Starting phenix.real_space_refine
on Tue Feb  3 19:12:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9prc_71807/02_2026/9prc_71807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9prc_71807/02_2026/9prc_71807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9prc_71807/02_2026/9prc_71807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9prc_71807/02_2026/9prc_71807.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9prc_71807/02_2026/9prc_71807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9prc_71807/02_2026/9prc_71807.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.000
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: 4
    Type Number    sf(0)   Gaussians
     P     152      5.49       5
     C    3543      2.51       5
     N    1149      2.21       5
     O    1649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6493
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 422
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 422
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 412
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "D"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 407
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "E"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 412
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "F"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 407
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "G"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 412
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "H"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 407
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "J"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 756
          Classifications: {'RNA': 36}
          Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18}
          Link IDs: {'rna3p': 35}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 840
          Classifications: {'RNA': 40}
          Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 20}
          Link IDs: {'rna3p': 39}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 756
          Classifications: {'RNA': 36}
          Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18}
          Link IDs: {'rna3p': 35}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 840
          Classifications: {'RNA': 40}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 19, 'rna3p_pyr': 16}
          Link IDs: {'rna2p': 4, 'rna3p': 35}
          Chain breaks: 1
  Time building chain proxies: 1.38, per 1000 atoms: 0.21
  Number of scatterers: 6493
  At special positions: 0
  Unit cell: (120.285, 106.434, 85.293, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     P     152     15.00
     O    1649      8.00
     N    1149      7.00
     C    3543      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 267.9 milliseconds
  

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  722

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      96.5% alpha, 0.0% beta
      64 base pairs and 82 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 48
      removed outlier: 3.881A  pdb=" N   VAL A  16 " --> pdb=" O   GLY A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 60
      removed outlier: 4.224A  pdb=" N   ASN A  53 " --> pdb=" O   PRO A  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 48
    Processing helix  chain 'B' and resid 49 through 59
      removed outlier: 4.133A  pdb=" N   ASN B  53 " --> pdb=" O   PRO B  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 48
      removed outlier: 3.651A  pdb=" N   HIS C  48 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 60
      removed outlier: 3.627A  pdb=" N   GLY C  52 " --> pdb=" O   HIS C  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 48
    Processing helix  chain 'D' and resid 48 through 60
      removed outlier: 3.792A  pdb=" N   GLY D  52 " --> pdb=" O   HIS D  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 13 through 47
      removed outlier: 4.222A  pdb=" N   GLU E  47 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 48 through 59
    Processing helix  chain 'F' and resid 13 through 47
      removed outlier: 4.471A  pdb=" N   GLU F  47 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 60
    Processing helix  chain 'G' and resid 13 through 48
    Processing helix  chain 'G' and resid 48 through 61
      removed outlier: 3.626A  pdb=" N   GLY G  52 " --> pdb=" O   HIS G  48 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS G  61 " --> pdb=" O   ILE G  57 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 13 through 47
    Processing helix  chain 'H' and resid 48 through 60
      removed outlier: 3.532A  pdb=" N   GLY H  52 " --> pdb=" O   HIS H  48 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS H  60 " --> pdb=" O   GLY H  56 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      128 hydrogen bonds
      256 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      82 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.29: 729
        1.29 -     1.38: 1447
        1.38 -     1.46: 1511
        1.46 -     1.54: 2899
        1.54 -     1.62: 319
  Bond restraints: 6905
  Sorted by residual:
  bond pdb=" CG  LYS F  26 "
       pdb=" CD  LYS F  26 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.89e+00
  bond pdb=" C3'   U P  32 "
       pdb=" O3'   U P  32 "
    ideal  model  delta    sigma   weight residual
    1.427  1.447 -0.020 1.50e-02 4.44e+03 1.76e+00
  bond pdb=" CG  LYS E  26 "
       pdb=" CD  LYS E  26 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" CB  LYS F  26 "
