Starting phenix.real_space_refine
on Mon Jul 28 15:14:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lv8_23529/07_2025/7lv8_23529.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lv8_23529/07_2025/7lv8_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_23529/07_2025/7lv8_23529.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lv8_23529/07_2025/7lv8_23529.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lv8_23529/07_2025/7lv8_23529.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lv8_23529/07_2025/7lv8_23529.cif"
  }
  resolution = 3.4
  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=   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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ASP:plan': 1, 'HIS: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, 'ASP:plan': 1, 'HIS: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: 7.19, per 1000 atoms: 0.68
  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: 3.00
  Conformation dependent library (CDL) restraints added in 795.4 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: 5.15
  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: 4.54

  Time building geometry restraints manager: 3.56 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:             1.060
  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:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     32.050
  Find NCS groups from input model:        0.290
  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:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.850
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.26 (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
 HIS   0.003   0.001   HIS B  57 
 PHE   0.024   0.002   PHE G 152 
 TYR   0.024   0.003   TYR H 100 
 ARG   0.012   0.001   ARG C 129 

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

*********************** 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  : 0.797 
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: 0.2458
  time to fit residues: 36.9750
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  : 0.834 
-------------------------------------------------------------------------------
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 81 optimal weight:    7.9990
   chunk 72 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 49 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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
A 128 ASN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 182 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.131655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.096457 restraints weight = 18058.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.40
r_work: 0.3168 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11316  Z= 0.198
  Angle     :  0.592   7.983  16301  Z= 0.352
  Chirality :  0.035   0.135   1891
  Planarity :  0.004   0.041   1211
  Dihedral  : 29.659 170.418   3432
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  :  8.85 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.28), residues: 748
  helix:  0.61 (0.21), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.29 (0.34), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  57 
 PHE   0.035   0.003   PHE G 152 
 TYR   0.019   0.002   TYR H  81 
 ARG   0.008   0.001   ARG C 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00142 (    4)
  link_TRANS           : angle       0.44698 (   12)
  hydrogen bonds       : bond        0.05306 (  641)
  hydrogen bonds       : angle       2.98099 ( 1628)
  covalent geometry    : bond        0.00441 (11312)
  covalent geometry    : angle       0.59244 (16289)

*********************** 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
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.940 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9302 (t) cc_final: 0.8919 (p)
REVERT: A  186 GLU cc_start: 0.7711 (tt0) cc_final: 0.7388 (mt-10)
REVERT: C  118 GLN cc_start: 0.8673 (mt0) cc_final: 0.8428 (mt0)
REVERT: C  125 GLU cc_start: 0.8238 (tt0) cc_final: 0.7919 (tt0)
REVERT: F   89 GLU cc_start: 0.8883 (pp20) cc_final: 0.8292 (pt0)
REVERT: E  120 SER cc_start: 0.8240 (t) cc_final: 0.7906 (p)
REVERT: G  169 LYS cc_start: 0.6802 (mmtp) cc_final: 0.6405 (mtpt)
  outliers start: 11
  outliers final: 7
  residues processed: 86
  average time/residue: 0.2473
  time to fit residues: 29.6857
Evaluate side-chains
  78 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 SER
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 E residue  202 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 13 optimal weight:    0.0570
   chunk 51 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 94 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 52 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
D  16 ASN
D  27 GLN
F  72 GLN
** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.133733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.098882 restraints weight = 18183.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.37
r_work: 0.3201 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11316  Z= 0.146
  Angle     :  0.526   6.070  16301  Z= 0.319
  Chirality :  0.033   0.204   1891
  Planarity :  0.003   0.041   1211
  Dihedral  : 29.464 168.471   3430
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.35 %
    Favored  : 87.15 %
  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:  1.38 (0.30), residues: 748
  helix:  1.95 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -1.22 (0.34), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  55 
 PHE   0.026   0.002   PHE G 152 
 TYR   0.018   0.001   TYR H  81 
 ARG   0.007   0.000   ARG C 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00143 (    4)
  link_TRANS           : angle       0.24270 (   12)
  hydrogen bonds       : bond        0.03966 (  641)
  hydrogen bonds       : angle       2.65665 ( 1628)
  covalent geometry    : bond        0.00313 (11312)
  covalent geometry    : angle       0.52589 (16289)

