Starting phenix.real_space_refine
on Tue Jun 10 16:44:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qzm_18778/06_2025/8qzm_18778.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qzm_18778/06_2025/8qzm_18778.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qzm_18778/06_2025/8qzm_18778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qzm_18778/06_2025/8qzm_18778.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qzm_18778/06_2025/8qzm_18778.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qzm_18778/06_2025/8qzm_18778.cif"
  }
  resolution = 3.1
  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=   0.024
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     290      5.49       5
     S      11      5.16       5
     C    6718      2.51       5
     N    2292      2.21       5
     O    2830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12141
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 833
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "G"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "I"
      Number of atoms: 2988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2988
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 189
          Classifications: {'peptide': 24}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 21}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 7.80, per 1000 atoms: 0.64
  Number of scatterers: 12141
  At special positions: 0
  Unit cell: (77.926, 121.863, 117.718, 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      11     16.00
     P     290     15.00
     O    2830      8.00
     N    2292      7.00
     C    6718      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: 2.99
  Conformation dependent library (CDL) restraints added in 888.5 milliseconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1462

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      69.7% alpha, 2.8% beta
      137 base pairs and 256 stacking pairs defined.
    Time for finding SS restraints: 5.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.680A  pdb=" N   SER A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.610A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.554A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.560A  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 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    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 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.842A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (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 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.586A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.787A  pdb=" N   ILE H  61 " --> pdb=" O   LYS H  57 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 3.671A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.969A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.499A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (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
      removed outlier: 6.643A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.216A  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: 7.396A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (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

    406 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      355 hydrogen bonds
      710 hydrogen bond angles
      0 basepair planarities
      137 basepair parallelities
      256 stacking parallelities
  Total time for adding SS restraints: 4.30

  Time building geometry restraints manager: 3.38 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: 2357
        1.33 -     1.45: 4234
        1.45 -     1.57: 5753
        1.57 -     1.69: 578
        1.69 -     1.81: 22
  Bond restraints: 12944
  Sorted by residual:
  bond pdb=" P    DG I  20 "
       pdb=" OP2  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.480  1.520 -0.040 2.00e-02 2.50e+03 4.03e+00
  bond pdb=" P    DT I -59 "
       pdb=" OP2  DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.480  1.520 -0.040 2.00e-02 2.50e+03 4.00e+00
  bond pdb=" P    DC I  52 "
       pdb=" OP2  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.480  1.519 -0.039 2.00e-02 2.50e+03 3.81e+00
  bond pdb=" P    DG I  21 "
       pdb=" OP1  DG I  21 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.66e+00
  bond pdb=" P    DC I  53 "
       pdb=" OP1  DC I  53 "
    ideal  model  delta    sigma   weight residual
    1.480  1.518 -0.038 2.00e-02 2.50e+03 3.64e+00
  ... (remaining 12939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 18376
        1.93 -     3.85: 309
        3.85 -     5.78: 16
        5.78 -     7.71: 14
        7.71 -     9.64: 2
  Bond angle restraints: 18717
  Sorted by residual:
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     111.02  116.92   -5.90 1.86e+00 2.89e-01 1.00e+01
  angle pdb=" CA  LEU D 101 "
        pdb=" CB  LEU D 101 "
        pdb=" CG  LEU D 101 "
      ideal   model   delta    sigma   weight residual
     116.30  125.94   -9.64 3.50e+00 8.16e-02 7.58e+00