       pdb=" CG  LYS F  26 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.58e+00
  bond pdb=" CB  LYS E  26 "
       pdb=" CG  LYS E  26 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.30e+00
  ... (remaining 6900 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 9762
        1.89 -     3.78: 143
        3.78 -     5.67: 32
        5.67 -     7.56: 8
        7.56 -     9.45: 2
  Bond angle restraints: 9947
  Sorted by residual:
  angle pdb=" CB  LYS F  26 "
        pdb=" CG  LYS F  26 "
        pdb=" CD  LYS F  26 "
      ideal   model   delta    sigma   weight residual
     111.30  120.75   -9.45 2.30e+00 1.89e-01 1.69e+01
  angle pdb=" CB  LYS E  26 "
        pdb=" CG  LYS E  26 "
        pdb=" CD  LYS E  26 "
      ideal   model   delta    sigma   weight residual
     111.30  120.59   -9.29 2.30e+00 1.89e-01 1.63e+01
  angle pdb=" C3'   U P  32 "
        pdb=" O3'   U P  32 "
        pdb=" P     A P  33 "
      ideal   model   delta    sigma   weight residual
     120.20  125.76   -5.56 1.50e+00 4.44e-01 1.37e+01
  angle pdb=" CA  LYS C  42 "
        pdb=" CB  LYS C  42 "
        pdb=" CG  LYS C  42 "
      ideal   model   delta    sigma   weight residual
     114.10  120.50   -6.40 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" CA  GLU A  28 "
        pdb=" CB  GLU A  28 "
        pdb=" CG  GLU A  28 "
      ideal   model   delta    sigma   weight residual
     114.10  119.87   -5.77 2.00e+00 2.50e-01 8.33e+00
  ... (remaining 9942 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.69: 3876
       35.69 -    71.39: 301
       71.39 -   107.08: 14
      107.08 -   142.78: 1
      142.78 -   178.47: 3
  Dihedral angle restraints: 4195
    sinusoidal: 3080
      harmonic: 1115
  Sorted by residual:
  dihedral pdb=" O4'   U P  34 "
           pdb=" C1'   U P  34 "
           pdb=" N1    U P  34 "
           pdb=" C2    U P  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   18.47 -178.47     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U P  32 "
           pdb=" C1'   U P  32 "
           pdb=" N1    U P  32 "
           pdb=" C2    U P  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   66.49  165.51     1      1.70e+01 3.46e-03 6.54e+01
  dihedral pdb=" O4'   U P  26 "
           pdb=" C1'   U P  26 "
           pdb=" N1    U P  26 "
           pdb=" C2    U P  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -24.01 -103.99     1      1.70e+01 3.46e-03 4.13e+01
  ... (remaining 4192 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1054
       0.034 -    0.068: 137
       0.068 -    0.102: 24
       0.102 -    0.135: 5
       0.135 -    0.169: 5
  Chirality restraints: 1225
  Sorted by residual:
  chirality pdb=" C1'   A P  41 "
            pdb=" O4'   A P  41 "
            pdb=" C2'   A P  41 "
            pdb=" N9    A P  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" C1'   U P  32 "
            pdb=" O4'   U P  32 "
            pdb=" C2'   U P  32 "
            pdb=" N1    U P  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.29    0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" P     A P  33 "
            pdb=" OP1   A P  33 "
            pdb=" OP2   A P  33 "
            pdb=" O5'   A P  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.56   -0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 1222 not shown)

  Planarity restraints: 705
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D  28 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.22e+00
        pdb=" CD  GLU D  28 "   -0.031 2.00e-02 2.50e+03
        pdb=" OE1 GLU D  28 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU D  28 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D  15 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.08e+00
        pdb=" CD  GLU D  15 "    0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU D  15 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU D  15 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU G  28 "    0.009 2.00e-02 2.50e+03   1.73e-02 3.01e+00
        pdb=" CD  GLU G  28 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU G  28 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU G  28 "    0.011 2.00e-02 2.50e+03
  ... (remaining 702 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 838
        2.75 -     3.29: 6294
        3.29 -     3.82: 12980
        3.82 -     4.36: 13699
        4.36 -     4.90: 19686
  Nonbonded interactions: 53497
  Sorted by model distance:
  nonbonded pdb=" O4    U P  12 "
            pdb=" N6    A P  33 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OD1 ASN D  53 "
            pdb=" O2'   U J  32 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OE2 GLU B  31 "
            pdb=" NH1 ARG B  35 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OE2 GLU B  29 "
            pdb=" NH1 ARG B  32 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O2    U P  10 "
            pdb=" N6    A P  35 "
     model   vdw
     2.302 3.120
  ... (remaining 53492 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' and resid 12 through 60)
  selection = (chain 'B' and resid 12 through 60)
  selection = (chain 'C' and resid 12 through 60)
  selection = chain 'D'
  selection = (chain 'E' and resid 12 through 60)
  selection = chain 'F'
  selection = (chain 'G' and resid 12 through 60)
  selection = chain 'H'
}
ncs_group {
  reference = chain 'J'
  selection = (chain 'K' and resid 5 through 44)
  selection = chain 'M'
  selection = (chain 'P' and resid 5 through 44)
}

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:             8.420
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.460
