Starting phenix.real_space_refine
on Wed Mar  4 03:23:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lv8_23529/03_2026/7lv8_23529.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lv8_23529/03_2026/7lv8_23529.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lv8_23529/03_2026/7lv8_23529.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lv8_23529/03_2026/7lv8_23529.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lv8_23529/03_2026/7lv8_23529.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lv8_23529/03_2026/7lv8_23529.cif"
  }
  resolution = 3.4
  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=   1.001
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     242      5.49       5
     S      30      5.16       5
     C    5913      2.51       5
     N    1961      2.21       5
     O    2505      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10651
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "B"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 731
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "A"
      Number of atoms: 770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 770
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "D"
      Number of atoms: 659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 659
          Classifications: {'peptide': 89}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 688
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 93}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "F"
      Number of atoms: 731
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 731
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 772
          Classifications: {'peptide': 102}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "H"
      Number of atoms: 659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 659
          Classifications: {'peptide': 89}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "G"
      Number of atoms: 680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 680
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 93}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "I"
      Number of atoms: 2495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2495
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
    Chain: "J"
      Number of atoms: 2466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2466
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
  Time building chain proxies: 1.91, per 1000 atoms: 0.18
  Number of scatterers: 10651
  At special positions: 0
  Unit cell: (82.84, 115.54, 118.81, 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      30     16.00
     P     242     15.00
     O    2505      8.00
     N    1961      7.00
     C    5913      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
  Links applied
    TRANS
      " CYS A 113 " - " SER B 112 "
      " GLU C 105 " - " LYS D 104 "
      " CYS E 113 " - " SER F 112 "
      " GLU G 105 " - " LYS H 104 "
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 319.6 milliseconds
  

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1404

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 7 sheets defined
      67.8% alpha, 1.8% beta
      112 base pairs and 205 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 39
      removed outlier: 3.660A  pdb=" N   LEU B  36 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 74
      removed outlier: 3.675A  pdb=" N   LEU B  69 " --> pdb=" O   GLN B  65 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA B  74 " --> pdb=" O   ALA B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 91
      removed outlier: 3.554A  pdb=" N   VAL B  84 " --> pdb=" O   MET B  80 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   MET B  91 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 136
      removed outlier: 3.511A  pdb=" N   VAL A 132 " --> pdb=" O   ASN A 128 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ARG A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 158
      removed outlier: 3.739A  pdb=" N   LYS A 158 " --> pdb=" O   GLU A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 195
      removed outlier: 3.503A  pdb=" N   ILE A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 211
      removed outlier: 3.603A  pdb=" N   ILE A 205 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 29
    Processing helix  chain 'D' and resid 35 through 61
    Processing helix  chain 'D' and resid 69 through 81
      removed outlier: 3.753A  pdb=" N   VAL D  73 " --> pdb=" O   LYS D  69 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASP D  79 " --> pdb=" O   LEU D  75 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU D  80 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 103