*********************** 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
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.782 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9260 (t) cc_final: 0.8922 (p)
REVERT: A  128 ASN cc_start: 0.7458 (t0) cc_final: 0.7197 (t0)
REVERT: A  186 GLU cc_start: 0.7491 (tt0) cc_final: 0.7249 (mt-10)
REVERT: D   63 GLU cc_start: 0.7458 (pm20) cc_final: 0.6992 (pt0)
REVERT: C  118 GLN cc_start: 0.8648 (mt0) cc_final: 0.8312 (mt0)
REVERT: C  125 GLU cc_start: 0.8038 (tt0) cc_final: 0.7665 (tt0)
REVERT: E  120 SER cc_start: 0.8270 (t) cc_final: 0.8034 (p)
REVERT: H   31 ASP cc_start: 0.8484 (p0) cc_final: 0.8225 (p0)
REVERT: H   63 GLU cc_start: 0.7145 (pm20) cc_final: 0.6715 (mm-30)
REVERT: G  169 LYS cc_start: 0.6457 (mmtp) cc_final: 0.6013 (mtpt)
  outliers start: 9
  outliers final: 6
  residues processed: 86
  average time/residue: 0.2449
  time to fit residues: 29.2255
Evaluate side-chains
  77 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
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 H residue   65 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 42 optimal weight:    0.3980
   chunk 88 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.133153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.098226 restraints weight = 18153.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.39
r_work: 0.3195 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2501

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= 0.146
  Angle     :  0.517   7.616  16301  Z= 0.313
  Chirality :  0.032   0.131   1891
  Planarity :  0.003   0.044   1211
  Dihedral  : 29.432 167.723   3430
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.52 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.90 (0.30), residues: 748
  helix:  2.36 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.07 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS D  55 
 PHE   0.028   0.002   PHE G 152 
 TYR   0.018   0.001   TYR H  81 
 ARG   0.007   0.000   ARG F  37 

Details of bonding type rmsd
  link_TRANS           : bond        0.00069 (    4)
  link_TRANS           : angle       0.19559 (   12)
  hydrogen bonds       : bond        0.03778 (  641)
  hydrogen bonds       : angle       2.56602 ( 1628)
  covalent geometry    : bond        0.00314 (11312)
  covalent geometry    : angle       0.51740 (16289)

*********************** 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
  90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.781 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9315 (t) cc_final: 0.8992 (p)
REVERT: A  128 ASN cc_start: 0.7427 (t0) cc_final: 0.6585 (t0)
REVERT: D  104 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7235 (tmtt)
REVERT: C  118 GLN cc_start: 0.8696 (mt0) cc_final: 0.8357 (mt0)
REVERT: C  125 GLU cc_start: 0.8147 (tt0) cc_final: 0.7710 (tt0)
REVERT: C  153 MET cc_start: 0.8680 (mmm) cc_final: 0.8465 (mmm)
REVERT: E  120 SER cc_start: 0.8257 (t) cc_final: 0.7979 (p)
REVERT: E  172 MET cc_start: 0.8309 (ttm) cc_final: 0.8086 (ttp)
REVERT: H   31 ASP cc_start: 0.8510 (p0) cc_final: 0.8271 (p0)
REVERT: G  169 LYS cc_start: 0.6688 (mmtp) cc_final: 0.6220 (mtpt)
  outliers start: 10
  outliers final: 6
  residues processed: 87
  average time/residue: 0.2325
  time to fit residues: 28.6754
Evaluate side-chains
  82 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  100 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  104 LYS
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain H residue   59 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 81 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.128586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.093495 restraints weight = 17845.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.29
r_work: 0.3128 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2883

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= 0.198
  Angle     :  0.568   6.881  16301  Z= 0.337
  Chirality :  0.035   0.157   1891
  Planarity :  0.003   0.038   1211
  Dihedral  : 29.561 168.650   3430
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.36 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.30), residues: 748
  helix:  2.38 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.91 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  55 
 PHE   0.035   0.003   PHE G 152 
 TYR   0.024   0.002   TYR H  81 
 ARG   0.007   0.001   ARG F  37 