  angle pdb=" C3'  DC I  53 "
        pdb=" C2'  DC I  53 "
        pdb=" C1'  DC I  53 "
      ideal   model   delta    sigma   weight residual
     101.60  105.63   -4.03 1.50e+00 4.44e-01 7.20e+00
  angle pdb=" CB  MET A  90 "
        pdb=" CG  MET A  90 "
        pdb=" SD  MET A  90 "
      ideal   model   delta    sigma   weight residual
     112.70  120.68   -7.98 3.00e+00 1.11e-01 7.08e+00
  angle pdb=" C4   DT I -59 "
        pdb=" C5   DT I -59 "
        pdb=" C7   DT I -59 "
      ideal   model   delta    sigma   weight residual
     122.40  118.56    3.84 1.50e+00 4.44e-01 6.56e+00
  ... (remaining 18712 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.29: 5477
       32.29 -    64.58: 1525
       64.58 -    96.87: 40
       96.87 -   129.16: 0
      129.16 -   161.45: 3
  Dihedral angle restraints: 7045
    sinusoidal: 4780
      harmonic: 2265
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.55  161.45     1      3.50e+01 8.16e-04 1.53e+01
  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   66.42  153.58     1      3.50e+01 8.16e-04 1.49e+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   69.26  150.74     1      3.50e+01 8.16e-04 1.47e+01
  ... (remaining 7042 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 2113
       0.120 -    0.239: 8
       0.239 -    0.359: 1
       0.359 -    0.478: 0
       0.478 -    0.598: 6
  Chirality restraints: 2128
  Sorted by residual:
  chirality pdb=" P    DC I -58 "
            pdb=" OP1  DC I -58 "
            pdb=" OP2  DC I -58 "
            pdb=" O5'  DC I -58 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.94   -0.60 2.00e-01 2.50e+01 8.94e+00
  chirality pdb=" P    DG I  21 "
            pdb=" OP1  DG I  21 "
            pdb=" OP2  DG I  21 "
            pdb=" O5'  DG I  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.92   -0.58 2.00e-01 2.50e+01 8.34e+00
  chirality pdb=" P    DC I  53 "
            pdb=" OP1  DC I  53 "
            pdb=" OP2  DC I  53 "
            pdb=" O5'  DC I  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.89   -0.55 2.00e-01 2.50e+01 7.52e+00
  ... (remaining 2125 not shown)

  Planarity restraints: 1366
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.56e+00
        pdb=" N   PRO H 103 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -55 "   -0.023 2.00e-02 2.50e+03   9.99e-03 2.74e+00
        pdb=" N9   DA I -55 "    0.020 2.00e-02 2.50e+03
        pdb=" C8   DA I -55 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I -55 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -55 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -55 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I -55 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -55 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I -55 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DA I -55 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -55 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  57 "    0.023 2.00e-02 2.50e+03   9.44e-03 2.67e+00
        pdb=" N9   DG I  57 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DG I  57 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DG I  57 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  57 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  57 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  57 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  57 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  57 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  57 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  57 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1363 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2319
        2.79 -     3.31: 10898
        3.31 -     3.84: 23587
        3.84 -     4.37: 28097
        4.37 -     4.90: 40245
  Nonbonded interactions: 105146
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU G  61 "
            pdb=" NH1 ARG K 181 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" NE2 GLN E 125 "
            pdb=" OE2 GLU F  53 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OG1 THR F  30 "
            pdb=" OP2  DC J -12 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   LEU A  92 "
            pdb=" OG  SER A  96 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" NH2 ARG F  35 "
            pdb=" OP2  DG I   8 "
     model   vdw
     2.315 3.120
  ... (remaining 105141 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 39 through 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 24 through 101))
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ 
e C or name O or name CB ))))
}
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:             2.410
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     32.680
  Find NCS groups from input model:        0.260
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
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   0.040  12944  Z= 0.196
  Angle     :  0.600   9.637  18717  Z= 0.350
  Chirality :  0.046   0.598   2128
  Planarity :  0.004   0.047   1366