      removed outlier: 3.745A  pdb=" N   GLY D  91 " --> pdb=" O   ARG D  87 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU D  92 " --> pdb=" O   HIS D  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 115
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 138 through 167
      removed outlier: 3.561A  pdb=" N   ALA C 142 " --> pdb=" O   SER C 138 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL C 143 " --> pdb=" O   GLU C 139 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE C 152 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 184
      removed outlier: 3.592A  pdb=" N   ASP C 184 " --> pdb=" O   ALA C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 192
      removed outlier: 3.538A  pdb=" N   ALA C 189 " --> pdb=" O   ALA C 185 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   VAL C 190 " --> pdb=" O   ALA C 186 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL C 191 " --> pdb=" O   LEU C 187 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 28 through 40
      removed outlier: 3.570A  pdb=" N   GLN F  33 " --> pdb=" O   LYS F  29 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA F  39 " --> pdb=" O   LEU F  35 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 74
      removed outlier: 3.595A  pdb=" N   LEU F  69 " --> pdb=" O   GLN F  65 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 80 through 89
      removed outlier: 3.545A  pdb=" N   VAL F  84 " --> pdb=" O   MET F  80 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 92
      No H-bonds generated for 'chain 'F' and resid 90 through 92'
    Processing helix  chain 'E' and resid 127 through 136
      removed outlier: 3.525A  pdb=" N   VAL E 132 " --> pdb=" O   ASN E 128 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ARG E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET E 136 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 144 through 160
      removed outlier: 3.848A  pdb=" N   GLU E 159 " --> pdb=" O   ILE E 155 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 166 through 195
      removed outlier: 3.586A  pdb=" N   ILE E 191 " --> pdb=" O   LYS E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 211
      removed outlier: 3.717A  pdb=" N   ILE E 205 " --> pdb=" O   THR E 201 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 17 through 29
    Processing helix  chain 'H' and resid 35 through 61
    Processing helix  chain 'H' and resid 69 through 81
      removed outlier: 3.698A  pdb=" N   VAL H  73 " --> pdb=" O   LYS H  69 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 103
      removed outlier: 3.547A  pdb=" N   GLY H  91 " --> pdb=" O   ARG H  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 110 through 115
    Processing helix  chain 'G' and resid 120 through 130
    Processing helix  chain 'G' and resid 138 through 167
      removed outlier: 3.771A  pdb=" N   ALA G 142 " --> pdb=" O   SER G 138 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL G 143 " --> pdb=" O   GLU G 139 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE G 152 " --> pdb=" O   ALA G 148 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 173 through 183
      removed outlier: 3.545A  pdb=" N   ILE G 181 " --> pdb=" O   ILE G 177 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN G 182 " --> pdb=" O   THR G 178 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASN G 183 " --> pdb=" O   LEU G 179 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 184 through 189
      removed outlier: 3.735A  pdb=" N   ALA G 189 " --> pdb=" O   ALA G 185 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 78 through 79
    Processing sheet with id=AA2, first strand: chain 'D' and resid 33 through 34
      removed outlier: 7.315A  pdb=" N   SER D  33 " --> pdb=" O   ILE C 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'D' and resid 67 through 68
    Processing sheet with id=AA4, first strand: chain 'F' and resid 43 through 44
      removed outlier: 6.959A  pdb=" N   SER F  43 " --> pdb=" O   VAL E 200 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 34
      removed outlier: 7.202A  pdb=" N   SER H  33 " --> pdb=" O   ILE G 172 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 67 through 68

    350 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      291 hydrogen bonds
      578 hydrogen bond angles
      0 basepair planarities
      112 basepair parallelities
      205 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2538
        1.34 -     1.46: 3383
        1.46 -     1.58: 4857
        1.58 -     1.70: 482
        1.70 -     1.82: 52
  Bond restraints: 11312
  Sorted by residual:
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.484 -0.062 3.00e-02 1.11e+03 4.34e+00
  bond pdb=" CB  ASP F  47 "
       pdb=" CG  ASP F  47 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.33e+00
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.78e+00