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
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      :  0.004   0.041   6905  Z= 0.162
  Angle     :  0.597   9.447   9947  Z= 0.297
  Chirality :  0.027   0.169   1225
  Planarity :  0.004   0.034    705
  Dihedral  : 19.631 178.472   3473
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 37.21 %
    Favored  : 60.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.49 (0.40), residues: 385
  helix:  3.77 (0.25), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.31 (1.03), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  32 
 TRP   0.016   0.002   TRP H  20 
 HIS   0.011   0.002   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6905)
  covalent geometry    : angle       0.59705 ( 9947)
  hydrogen bonds       : bond        0.07560 (  439)
  hydrogen bonds       : angle       3.57558 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7302 (tm-30)
REVERT: B   29 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7600 (mm-30)
REVERT: E   45 GLU cc_start: 0.8032 (tp30) cc_final: 0.7684 (tm-30)
REVERT: E   55 LYS cc_start: 0.6364 (tptm) cc_final: 0.5896 (tptm)
REVERT: F   42 LYS cc_start: 0.8368 (tppt) cc_final: 0.8126 (mmtm)
REVERT: G   46 ASP cc_start: 0.7738 (t0) cc_final: 0.7383 (t0)
REVERT: H   18 GLU cc_start: 0.7717 (tp30) cc_final: 0.7216 (tp30)
  outliers start: 9
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1409
  time to fit residues: 18.8710
Evaluate side-chains
  110 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0770
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    8.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  48 HIS
F  53 ASN
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.124050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.100842 restraints weight = 18742.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.102680 restraints weight = 9336.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.103951 restraints weight = 5905.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.104719 restraints weight = 4455.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.105271 restraints weight = 3773.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.0458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6905  Z= 0.145
  Angle     :  0.540   6.218   9947  Z= 0.268
  Chirality :  0.026   0.161   1225
  Planarity :  0.004   0.036    705
  Dihedral  : 17.739 179.206   2543
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 33.72 %
    Favored  : 62.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.28 (0.39), residues: 385
  helix:  3.62 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.10 (1.05), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  32 
 TRP   0.011   0.001   TRP H  20 
 HIS   0.006   0.002   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6905)
  covalent geometry    : angle       0.54011 ( 9947)
  hydrogen bonds       : bond        0.04754 (  439)
  hydrogen bonds       : angle       3.23476 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7347 (tm-30)
REVERT: E   45 GLU cc_start: 0.8081 (tp30) cc_final: 0.7721 (tm-30)
REVERT: E   55 LYS cc_start: 0.6569 (tptm) cc_final: 0.6045 (tptm)
REVERT: F   32 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7645 (mtm110)
REVERT: F   42 LYS cc_start: 0.8492 (tppt) cc_final: 0.8256 (mmtm)
REVERT: G   46 ASP cc_start: 0.7963 (t0) cc_final: 0.7606 (t0)
REVERT: H   18 GLU cc_start: 0.7833 (tp30) cc_final: 0.7253 (tp30)
  outliers start: 14
  outliers final: 10
  residues processed: 116
  average time/residue: 0.1303
  time to fit residues: 17.6470
Evaluate side-chains
  115 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   29 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0170
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0270
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.3276

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

Flipped N/Q/H residues before XYZ refinement:
** B  48 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 = 0.4225 r_free = 0.4225 target = 0.125678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.103669 restraints weight = 19388.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.105498 restraints weight = 9693.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.106729 restraints weight = 6118.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.107462 restraints weight = 4595.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.107967 restraints weight = 3893.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.0913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6905  Z= 0.119
  Angle     :  0.509   7.025   9947  Z= 0.249
  Chirality :  0.025   0.160   1225
  Planarity :  0.003   0.034    705
  Dihedral  : 17.393 174.779   2539
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 32.27 %
    Favored  : 62.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.59 (0.39), residues: 385
  helix:  3.82 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -1.96 (1.08), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  32 
 TRP   0.010   0.001   TRP H  20 
 HIS   0.011   0.002   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6905)
  covalent geometry    : angle       0.50944 ( 9947)
  hydrogen bonds       : bond        0.04217 (  439)
  hydrogen bonds       : angle       3.00393 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.114 
Fit side-chains
REVERT: B   28 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7252 (tm-30)
REVERT: C   47 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6020 (mp0)