  Dihedral  : 28.215 161.446   5583
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 11.04 %
    Favored  : 88.65 %
  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:  1.83 (0.30), residues: 763
  helix:  1.82 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.22 (0.37), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.008   0.001   PHE H  70 
 TYR   0.015   0.001   TYR A  41 
 ARG   0.005   0.000   ARG F  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10831 (  761)
  hydrogen bonds       : angle       4.01260 ( 1913)
  covalent geometry    : bond        0.00438 (12944)
  covalent geometry    : angle       0.59968 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 136
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  108 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8392 (ttmt)
  outliers start: 2
  outliers final: 1
  residues processed: 136
  average time/residue: 0.3894
  time to fit residues: 67.1181
Evaluate side-chains
  118 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   90 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.057202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.043142 restraints weight = 46524.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 1.79
r_work: 0.2728 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.1025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12944  Z= 0.181
  Angle     :  0.551   8.288  18717  Z= 0.330
  Chirality :  0.034   0.159   2128
  Planarity :  0.004   0.043   1366
  Dihedral  : 30.405 163.858   4044
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 11.66 %
    Favored  : 86.94 %
  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:  2.34 (0.30), residues: 763
  helix:  2.21 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.22 (0.38), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.012   0.001   TYR H  40 
 ARG   0.003   0.000   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  761)
  hydrogen bonds       : angle       2.96415 ( 1913)
  covalent geometry    : bond        0.00402 (12944)
  covalent geometry    : angle       0.55072 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9031 (m-30) cc_final: 0.8760 (t0)
REVERT: A  105 GLU cc_start: 0.7889 (tp30) cc_final: 0.7516 (tp30)
REVERT: C   41 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: E   49 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8518 (ptp-170)
REVERT: F   68 ASP cc_start: 0.9002 (m-30) cc_final: 0.8795 (m-30)
REVERT: K  187 ARG cc_start: 0.8650 (tpt-90) cc_final: 0.7937 (tpt-90)
  outliers start: 9
  outliers final: 5
  residues processed: 139
  average time/residue: 0.3669
  time to fit residues: 65.4670
Evaluate side-chains
  127 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 99 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 100 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
G  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.056282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.042137 restraints weight = 46720.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 1.78
r_work: 0.2707 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12944  Z= 0.216
  Angle     :  0.557   5.499  18717  Z= 0.335
  Chirality :  0.035   0.147   2128
  Planarity :  0.004   0.041   1366
  Dihedral  : 30.429 165.352   4041
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.53 %
    Favored  : 84.76 %
  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:  2.42 (0.30), residues: 763
  helix:  2.31 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.32 (0.38), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.011   0.001   TYR A  41 
 ARG   0.004   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  761)
  hydrogen bonds       : angle       2.91128 ( 1913)
  covalent geometry    : bond        0.00488 (12944)
  covalent geometry    : angle       0.55683 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9020 (m-30) cc_final: 0.8680 (t0)
REVERT: C   41 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8054 (tm-30)
REVERT: D   76 GLU cc_start: 0.9252 (mm-30) cc_final: 0.9017 (tp30)
REVERT: D   93 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8142 (mp0)
REVERT: E   49 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8508 (ptp-170)
REVERT: E   59 GLU cc_start: 0.9035 (pm20) cc_final: 0.8730 (pm20)
REVERT: F   68 ASP cc_start: 0.9007 (m-30) cc_final: 0.8805 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 138
  average time/residue: 0.3681
  time to fit residues: 65.2941
Evaluate side-chains
  132 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  125 GLN
Chi-restraints excluded: chain K residue  181 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 85 optimal weight:    6.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.055868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.041794 restraints weight = 46860.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 1.80
r_work: 0.2691 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12944  Z= 0.233
  Angle     :  0.563   5.338  18717  Z= 0.338
  Chirality :  0.035   0.150   2128