  bond pdb=" C3'  DT I -59 "
       pdb=" O3'  DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.467 -0.045 3.00e-02 1.11e+03 2.26e+00
  bond pdb=" CB  ASN D  16 "
       pdb=" CG  ASN D  16 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.81e+00
  ... (remaining 11307 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 16130
        2.33 -     4.66: 142
        4.66 -     6.99: 15
        6.99 -     9.32: 1
        9.32 -    11.65: 1
  Bond angle restraints: 16289
  Sorted by residual:
  angle pdb=" CB  MET C 153 "
        pdb=" CG  MET C 153 "
        pdb=" SD  MET C 153 "
      ideal   model   delta    sigma   weight residual
     112.70  124.35  -11.65 3.00e+00 1.11e-01 1.51e+01
  angle pdb=" C   LYS C 107 "
        pdb=" N   GLU C 108 "
        pdb=" CA  GLU C 108 "
      ideal   model   delta    sigma   weight residual
     121.54  127.66   -6.12 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" C3'  DG I  20 "
        pdb=" O3'  DG I  20 "
        pdb=" P    DG I  21 "
      ideal   model   delta    sigma   weight residual
     120.20  124.92   -4.72 1.50e+00 4.44e-01 9.89e+00
  angle pdb=" CA  LYS C 107 "
        pdb=" CB  LYS C 107 "
        pdb=" CG  LYS C 107 "
      ideal   model   delta    sigma   weight residual
     114.10  120.11   -6.01 2.00e+00 2.50e-01 9.02e+00
  angle pdb=" CB  ASP F  47 "
        pdb=" CG  ASP F  47 "
        pdb=" OD1 ASP F  47 "
      ideal   model   delta    sigma   weight residual
     118.40  124.93   -6.53 2.30e+00 1.89e-01 8.05e+00
  ... (remaining 16284 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.62: 5040
       34.62 -    69.24: 1127
       69.24 -   103.86: 18
      103.86 -   138.48: 0
      138.48 -   173.11: 3
  Dihedral angle restraints: 6188
    sinusoidal: 4016
      harmonic: 2172
  Sorted by residual:
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.89  173.11     1      3.50e+01 8.16e-04 1.56e+01
  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   76.29  143.71     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   80.70  139.30     1      3.50e+01 8.16e-04 1.38e+01
  ... (remaining 6185 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1332
       0.033 -    0.066: 410
       0.066 -    0.098: 106
       0.098 -    0.131: 37
       0.131 -    0.164: 6
  Chirality restraints: 1891
  Sorted by residual:
  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   -2.51   -0.16 2.00e-01 2.50e+01 6.74e-01
  chirality pdb=" CA  ILE F  27 "
            pdb=" N   ILE F  27 "
            pdb=" C   ILE F  27 "
            pdb=" CB  ILE F  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  ASN D  16 "
            pdb=" N   ASN D  16 "
            pdb=" C   ASN D  16 "
            pdb=" CB  ASN D  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.07e-01
  ... (remaining 1888 not shown)

  Planarity restraints: 1215
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F  47 "   -0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   ASP F  47 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ASP F  47 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   THR F  48 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 178 "   -0.009 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" CD  GLU A 178 "    0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 178 "   -0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 178 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  36 "    0.023 2.00e-02 2.50e+03   1.13e-02 2.88e+00
        pdb=" N1   DC J  36 "   -0.017 2.00e-02 2.50e+03
        pdb=" C2   DC J  36 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DC J  36 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DC J  36 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DC J  36 "    0.005 2.00e-02 2.50e+03
        pdb=" N4   DC J  36 "    0.009 2.00e-02 2.50e+03
        pdb=" C5   DC J  36 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6   DC J  36 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1212 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 941
        2.74 -     3.28: 9222
        3.28 -     3.82: 20333
        3.82 -     4.36: 23381
        4.36 -     4.90: 33904
  Nonbonded interactions: 87781
  Sorted by model distance:
  nonbonded pdb=" O   LYS B  29 "
            pdb=" OG1 THR B  32 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OG1 THR E 123 "
            pdb=" OP2  DA I -14 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   LEU B  42 "
            pdb=" ND2 ASN A 128 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OE2 GLU H  37 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" NH1 ARG C 111 "
            pdb=" OE1 GLU C 125 "
     model   vdw
     2.360 3.120
