REVERT: A   90 MET cc_start: 0.5995 (mmt) cc_final: 0.5182 (ttm)
REVERT: A  125 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7212 (mp10)
REVERT: C   99 ARG cc_start: 0.7850 (mpt180) cc_final: 0.7563 (mpp-170)
REVERT: F   68 ASP cc_start: 0.7869 (m-30) cc_final: 0.7458 (m-30)
REVERT: H   68 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7172 (mp0)
REVERT: H   90 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7299 (mp0)
  outliers start: 33
  outliers final: 13
  residues processed: 128
  average time/residue: 1.5469
  time to fit residues: 210.4832
Evaluate side-chains
  123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
** G  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.128015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.112317 restraints weight = 24107.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 0.98
r_work: 0.3817 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3723 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12741  Z= 0.182
  Angle     :  0.588   8.013  18484  Z= 0.351
  Chirality :  0.035   0.141   2110
  Planarity :  0.004   0.047   1312
  Dihedral  : 31.232 162.313   4054
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 21.92 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.16 (0.30), residues: 722
  helix:  2.15 (0.21), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.82 (0.41), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS C  82 
 PHE   0.025   0.002   PHE A  67 
 TYR   0.013   0.002   TYR F  51 
 ARG   0.004   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04309 (  791)
  hydrogen bonds       : angle       2.93025 ( 1969)
  covalent geometry    : bond        0.00404 (12741)
  covalent geometry    : angle       0.58845 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7545 (t)
REVERT: A   90 MET cc_start: 0.5954 (mmt) cc_final: 0.5203 (ttm)
REVERT: A  120 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6871 (mtt)
REVERT: A  125 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7283 (mp10)
REVERT: A  131 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7768 (mtt180)
REVERT: B   92 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6536 (ptm160)
REVERT: B   95 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7671 (mtp85)
REVERT: C   99 ARG cc_start: 0.7806 (mpt180) cc_final: 0.7539 (mpp-170)
REVERT: F   68 ASP cc_start: 0.7828 (m-30) cc_final: 0.7374 (m-30)
REVERT: F   74 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7640 (tp30)
REVERT: H   68 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7317 (mp0)
REVERT: H   90 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7315 (mp0)
  outliers start: 33
  outliers final: 16
  residues processed: 121
  average time/residue: 1.7142
  time to fit residues: 220.2409
Evaluate side-chains
  122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  125 GLN
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0270
   chunk 70 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0970
   chunk 60 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0170
   chunk 16 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
F  27 GLN
H  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.130299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.114727 restraints weight = 24142.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 0.98
r_work: 0.3859 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12741  Z= 0.152
  Angle     :  0.564   7.339  18484  Z= 0.338
  Chirality :  0.033   0.136   2110
  Planarity :  0.004   0.058   1312
  Dihedral  : 31.026 162.752   4054
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.38 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.40 (0.30), residues: 722
  helix:  2.29 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.70 (0.42), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.001   HIS G  82 
 PHE   0.027   0.002   PHE A  67 
 TYR   0.015   0.001   TYR G  50 
 ARG   0.009   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  791)
  hydrogen bonds       : angle       2.83067 ( 1969)
  covalent geometry    : bond        0.00326 (12741)
  covalent geometry    : angle       0.56381 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7521 (t)
REVERT: A   90 MET cc_start: 0.5841 (mmt) cc_final: 0.5110 (ttm)
REVERT: A  125 GLN cc_start: 0.7817 (mt0) cc_final: 0.7229 (mp10)
REVERT: A  131 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7465 (mtt180)
REVERT: C   99 ARG cc_start: 0.7876 (mpt180) cc_final: 0.7606 (mpp-170)
REVERT: F   68 ASP cc_start: 0.7817 (m-30) cc_final: 0.7400 (m-30)
REVERT: H   90 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7315 (mp0)
  outliers start: 25
  outliers final: 10
  residues processed: 116
  average time/residue: 1.6225
  time to fit residues: 200.2704
Evaluate side-chains
  108 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0570
   chunk 41 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 64 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:
A  85 GLN
B  27 GLN
E 125 GLN
H  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.128882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.113182 restraints weight = 24142.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 0.98
r_work: 0.3834 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3740 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12741  Z= 0.178
  Angle     :  0.592  10.713  18484  Z= 0.350
  Chirality :  0.034   0.140   2110
  Planarity :  0.005   0.046   1312
  Dihedral  : 31.050 161.640   4051
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.70 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.27 (0.30), residues: 722
  helix:  2.18 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.72 (0.43), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS G  82 
 PHE   0.026   0.002   PHE A  67 
 TYR   0.018   0.002   TYR G  50 
 ARG   0.010   0.001   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04153 (  791)
  hydrogen bonds       : angle       2.90185 ( 1969)
  covalent geometry    : bond        0.00393 (12741)
  covalent geometry    : angle       0.59169 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.5892 (mmt) cc_final: 0.5156 (ttm)
REVERT: A  120 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6896 (mtt)
REVERT: A  125 GLN cc_start: 0.7806 (mt0) cc_final: 0.7196 (mp10)
REVERT: A  131 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7438 (mtt180)
REVERT: C   99 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7530 (mpp-170)
REVERT: D   30 ARG cc_start: 0.7152 (ttm110) cc_final: 0.6801 (ttt180)
REVERT: F   68 ASP cc_start: 0.7846 (m-30) cc_final: 0.7462 (m-30)
REVERT: H   40 LYS cc_start: 0.7180 (mtmt) cc_final: 0.6810 (mtmt)
REVERT: H   90 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7297 (mp0)
  outliers start: 28
  outliers final: 14
  residues processed: 119
  average time/residue: 1.9175
  time to fit residues: 243.3768
Evaluate side-chains
  114 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.127634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.111900 restraints weight = 24192.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 0.99
r_work: 0.3809 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12741  Z= 0.207
  Angle     :  0.633  13.275  18484  Z= 0.370
  Chirality :  0.036   0.202   2110
  Planarity :  0.005   0.048   1312
  Dihedral  : 31.176 161.097   4051
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 23.70 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.96 (0.30), residues: 722
  helix:  1.95 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.81 (0.43), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS G  82 
 PHE   0.027   0.002   PHE A  67 
 TYR   0.020   0.002   TYR G  50 
 ARG   0.008   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04660 (  791)
  hydrogen bonds       : angle       3.03555 ( 1969)
  covalent geometry    : bond        0.00465 (12741)
  covalent geometry    : angle       0.63266 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 1.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.5939 (mmt) cc_final: 0.5193 (ttm)
REVERT: A  120 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6879 (mtt)
REVERT: A  125 GLN cc_start: 0.7879 (mt0) cc_final: 0.7295 (mp10)
REVERT: A  131 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7449 (mtt180)
REVERT: C   99 ARG cc_start: 0.7758 (mpt180) cc_final: 0.7508 (mpp-170)
REVERT: D   30 ARG cc_start: 0.7149 (ttm110) cc_final: 0.6847 (ttt180)
REVERT: F   68 ASP cc_start: 0.7848 (m-30) cc_final: 0.7409 (m-30)
REVERT: F   79 LYS cc_start: 0.8287 (mtmp) cc_final: 0.8077 (mtmt)
REVERT: H   90 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7302 (mp0)
  outliers start: 29
  outliers final: 21
  residues processed: 116
  average time/residue: 3.1760
  time to fit residues: 401.8690
Evaluate side-chains
  119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   61 SER
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 53 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
** H  44 GLN ** 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 = 0.4149 r_free = 0.4149 target = 0.127997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.112342 restraints weight = 23975.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 0.98
r_work: 0.3818 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3724 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12741  Z= 0.181
  Angle     :  0.623  13.557  18484  Z= 0.367
  Chirality :  0.035   0.237   2110
  Planarity :  0.005   0.053   1312
  Dihedral  : 31.173 161.255   4051
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.35 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  1.98 (0.30), residues: 722
  helix:  1.98 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.85 (0.43), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS G  82 
 PHE   0.031   0.002   PHE A  67 
 TYR   0.029   0.002   TYR G  50 
 ARG   0.009   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04435 (  791)
  hydrogen bonds       : angle       3.04143 ( 1969)
  covalent geometry    : bond        0.00398 (12741)
  covalent geometry    : angle       0.62313 (18484)