REVERT: E   45 GLU cc_start: 0.8057 (tp30) cc_final: 0.7774 (tm-30)
REVERT: E   55 LYS cc_start: 0.6452 (tptm) cc_final: 0.5986 (tptm)
REVERT: F   42 LYS cc_start: 0.8409 (tppt) cc_final: 0.8171 (mmtm)
REVERT: G   46 ASP cc_start: 0.7948 (t0) cc_final: 0.7631 (t0)
REVERT: H   18 GLU cc_start: 0.7808 (tp30) cc_final: 0.7238 (tp30)
  outliers start: 17
  outliers final: 13
  residues processed: 126
  average time/residue: 0.1324
  time to fit residues: 19.6338
Evaluate side-chains
  116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   35 ARG
Chi-restraints excluded: chain H residue   39 LYS
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** D  48 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 = 0.4158 r_free = 0.4158 target = 0.124051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.100367 restraints weight = 18495.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.102224 restraints weight = 9129.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.103480 restraints weight = 5766.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.104207 restraints weight = 4319.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.104810 restraints weight = 3676.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6905  Z= 0.149
  Angle     :  0.530   6.418   9947  Z= 0.261
  Chirality :  0.026   0.159   1225
  Planarity :  0.003   0.030    705
  Dihedral  : 17.323 170.080   2539
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 32.85 %
    Favored  : 61.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.64 (0.39), residues: 385
  helix:  3.85 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.04 (1.08), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  32 
 TRP   0.013   0.002   TRP F  50 
 HIS   0.007   0.002   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6905)
  covalent geometry    : angle       0.52966 ( 9947)
  hydrogen bonds       : bond        0.04512 (  439)
  hydrogen bonds       : angle       3.02722 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.139 
Fit side-chains
REVERT: B   28 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7346 (tm-30)
REVERT: C   47 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.6052 (mp0)
REVERT: E   55 LYS cc_start: 0.6459 (tptm) cc_final: 0.5887 (tptm)
REVERT: F   42 LYS cc_start: 0.8475 (tppt) cc_final: 0.8020 (mmtm)
REVERT: G   46 ASP cc_start: 0.7939 (t0) cc_final: 0.7610 (t0)
REVERT: H   18 GLU cc_start: 0.7832 (tp30) cc_final: 0.7253 (tp30)
  outliers start: 19
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1331
  time to fit residues: 18.6289
Evaluate side-chains
  116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   35 ARG
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 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 = 0.4143 r_free = 0.4143 target = 0.123150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.099571 restraints weight = 18849.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.101404 restraints weight = 9487.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.102684 restraints weight = 6049.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.103532 restraints weight = 4546.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.103989 restraints weight = 3819.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6905  Z= 0.179
  Angle     :  0.564   7.042   9947  Z= 0.277
  Chirality :  0.027   0.156   1225
  Planarity :  0.003   0.025    705
  Dihedral  : 17.335 167.163   2539
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 36.05 %
    Favored  : 59.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.53 (0.39), residues: 385
  helix:  3.79 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.15 (1.09), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  24 
 TRP   0.010   0.001   TRP F  50 
 HIS   0.008   0.002   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6905)
  covalent geometry    : angle       0.56424 ( 9947)
  hydrogen bonds       : bond        0.04970 (  439)
  hydrogen bonds       : angle       3.09711 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B   28 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7341 (tm-30)
REVERT: C   18 GLU cc_start: 0.7985 (tp30) cc_final: 0.7457 (tp30)
REVERT: C   47 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6135 (mp0)
REVERT: E   55 LYS cc_start: 0.6538 (tptm) cc_final: 0.5915 (tptm)
REVERT: F   42 LYS cc_start: 0.8427 (tppt) cc_final: 0.8208 (mmtm)
REVERT: G   46 ASP cc_start: 0.7969 (t0) cc_final: 0.7646 (t0)
REVERT: H   18 GLU cc_start: 0.7849 (tp30) cc_final: 0.7260 (tp30)
  outliers start: 14
  outliers final: 11
  residues processed: 113
  average time/residue: 0.1359
  time to fit residues: 17.9718
Evaluate side-chains
  114 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9990
   chunk 40 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7224

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.124530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.102072 restraints weight = 19341.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.104062 restraints weight = 9283.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.105375 restraints weight = 5731.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.106166 restraints weight = 4210.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.106754 restraints weight = 3540.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6905  Z= 0.145
  Angle     :  0.542   7.588   9947  Z= 0.267
  Chirality :  0.026   0.158   1225
  Planarity :  0.003   0.025    705
  Dihedral  : 17.239 166.184   2539
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 35.47 %