  ... (remaining 87776 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and (resid 113 through 122 or (resid 123 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 124 through 214))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and (resid 105 through 106 or (resid 107 through 108 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 109 through 157 or (resid 158  \ 
and (name N or name CA or name C or name O or name CB )) or resid 159 through 19 \ 
8))
  selection = chain 'G'
}
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:             1.650
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.630
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
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      :  0.003   0.062  11316  Z= 0.166
  Angle     :  0.646  11.653  16301  Z= 0.388
  Chirality :  0.037   0.164   1891
  Planarity :  0.004   0.046   1211
  Dihedral  : 27.117 173.105   4772
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.00 %
    Favored  : 99.83 %
  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: -3.26 (0.22), residues: 748
  helix: -2.34 (0.15), residues: 488
  sheet:  None (None), residues: 0
  loop : -1.37 (0.32), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 129 
 TYR   0.024   0.003   TYR H 100 
 PHE   0.024   0.002   PHE G 152 
 HIS   0.003   0.001   HIS B  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (11312)
  covalent geometry    : angle       0.64573 (16289)
  hydrogen bonds       : bond        0.20718 (  641)
  hydrogen bonds       : angle       5.81533 ( 1628)
  link_TRANS           : bond        0.00665 (    4)
  link_TRANS           : angle       0.95169 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.162 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9244 (t) cc_final: 0.8839 (p)
REVERT: F   41 SER cc_start: 0.9270 (m) cc_final: 0.8805 (p)
REVERT: F   80 MET cc_start: 0.7904 (mtp) cc_final: 0.7522 (mtt)
REVERT: E  131 GLU cc_start: 0.8253 (tp30) cc_final: 0.7496 (tt0)
REVERT: G  169 LYS cc_start: 0.7190 (mmtp) cc_final: 0.6789 (mtpt)
REVERT: G  184 ASP cc_start: 0.7671 (t70) cc_final: 0.7159 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 110
  average time/residue: 0.1102
  time to fit residues: 16.6011
Evaluate side-chains
  70 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   16 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 182 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.133083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.098204 restraints weight = 18258.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.38
r_work: 0.3190 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11316  Z= 0.177
  Angle     :  0.578   7.731  16301  Z= 0.346
  Chirality :  0.035   0.136   1891
  Planarity :  0.004   0.042   1211
  Dihedral  : 29.593 169.706   3432
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  :  9.02 %
    Favored  : 89.48 %
  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: -0.05 (0.28), residues: 748
  helix:  0.63 (0.21), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.29 (0.33), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 129 
 TYR   0.014   0.002   TYR D  81 
 PHE   0.033   0.002   PHE G 152 
 HIS   0.003   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (11312)
  covalent geometry    : angle       0.57794 (16289)
  hydrogen bonds       : bond        0.05163 (  641)
  hydrogen bonds       : angle       2.93354 ( 1628)
  link_TRANS           : bond        0.00085 (    4)
  link_TRANS           : angle       0.41063 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9266 (t) cc_final: 0.8881 (p)
REVERT: A  186 GLU cc_start: 0.7513 (tt0) cc_final: 0.7207 (mt-10)
REVERT: C  118 GLN cc_start: 0.8627 (mt0) cc_final: 0.8353 (mt0)
REVERT: C  125 GLU cc_start: 0.8102 (tt0) cc_final: 0.7793 (tt0)
REVERT: F   89 GLU cc_start: 0.8816 (pp20) cc_final: 0.8282 (pt0)
REVERT: E  120 SER cc_start: 0.8221 (t) cc_final: 0.7898 (p)
REVERT: H  100 TYR cc_start: 0.8731 (t80) cc_final: 0.8431 (t80)
REVERT: G  169 LYS cc_start: 0.6591 (mmtp) cc_final: 0.6129 (mtpt)
  outliers start: 9
  outliers final: 5
  residues processed: 93
  average time/residue: 0.0971
  time to fit residues: 12.6337
Evaluate side-chains
  79 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain G residue  182 GLN
Chi-restraints excluded: chain G residue  187 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 46 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  57 HIS
A 115 GLN
D  16 ASN
D  27 GLN
D  35 GLN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.123385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.088111 restraints weight = 18330.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.33
r_work: 0.3038 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  11316  Z= 0.313
  Angle     :  0.703   8.115  16301  Z= 0.404
  Chirality :  0.041   0.171   1891
  Planarity :  0.005   0.047   1211
  Dihedral  : 29.995 170.796   3430