  Planarity :  0.004   0.038   1366
  Dihedral  : 30.496 165.387   4041
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 14.15 %
    Favored  : 83.51 %
  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:  2.48 (0.30), residues: 763
  helix:  2.37 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.36 (0.38), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.011   0.001   TYR A  41 
 ARG   0.004   0.000   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  761)
  hydrogen bonds       : angle       2.89705 ( 1913)
  covalent geometry    : bond        0.00529 (12944)
  covalent geometry    : angle       0.56345 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9050 (m-30) cc_final: 0.8705 (t0)
REVERT: C   41 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: D   93 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8127 (mp0)
REVERT: E   49 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8512 (ptp-170)
REVERT: E   59 GLU cc_start: 0.8988 (pm20) cc_final: 0.8756 (pm20)
REVERT: E  125 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.9066 (mm-40)
REVERT: F   68 ASP cc_start: 0.9010 (m-30) cc_final: 0.8805 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 135
  average time/residue: 0.3632
  time to fit residues: 63.2467
Evaluate side-chains
  131 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  125 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.3980
   chunk 9 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.057831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.043893 restraints weight = 46618.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 1.83
r_work: 0.2756 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12944  Z= 0.155
  Angle     :  0.530   5.725  18717  Z= 0.321
  Chirality :  0.032   0.157   2128
  Planarity :  0.003   0.035   1366
  Dihedral  : 30.077 164.299   4041
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.40 %
    Favored  : 82.43 %
  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:  2.81 (0.30), residues: 763
  helix:  2.56 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.07 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.011   0.001   TYR H  40 
 ARG   0.004   0.000   ARG H  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03483 (  761)
  hydrogen bonds       : angle       2.62869 ( 1913)
  covalent geometry    : bond        0.00338 (12944)
  covalent geometry    : angle       0.53042 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9001 (m-30) cc_final: 0.8672 (t0)
REVERT: C   41 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: D   68 ASP cc_start: 0.9202 (t0) cc_final: 0.8846 (t0)
REVERT: E   49 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8512 (ptp-170)
REVERT: E   59 GLU cc_start: 0.8967 (pm20) cc_final: 0.8751 (pm20)
REVERT: F   68 ASP cc_start: 0.8982 (m-30) cc_final: 0.8762 (m-30)
REVERT: F   84 MET cc_start: 0.9155 (tpp) cc_final: 0.8841 (mmm)
REVERT: G  101 THR cc_start: 0.9367 (m) cc_final: 0.9139 (t)
REVERT: K  187 ARG cc_start: 0.8739 (tpt-90) cc_final: 0.8002 (tpt-90)
  outliers start: 14
  outliers final: 10
  residues processed: 151
  average time/residue: 0.3454
  time to fit residues: 67.5261
Evaluate side-chains
  134 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  124 ILE
Chi-restraints excluded: chain E residue  125 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0060
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 93 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.8998

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

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** 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 = 0.3327 r_free = 0.3327 target = 0.057486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.043378 restraints weight = 46954.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 1.86
r_work: 0.2735 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12944  Z= 0.162
  Angle     :  0.534   6.132  18717  Z= 0.322
  Chirality :  0.033   0.153   2128
  Planarity :  0.003   0.037   1366
  Dihedral  : 30.112 164.113   4041
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 16.64 %
    Favored  : 81.80 %
  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:  2.90 (0.30), residues: 763
  helix:  2.62 (0.22), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.01 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.010   0.001   TYR H  40 
 ARG   0.004   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03545 (  761)
  hydrogen bonds       : angle       2.64269 ( 1913)
  covalent geometry    : bond        0.00358 (12944)
  covalent geometry    : angle       0.53373 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9073 (m-30) cc_final: 0.8711 (t0)
REVERT: C   41 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8235 (tm-30)
REVERT: C   56 GLU cc_start: 0.9002 (tt0) cc_final: 0.8788 (tt0)
REVERT: D   76 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9080 (tp30)
REVERT: E   49 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8472 (ptp-170)
REVERT: E   59 GLU cc_start: 0.8940 (pm20) cc_final: 0.8669 (pm20)