    Favored  : 60.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.67 (0.39), residues: 385
  helix:  3.87 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.11 (1.10), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  32 
 TRP   0.010   0.001   TRP H  20 
 HIS   0.009   0.002   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6905)
  covalent geometry    : angle       0.54192 ( 9947)
  hydrogen bonds       : bond        0.04627 (  439)
  hydrogen bonds       : angle       3.01862 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: B   28 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7333 (tm-30)
REVERT: C   47 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6092 (mp0)
REVERT: E   29 GLU cc_start: 0.7385 (tp30) cc_final: 0.6979 (tp30)
REVERT: E   55 LYS cc_start: 0.6529 (tptm) cc_final: 0.5935 (tptm)
REVERT: F   42 LYS cc_start: 0.8467 (tppt) cc_final: 0.8264 (mmtm)
REVERT: G   46 ASP cc_start: 0.7997 (t0) cc_final: 0.7682 (t0)
REVERT: H   18 GLU cc_start: 0.7873 (tp30) cc_final: 0.7283 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 115
  average time/residue: 0.1490
  time to fit residues: 19.8811
Evaluate side-chains
  112 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.124007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.100453 restraints weight = 18754.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.102276 restraints weight = 9481.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.103524 restraints weight = 6037.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.104240 restraints weight = 4538.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.104844 restraints weight = 3863.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6905  Z= 0.162
  Angle     :  0.568   7.869   9947  Z= 0.280
  Chirality :  0.027   0.153   1225
  Planarity :  0.003   0.028    705
  Dihedral  : 17.219 166.058   2539
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 35.17 %
    Favored  : 59.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.64 (0.39), residues: 385
  helix:  3.86 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.24 (1.09), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  32 
 TRP   0.012   0.001   TRP C  50 
 HIS   0.007   0.002   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 6905)
  covalent geometry    : angle       0.56762 ( 9947)
  hydrogen bonds       : bond        0.04821 (  439)
  hydrogen bonds       : angle       3.04924 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.192 
Fit side-chains
REVERT: C   47 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.6186 (mp0)
REVERT: D   13 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6043 (ptm160)
REVERT: E   55 LYS cc_start: 0.6423 (tptm) cc_final: 0.5904 (tptm)
REVERT: F   42 LYS cc_start: 0.8356 (tppt) cc_final: 0.8144 (mmtm)
REVERT: G   46 ASP cc_start: 0.7846 (t0) cc_final: 0.7546 (t0)
REVERT: H   18 GLU cc_start: 0.7798 (tp30) cc_final: 0.7281 (tp30)
  outliers start: 17
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1299
  time to fit residues: 17.6953
Evaluate side-chains
  115 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   36 LYS
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   13 ARG
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   15 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  48 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.124695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.102561 restraints weight = 19394.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.104433 restraints weight = 9664.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.105636 restraints weight = 6053.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.106472 restraints weight = 4530.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.106810 restraints weight = 3797.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.1655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6905  Z= 0.150
  Angle     :  0.577   8.387   9947  Z= 0.284
  Chirality :  0.026   0.157   1225
  Planarity :  0.003   0.027    705
  Dihedral  : 17.141 165.831   2539
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 37.21 %
    Favored  : 58.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.67 (0.39), residues: 385
  helix:  3.88 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.28 (1.10), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  32 
 TRP   0.014   0.001   TRP C  50 
 HIS   0.007   0.002   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6905)
  covalent geometry    : angle       0.57687 ( 9947)
  hydrogen bonds       : bond        0.04714 (  439)
  hydrogen bonds       : angle       3.01248 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.180 
Fit side-chains
REVERT: C   47 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.6089 (mp0)
REVERT: E   29 GLU cc_start: 0.6958 (tp30) cc_final: 0.6674 (tp30)
REVERT: E   55 LYS cc_start: 0.6470 (tptm) cc_final: 0.5992 (tptm)
REVERT: F   28 GLU cc_start: 0.6959 (tp30) cc_final: 0.6677 (tp30)
REVERT: F   42 LYS cc_start: 0.8406 (tppt) cc_final: 0.8193 (mmtm)
REVERT: G   46 ASP cc_start: 0.7909 (t0) cc_final: 0.7600 (t0)
REVERT: H   18 GLU cc_start: 0.7825 (tp30) cc_final: 0.7274 (tp30)
  outliers start: 15
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1373
  time to fit residues: 18.6125
Evaluate side-chains
  114 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   15 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0010
   chunk 25 optimal weight:    0.7980
   chunk 29 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0010