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 11.35 %
    Favored  : 84.97 %
  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:  0.75 (0.30), residues: 748
  helix:  1.39 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -1.29 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 129 
 TYR   0.033   0.002   TYR H  81 
 PHE   0.045   0.004   PHE G 152 
 HIS   0.005   0.001   HIS B  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00723 (11312)
  covalent geometry    : angle       0.70291 (16289)
  hydrogen bonds       : bond        0.05681 (  641)
  hydrogen bonds       : angle       3.22903 ( 1628)
  link_TRANS           : bond        0.00109 (    4)
  link_TRANS           : angle       0.28833 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.232 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9331 (t) cc_final: 0.8959 (p)
REVERT: D   16 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6525 (p0)
REVERT: D   63 GLU cc_start: 0.7488 (pm20) cc_final: 0.6784 (pt0)
REVERT: C  118 GLN cc_start: 0.8708 (mt0) cc_final: 0.8296 (mt0)
REVERT: H   31 ASP cc_start: 0.8571 (p0) cc_final: 0.8325 (p0)
REVERT: G  169 LYS cc_start: 0.7063 (mmtp) cc_final: 0.6719 (mtpt)
  outliers start: 22
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0907
  time to fit residues: 11.8811
Evaluate side-chains
  87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain D residue   16 ASN
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain D residue   47 VAL
Chi-restraints excluded: chain D residue   67 THR
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  192 THR
Chi-restraints excluded: chain E residue  202 SER
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain G residue  134 CYS
Chi-restraints excluded: chain G residue  139 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 72 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D  16 ASN
** E 128 ASN ** 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 = 0.3809 r_free = 0.3809 target = 0.128423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.093547 restraints weight = 17923.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.27
r_work: 0.3122 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11316  Z= 0.153
  Angle     :  0.545   7.269  16301  Z= 0.328
  Chirality :  0.034   0.132   1891
  Planarity :  0.003   0.040   1211
  Dihedral  : 29.710 170.761   3430
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.02 %
    Favored  : 83.81 %
  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:  1.63 (0.30), residues: 748
  helix:  2.13 (0.23), residues: 492
  sheet:  None (None), residues: 0
  loop : -1.06 (0.35), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 129 
 TYR   0.020   0.001   TYR H  81 
 PHE   0.029   0.002   PHE G 152 
 HIS   0.003   0.001   HIS D  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (11312)
  covalent geometry    : angle       0.54520 (16289)
  hydrogen bonds       : bond        0.04062 (  641)
  hydrogen bonds       : angle       2.70854 ( 1628)
  link_TRANS           : bond        0.00116 (    4)
  link_TRANS           : angle       0.24702 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.271 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9333 (t) cc_final: 0.9003 (p)
REVERT: C  118 GLN cc_start: 0.8722 (mt0) cc_final: 0.8269 (mt0)
REVERT: E  206 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8059 (mm-30)
REVERT: H   31 ASP cc_start: 0.8499 (p0) cc_final: 0.8267 (p0)
REVERT: H  100 TYR cc_start: 0.8633 (t80) cc_final: 0.8311 (t80)
REVERT: G  169 LYS cc_start: 0.6711 (mmtp) cc_final: 0.6378 (mtpt)
  outliers start: 13
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0980
  time to fit residues: 12.2896
Evaluate side-chains
  81 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain H residue   61 LEU
Chi-restraints excluded: chain H residue   65 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 79 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 57 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 82 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
D  16 ASN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  16 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.122326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.087232 restraints weight = 17937.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 2.24
r_work: 0.3028 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  11316  Z= 0.279
  Angle     :  0.664   7.929  16301  Z= 0.384
  Chirality :  0.040   0.169   1891
  Planarity :  0.004   0.040   1211
  Dihedral  : 29.965 171.028   3430
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 15.03 %
    Favored  : 80.97 %
  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:  1.44 (0.30), residues: 748
  helix:  1.98 (0.23), residues: 492
  sheet:  None (None), residues: 0