REVERT: F   68 ASP cc_start: 0.8991 (m-30) cc_final: 0.8751 (m-30)
REVERT: F   84 MET cc_start: 0.9255 (tpp) cc_final: 0.8881 (mmm)
REVERT: G  101 THR cc_start: 0.9363 (m) cc_final: 0.9101 (t)
REVERT: H   34 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9022 (mmtm)
REVERT: K  187 ARG cc_start: 0.8776 (tpt-90) cc_final: 0.7988 (tpt-90)
  outliers start: 10
  outliers final: 6
  residues processed: 137
  average time/residue: 0.4242
  time to fit residues: 75.1887
Evaluate side-chains
  128 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 121
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain E residue  124 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 93 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.056049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.041798 restraints weight = 47289.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 1.83
r_work: 0.2693 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12944  Z= 0.213
  Angle     :  0.562   6.356  18717  Z= 0.335
  Chirality :  0.034   0.155   2128
  Planarity :  0.003   0.033   1366
  Dihedral  : 30.351 164.050   4041
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.02 %
    Favored  : 81.96 %
  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:  2.77 (0.30), residues: 763
  helix:  2.55 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.10 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.010   0.001   TYR A  54 
 ARG   0.007   0.000   ARG K 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  761)
  hydrogen bonds       : angle       2.77924 ( 1913)
  covalent geometry    : bond        0.00481 (12944)
  covalent geometry    : angle       0.56233 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.949 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9109 (m-30) cc_final: 0.8725 (t0)
REVERT: C   41 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: C   56 GLU cc_start: 0.9027 (tt0) cc_final: 0.8812 (tt0)
REVERT: E   49 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8462 (ptp-170)
REVERT: E   59 GLU cc_start: 0.9001 (pm20) cc_final: 0.8713 (pm20)
REVERT: F   68 ASP cc_start: 0.9001 (m-30) cc_final: 0.8771 (m-30)
REVERT: F   84 MET cc_start: 0.9263 (tpp) cc_final: 0.8863 (mmm)
REVERT: H   34 LYS cc_start: 0.9395 (mmmm) cc_final: 0.9011 (mmtm)
REVERT: K  187 ARG cc_start: 0.8793 (tpt-90) cc_final: 0.7996 (tpt-90)
  outliers start: 13
  outliers final: 9
  residues processed: 134
  average time/residue: 0.4005
  time to fit residues: 69.4103
Evaluate side-chains
  128 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 46 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 49 optimal weight:    0.4980
   chunk 98 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.055724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.041641 restraints weight = 47741.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 1.83
r_work: 0.2687 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12944  Z= 0.229
  Angle     :  0.576   9.077  18717  Z= 0.342
  Chirality :  0.035   0.209   2128
  Planarity :  0.004   0.038   1366
  Dihedral  : 30.483 163.813   4041
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 16.80 %
    Favored  : 81.34 %
  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:  2.67 (0.30), residues: 763
  helix:  2.48 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.15 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.011   0.001   PHE A  67 
 TYR   0.010   0.001   TYR A  41 
 ARG   0.008   0.000   ARG K 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (  761)
  hydrogen bonds       : angle       2.85749 ( 1913)
  covalent geometry    : bond        0.00518 (12944)
  covalent geometry    : angle       0.57589 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 1.189 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9141 (m-30) cc_final: 0.8742 (t0)
REVERT: C   41 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: C   56 GLU cc_start: 0.9039 (tt0) cc_final: 0.8806 (tt0)
REVERT: E   49 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8476 (ptp-170)
REVERT: E   59 GLU cc_start: 0.8994 (pm20) cc_final: 0.8700 (pm20)
REVERT: F   68 ASP cc_start: 0.9017 (m-30) cc_final: 0.8803 (m-30)
REVERT: H   34 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9006 (mmtm)
REVERT: K  187 ARG cc_start: 0.8806 (tpt-90) cc_final: 0.8010 (tpt-90)
  outliers start: 12
  outliers final: 8
  residues processed: 127
  average time/residue: 0.4679
  time to fit residues: 76.9271
Evaluate side-chains
  122 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 113
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   71 VAL
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  122 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 85 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.057520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.043505 restraints weight = 46877.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 1.85
r_work: 0.2742 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12944  Z= 0.162