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

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

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1444 Ramachandran restraints generated.
    722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.5907 (mmt) cc_final: 0.5168 (ttm)
REVERT: A  120 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6869 (mtt)
REVERT: A  125 GLN cc_start: 0.7865 (mt0) cc_final: 0.7292 (mp10)
REVERT: A  131 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7415 (mtt180)
REVERT: C   99 ARG cc_start: 0.7774 (mpt180) cc_final: 0.7519 (mpp-170)
REVERT: D   30 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6848 (ttt180)
REVERT: D   31 LYS cc_start: 0.5885 (OUTLIER) cc_final: 0.5634 (mptt)
REVERT: F   68 ASP cc_start: 0.7845 (m-30) cc_final: 0.7410 (m-30)
REVERT: F   79 LYS cc_start: 0.8279 (mtmp) cc_final: 0.8067 (mtmt)
REVERT: H   90 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7290 (mp0)
  outliers start: 25
  outliers final: 17
  residues processed: 116
  average time/residue: 1.6257
  time to fit residues: 200.8075
Evaluate side-chains
  116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   31 LYS
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   84 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   32 GLU
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue   54 LYS
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
E 125 GLN
** H  44 GLN ** 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 = 0.4133 r_free = 0.4133 target = 0.126938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.111234 restraints weight = 24002.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 0.99
r_work: 0.3798 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12741  Z= 0.218
  Angle     :  0.652  13.465  18484  Z= 0.381
  Chirality :  0.037   0.260   2110
  Planarity :  0.005   0.051   1312
  Dihedral  : 31.302 161.286   4051
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 24.03 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.74 (0.30), residues: 722
  helix:  1.85 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.00 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS G  82 
 PHE   0.030   0.002   PHE A  67 
 TYR   0.032   0.002   TYR G  50 
 ARG   0.009   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04877 (  791)
  hydrogen bonds       : angle       3.17670 ( 1969)
  covalent geometry    : bond        0.00491 (12741)
  covalent geometry    : angle       0.65224 (18484)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10619.55 seconds
wall clock time: 188 minutes 45.75 seconds (11325.75 seconds total)