  loop : -1.12 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  53 
 TYR   0.033   0.002   TYR H  81 
 PHE   0.046   0.004   PHE C 152 
 HIS   0.003   0.001   HIS D  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 (11312)
  covalent geometry    : angle       0.66461 (16289)
  hydrogen bonds       : bond        0.05196 (  641)
  hydrogen bonds       : angle       3.11320 ( 1628)
  link_TRANS           : bond        0.00106 (    4)
  link_TRANS           : angle       0.27685 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 73
  time to evaluate  : 0.262 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9348 (t) cc_final: 0.8966 (p)
REVERT: F   47 ASP cc_start: 0.8157 (t0) cc_final: 0.7928 (t0)
REVERT: E  172 MET cc_start: 0.8275 (ttm) cc_final: 0.8037 (ttp)
REVERT: H   16 ASN cc_start: 0.6049 (OUTLIER) cc_final: 0.5689 (p0)
REVERT: H   31 ASP cc_start: 0.8554 (p0) cc_final: 0.8338 (p0)
REVERT: G  169 LYS cc_start: 0.7106 (mmtp) cc_final: 0.6800 (mtpt)
  outliers start: 24
  outliers final: 15
  residues processed: 88
  average time/residue: 0.0926
  time to fit residues: 11.9362
Evaluate side-chains
  87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
Chi-restraints excluded: chain E residue  192 THR
Chi-restraints excluded: chain H residue   16 ASN
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain G residue  134 CYS
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  139 GLU
Chi-restraints excluded: chain G residue  187 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D  16 ASN
F  72 GLN
E 128 ASN
H  16 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.127475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.092788 restraints weight = 17960.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 2.29
r_work: 0.3117 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11316  Z= 0.152
  Angle     :  0.543   6.042  16301  Z= 0.326
  Chirality :  0.033   0.129   1891
  Planarity :  0.003   0.037   1211
  Dihedral  : 29.616 170.924   3430
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.86 %
    Favored  : 80.30 %
  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:  1.99 (0.31), residues: 748
  helix:  2.39 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.95 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 129 
 TYR   0.013   0.001   TYR H  81 
 PHE   0.029   0.002   PHE G 152 
 HIS   0.003   0.001   HIS D  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (11312)
  covalent geometry    : angle       0.54321 (16289)
  hydrogen bonds       : bond        0.03870 (  641)
  hydrogen bonds       : angle       2.59687 ( 1628)
  link_TRANS           : bond        0.00079 (    4)
  link_TRANS           : angle       0.19052 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.227 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9359 (t) cc_final: 0.9081 (p)
REVERT: B   71 MET cc_start: 0.8788 (ttp) cc_final: 0.8531 (tmm)
REVERT: C  118 GLN cc_start: 0.8746 (mt0) cc_final: 0.8355 (mt0)
REVERT: F  102 ASP cc_start: 0.8896 (t70) cc_final: 0.8518 (t0)
REVERT: E  172 MET cc_start: 0.8245 (ttm) cc_final: 0.8006 (ttp)
REVERT: E  206 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8023 (mm-30)
REVERT: H   16 ASN cc_start: 0.6033 (OUTLIER) cc_final: 0.5814 (p0)
REVERT: H  100 TYR cc_start: 0.8738 (t80) cc_final: 0.8419 (t80)
REVERT: G  169 LYS cc_start: 0.6935 (mmtp) cc_final: 0.6553 (mtpt)
  outliers start: 17
  outliers final: 14
  residues processed: 101
  average time/residue: 0.0854
  time to fit residues: 12.4646
Evaluate side-chains
  97 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain F residue   16 LEU
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
Chi-restraints excluded: chain E residue  202 SER
Chi-restraints excluded: chain H residue   16 ASN
Chi-restraints excluded: chain H residue   61 LEU
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  195 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0270
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   chunk 50 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
D  16 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.128479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.093970 restraints weight = 17812.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.25
r_work: 0.3132 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11316  Z= 0.145
  Angle     :  0.534   6.452  16301  Z= 0.321
  Chirality :  0.033   0.133   1891
  Planarity :  0.003   0.036   1211
  Dihedral  : 29.581 169.172   3430
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.03 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.25 (0.31), residues: 748
  helix:  2.61 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.88 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 129 
 TYR   0.011   0.001   TYR H  81 