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 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 = 0.4229 r_free = 0.4229 target = 0.126274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.104132 restraints weight = 19784.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.105985 restraints weight = 9800.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.107233 restraints weight = 6150.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.108057 restraints weight = 4578.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.108471 restraints weight = 3844.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6905  Z= 0.125
  Angle     :  0.560   8.993   9947  Z= 0.276
  Chirality :  0.025   0.164   1225
  Planarity :  0.003   0.029    705
  Dihedral  : 16.983 165.984   2539
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 37.50 %
    Favored  : 58.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.76 (0.39), residues: 385
  helix:  3.94 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.30 (1.09), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  32 
 TRP   0.015   0.001   TRP C  50 
 HIS   0.007   0.001   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6905)
  covalent geometry    : angle       0.55988 ( 9947)
  hydrogen bonds       : bond        0.04360 (  439)
  hydrogen bonds       : angle       2.92332 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.187 
Fit side-chains
REVERT: C   47 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6166 (mp0)
REVERT: E   55 LYS cc_start: 0.6390 (tptm) cc_final: 0.5913 (tptm)
REVERT: F   28 GLU cc_start: 0.6858 (tp30) cc_final: 0.6595 (tp30)
REVERT: F   42 LYS cc_start: 0.8350 (tppt) cc_final: 0.8136 (mmtm)
REVERT: G   46 ASP cc_start: 0.7898 (t0) cc_final: 0.7604 (t0)
REVERT: H   18 GLU cc_start: 0.7761 (tp30) cc_final: 0.7218 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1440
  time to fit residues: 19.0406
Evaluate side-chains
  111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   15 GLU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 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 = 0.4130 r_free = 0.4130 target = 0.122239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.098948 restraints weight = 18782.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.100655 restraints weight = 9659.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.101832 restraints weight = 6283.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.102530 restraints weight = 4810.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.103042 restraints weight = 4134.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.1959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6905  Z= 0.241
  Angle     :  0.666   9.470   9947  Z= 0.329
  Chirality :  0.030   0.149   1225
  Planarity :  0.004   0.026    705
  Dihedral  : 17.329 166.931   2539
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 37.21 %
    Favored  : 59.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.38 (0.39), residues: 385
  helix:  3.70 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.34 (1.09), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  32 
 TRP   0.010   0.002   TRP C  50 
 HIS   0.006   0.002   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 6905)
  covalent geometry    : angle       0.66552 ( 9947)
  hydrogen bonds       : bond        0.05647 (  439)
  hydrogen bonds       : angle       3.32416 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.181 
Fit side-chains
REVERT: C   18 GLU cc_start: 0.8011 (tp30) cc_final: 0.7469 (tp30)
REVERT: C   40 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7505 (mptt)
REVERT: E   55 LYS cc_start: 0.6600 (tptm) cc_final: 0.6133 (tptm)
REVERT: F   28 GLU cc_start: 0.7073 (tp30) cc_final: 0.6771 (tp30)
REVERT: F   42 LYS cc_start: 0.8464 (tppt) cc_final: 0.8236 (mmtm)
REVERT: G   46 ASP cc_start: 0.7960 (t0) cc_final: 0.7656 (t0)
REVERT: G   48 HIS cc_start: 0.7606 (m170) cc_final: 0.7345 (m170)
REVERT: H   18 GLU cc_start: 0.7889 (tp30) cc_final: 0.7326 (tp30)
  outliers start: 12
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1522
  time to fit residues: 20.4163
Evaluate side-chains
  117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  53 ASN
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.122681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.099485 restraints weight = 18381.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.101229 restraints weight = 9546.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.102450 restraints weight = 6186.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.103170 restraints weight = 4705.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.103657 restraints weight = 4008.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6905  Z= 0.165
  Angle     :  0.610   9.020   9947  Z= 0.302
  Chirality :  0.027   0.158   1225
  Planarity :  0.004   0.033    705
  Dihedral  : 17.148 165.505   2539
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 38.66 %
    Favored  : 58.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.51 (0.39), residues: 385
  helix:  3.78 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.39 (1.08), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  32 
 TRP   0.015   0.002   TRP C  50 
 HIS   0.005   0.001   HIS D  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6905)
  covalent geometry    : angle       0.60959 ( 9947)
  hydrogen bonds       : bond        0.04979 (  439)
  hydrogen bonds       : angle       3.14276 ( 1189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1286.55 seconds
wall clock time: 22 minutes 51.92 seconds (1371.92 seconds total)