  Angle     :  0.547   9.569  18717  Z= 0.326
  Chirality :  0.033   0.242   2128
  Planarity :  0.003   0.035   1366
  Dihedral  : 30.122 162.969   4041
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.80 %
    Favored  : 81.80 %
  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:  2.89 (0.30), residues: 763
  helix:  2.62 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop : -0.01 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.008   0.001   PHE H  70 
 TYR   0.011   0.001   TYR H  40 
 ARG   0.004   0.000   ARG H  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  761)
  hydrogen bonds       : angle       2.65248 ( 1913)
  covalent geometry    : bond        0.00356 (12944)
  covalent geometry    : angle       0.54704 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 1.582 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9113 (m-30) cc_final: 0.8718 (t0)
REVERT: C   41 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: C   56 GLU cc_start: 0.8998 (tt0) cc_final: 0.8743 (tt0)
REVERT: E   49 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8454 (ptp-170)
REVERT: E   59 GLU cc_start: 0.8940 (pm20) cc_final: 0.8661 (pm20)
REVERT: F   68 ASP cc_start: 0.9005 (m-30) cc_final: 0.8779 (m-30)
REVERT: F   84 MET cc_start: 0.9210 (tpp) cc_final: 0.8837 (mmm)
REVERT: G  101 THR cc_start: 0.9375 (m) cc_final: 0.9118 (t)
REVERT: H   34 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9003 (mmtm)
REVERT: K  187 ARG cc_start: 0.8774 (tpt-90) cc_final: 0.7976 (tpt-90)
  outliers start: 9
  outliers final: 6
  residues processed: 131
  average time/residue: 0.4920
  time to fit residues: 83.7539
Evaluate side-chains
  127 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   73 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.057361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.043280 restraints weight = 46574.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 1.86
r_work: 0.2736 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12944  Z= 0.167
  Angle     :  0.553   9.668  18717  Z= 0.328
  Chirality :  0.033   0.277   2128
  Planarity :  0.003   0.035   1366
  Dihedral  : 30.144 162.993   4041
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.95 %
    Favored  : 81.65 %
  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:  2.90 (0.30), residues: 763
  helix:  2.62 (0.22), residues: 553
  sheet:  None (None), residues: 0
  loop :  0.01 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.010   0.001   TYR H  40 
 ARG   0.005   0.000   ARG K 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03552 (  761)
  hydrogen bonds       : angle       2.67070 ( 1913)
  covalent geometry    : bond        0.00369 (12944)
  covalent geometry    : angle       0.55345 (18717)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.9124 (m-30) cc_final: 0.8720 (t0)
REVERT: C   41 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: C   56 GLU cc_start: 0.9005 (tt0) cc_final: 0.8749 (tt0)
REVERT: E   49 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8450 (ptp-170)
REVERT: E   59 GLU cc_start: 0.8937 (pm20) cc_final: 0.8660 (pm20)
REVERT: F   68 ASP cc_start: 0.9017 (m-30) cc_final: 0.8788 (m-30)
REVERT: F   84 MET cc_start: 0.9230 (tpp) cc_final: 0.8852 (mmm)
REVERT: G  101 THR cc_start: 0.9378 (m) cc_final: 0.9107 (t)
REVERT: H   34 LYS cc_start: 0.9386 (mmmm) cc_final: 0.9004 (mmtm)
REVERT: K  187 ARG cc_start: 0.8788 (tpt-90) cc_final: 0.7991 (tpt-90)
  outliers start: 9
  outliers final: 7
  residues processed: 127
  average time/residue: 0.4226
  time to fit residues: 69.7551
Evaluate side-chains
  127 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   15 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue   96 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 89 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** 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 = 0.3273 r_free = 0.3273 target = 0.054861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.040766 restraints weight = 46623.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 1.76
r_work: 0.2666 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  12944  Z= 0.302
  Angle     :  0.622   9.394  18717  Z= 0.363
  Chirality :  0.038   0.272   2128
  Planarity :  0.004   0.034   1366
  Dihedral  : 30.782 163.490   4041
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 17.26 %
    Favored  : 81.34 %
  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:  2.52 (0.30), residues: 763
  helix:  2.37 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.21 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  49 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.015   0.001   TYR A  54 
 ARG   0.007   0.000   ARG K 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04703 (  761)
  hydrogen bonds       : angle       3.01978 ( 1913)
  covalent geometry    : bond        0.00688 (12944)
  covalent geometry    : angle       0.62163 (18717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5538.22 seconds
wall clock time: 99 minutes 47.43 seconds (5987.43 seconds total)