 PHE   0.026   0.002   PHE G 152 
 HIS   0.003   0.000   HIS D  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (11312)
  covalent geometry    : angle       0.53466 (16289)
  hydrogen bonds       : bond        0.03657 (  641)
  hydrogen bonds       : angle       2.50536 ( 1628)
  link_TRANS           : bond        0.00086 (    4)
  link_TRANS           : angle       0.15594 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.187 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9344 (t) cc_final: 0.9023 (p)
REVERT: B   71 MET cc_start: 0.8584 (ttp) cc_final: 0.8369 (tmm)
REVERT: B   80 MET cc_start: 0.8671 (mmm) cc_final: 0.8352 (mmm)
REVERT: F  102 ASP cc_start: 0.8879 (t70) cc_final: 0.8435 (t0)
REVERT: G  169 LYS cc_start: 0.6207 (mmtp) cc_final: 0.5835 (mtpt)
  outliers start: 19
  outliers final: 15
  residues processed: 95
  average time/residue: 0.0849
  time to fit residues: 11.7866
Evaluate side-chains
  98 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain F residue   16 LEU
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
Chi-restraints excluded: chain E residue  202 SER
Chi-restraints excluded: chain H residue   61 LEU
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  195 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0030
   chunk 44 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0570
   chunk 58 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.3708

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

Flipped N/Q/H residues before XYZ refinement:
H  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.131483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.097279 restraints weight = 17879.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.27
r_work: 0.3182 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11316  Z= 0.137
  Angle     :  0.517   6.105  16301  Z= 0.311
  Chirality :  0.032   0.135   1891
  Planarity :  0.003   0.035   1211
  Dihedral  : 29.462 167.999   3430
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.70 %
    Favored  : 79.13 %
  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:  2.41 (0.31), residues: 748
  helix:  2.73 (0.23), residues: 498
  sheet:  None (None), residues: 0
  loop : -0.84 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  18 
 TYR   0.006   0.001   TYR D  81 
 PHE   0.020   0.002   PHE G 152 
 HIS   0.003   0.000   HIS D  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11312)
  covalent geometry    : angle       0.51677 (16289)
  hydrogen bonds       : bond        0.03457 (  641)
  hydrogen bonds       : angle       2.43220 ( 1628)
  link_TRANS           : bond        0.00091 (    4)
  link_TRANS           : angle       0.16288 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.231 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9301 (t) cc_final: 0.8880 (p)
REVERT: B   71 MET cc_start: 0.8531 (ttp) cc_final: 0.8324 (tmm)
REVERT: B   80 MET cc_start: 0.8757 (mmm) cc_final: 0.8496 (mmm)
REVERT: C  118 GLN cc_start: 0.8683 (mt0) cc_final: 0.8301 (mt0)
REVERT: F  102 ASP cc_start: 0.8917 (t70) cc_final: 0.8417 (t0)
REVERT: H   63 GLU cc_start: 0.7672 (pm20) cc_final: 0.6756 (mm-30)
REVERT: G  169 LYS cc_start: 0.6129 (mmtp) cc_final: 0.5706 (mtpt)
  outliers start: 13
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0980
  time to fit residues: 13.7212
Evaluate side-chains
  99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
Chi-restraints excluded: chain H residue   61 LEU
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  195 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0870
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.2162

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

Flipped N/Q/H residues before XYZ refinement:
D  16 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.128089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.093337 restraints weight = 17767.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.27
r_work: 0.3127 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.3936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11316  Z= 0.167
  Angle     :  0.546   6.574  16301  Z= 0.323
  Chirality :  0.033   0.132   1891
  Planarity :  0.003   0.046   1211
  Dihedral  : 29.591 168.093   3430
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 18.36 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.41 (0.31), residues: 748
  helix:  2.68 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.68 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F  37 
 TYR   0.009   0.001   TYR D  81 
 PHE   0.032   0.002   PHE G 152 
 HIS   0.003   0.001   HIS D  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (11312)
  covalent geometry    : angle       0.54644 (16289)
  hydrogen bonds       : bond        0.03812 (  641)
  hydrogen bonds       : angle       2.54130 ( 1628)
  link_TRANS           : bond        0.00074 (    4)
  link_TRANS           : angle       0.15121 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.279 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9277 (t) cc_final: 0.8988 (p)
REVERT: B   80 MET cc_start: 0.8853 (mmm) cc_final: 0.8604 (mmm)
REVERT: A  128 ASN cc_start: 0.7449 (t0) cc_final: 0.6553 (t0)
REVERT: C  118 GLN cc_start: 0.8712 (mt0) cc_final: 0.8346 (mt0)
REVERT: C  153 MET cc_start: 0.8718 (mmp) cc_final: 0.8458 (mmm)
REVERT: F  102 ASP cc_start: 0.8905 (t70) cc_final: 0.8421 (t0)
REVERT: G  169 LYS cc_start: 0.6473 (mmtp) cc_final: 0.6112 (mtpt)
  outliers start: 17
  outliers final: 14
  residues processed: 93
  average time/residue: 0.0867
  time to fit residues: 11.7838
Evaluate side-chains
  96 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain D residue   16 ASN
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
Chi-restraints excluded: chain E residue  202 SER
Chi-restraints excluded: chain H residue   61 LEU
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  195 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** D  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  16 ASN
G 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.124867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.090141 restraints weight = 17922.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.21
r_work: 0.3082 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11316  Z= 0.211
  Angle     :  0.596   7.569  16301  Z= 0.347
  Chirality :  0.036   0.161   1891
  Planarity :  0.004   0.050   1211
  Dihedral  : 29.726 169.702   3430
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.70 %
    Favored  : 78.30 %
  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:  2.17 (0.31), residues: 748
  helix:  2.44 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.65 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  37 
 TYR   0.011   0.001   TYR D  81 
 PHE   0.041   0.003   PHE G 152 
 HIS   0.004   0.001   HIS D  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 (11312)
  covalent geometry    : angle       0.59603 (16289)
  hydrogen bonds       : bond        0.04253 (  641)
  hydrogen bonds       : angle       2.76648 ( 1628)
  link_TRANS           : bond        0.00083 (    4)
  link_TRANS           : angle       0.21109 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.315 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9327 (t) cc_final: 0.8923 (p)
REVERT: B   80 MET cc_start: 0.8814 (mmm) cc_final: 0.8538 (mmm)
REVERT: A  128 ASN cc_start: 0.7308 (t0) cc_final: 0.6398 (t0)
REVERT: F  102 ASP cc_start: 0.8915 (t70) cc_final: 0.8460 (t0)
REVERT: H   16 ASN cc_start: 0.6304 (OUTLIER) cc_final: 0.6006 (p0)
REVERT: G  169 LYS cc_start: 0.6390 (mmtp) cc_final: 0.6073 (mtpt)
  outliers start: 18
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0921
  time to fit residues: 11.6238
Evaluate side-chains
  88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain F residue   16 LEU
Chi-restraints excluded: chain F residue   20 VAL
Chi-restraints excluded: chain F residue   73 LEU
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
Chi-restraints excluded: chain E residue  202 SER
Chi-restraints excluded: chain H residue   16 ASN
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   61 LEU
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain G residue  137 VAL
Chi-restraints excluded: chain G residue  195 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
H  16 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.126883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.092188 restraints weight = 17829.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.21
r_work: 0.3105 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11316  Z= 0.162
  Angle     :  0.548   6.771  16301  Z= 0.325
  Chirality :  0.033   0.147   1891
  Planarity :  0.003   0.035   1211
  Dihedral  : 29.662 169.333   3430
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 19.03 %
    Favored  : 78.46 %
  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:  2.26 (0.31), residues: 748
  helix:  2.58 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.80 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  37 
 TYR   0.010   0.001   TYR D  81 
 PHE   0.032   0.002   PHE G 152 
 HIS   0.003   0.001   HIS D  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (11312)
  covalent geometry    : angle       0.54789 (16289)
  hydrogen bonds       : bond        0.03820 (  641)
  hydrogen bonds       : angle       2.56246 ( 1628)
  link_TRANS           : bond        0.00063 (    4)
  link_TRANS           : angle       0.15130 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2040.11 seconds
wall clock time: 35 minutes 36.38 seconds (2136.38 seconds total)