Details of bonding type rmsd
  link_TRANS           : bond        0.00059 (    4)
  link_TRANS           : angle       0.16797 (   12)
  hydrogen bonds       : bond        0.04202 (  641)
  hydrogen bonds       : angle       2.72778 ( 1628)
  covalent geometry    : bond        0.00446 (11312)
  covalent geometry    : angle       0.56863 (16289)

*********************** 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
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.812 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9308 (t) cc_final: 0.8973 (p)
REVERT: B   71 MET cc_start: 0.8828 (ttp) cc_final: 0.8543 (tmm)
REVERT: D   16 ASN cc_start: 0.6760 (OUTLIER) cc_final: 0.6489 (p0)
REVERT: C  150 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: E  146 GLU cc_start: 0.8292 (tp30) cc_final: 0.8039 (tp30)
REVERT: H   31 ASP cc_start: 0.8551 (p0) cc_final: 0.8322 (p0)
REVERT: G  169 LYS cc_start: 0.6824 (mmtp) cc_final: 0.6430 (mtpt)
  outliers start: 13
  outliers final: 5
  residues processed: 85
  average time/residue: 0.2330
  time to fit residues: 28.5431
Evaluate side-chains
  76 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 E residue  138 SER
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   61 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3819 r_free = 0.3819 target = 0.129181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.094350 restraints weight = 18072.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.30
r_work: 0.3144 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11316  Z= 0.164
  Angle     :  0.535   6.380  16301  Z= 0.321
  Chirality :  0.033   0.147   1891
  Planarity :  0.003   0.038   1211
  Dihedral  : 29.526 168.745   3430
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 14.52 %
    Favored  : 83.64 %
  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:  2.18 (0.30), residues: 748
  helix:  2.55 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.87 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  55 
 PHE   0.031   0.002   PHE G 152 
 TYR   0.023   0.001   TYR H  81 
 ARG   0.005   0.000   ARG C 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00072 (    4)
  link_TRANS           : angle       0.13527 (   12)
  hydrogen bonds       : bond        0.03908 (  641)
  hydrogen bonds       : angle       2.60224 ( 1628)
  covalent geometry    : bond        0.00363 (11312)
  covalent geometry    : angle       0.53515 (16289)

*********************** 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
  93 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.806 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9315 (t) cc_final: 0.8973 (p)
REVERT: B   71 MET cc_start: 0.8697 (ttp) cc_final: 0.8424 (tmm)
REVERT: A  186 GLU cc_start: 0.7502 (tt0) cc_final: 0.7210 (mt-10)
REVERT: D   16 ASN cc_start: 0.6693 (OUTLIER) cc_final: 0.6366 (p0)
REVERT: C  118 GLN cc_start: 0.8720 (mt0) cc_final: 0.8314 (mt0)
REVERT: C  150 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: E  146 GLU cc_start: 0.8200 (tp30) cc_final: 0.7939 (tp30)
REVERT: E  172 MET cc_start: 0.8253 (ttm) cc_final: 0.8002 (ttp)
REVERT: H   31 ASP cc_start: 0.8517 (p0) cc_final: 0.8292 (p0)
REVERT: G  169 LYS cc_start: 0.6615 (mmtp) cc_final: 0.6208 (mtpt)
  outliers start: 11
  outliers final: 8
  residues processed: 89
  average time/residue: 0.2287
  time to fit residues: 29.8818
Evaluate side-chains
  86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain A residue  185 LEU
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 E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   61 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** E 128 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 = 0.3804 r_free = 0.3804 target = 0.127998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.093115 restraints weight = 18274.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.29
r_work: 0.3125 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11316  Z= 0.182
  Angle     :  0.551   6.231  16301  Z= 0.328
  Chirality :  0.034   0.163   1891
  Planarity :  0.003   0.041   1211
  Dihedral  : 29.542 168.933   3430
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.69 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.30), residues: 748
  helix:  2.53 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.87 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  55 
 PHE   0.035   0.003   PHE G 152 
 TYR   0.024   0.002   TYR H  81 
 ARG   0.005   0.000   ARG F  37 

Details of bonding type rmsd
  link_TRANS           : bond        0.00074 (    4)
  link_TRANS           : angle       0.15284 (   12)
  hydrogen bonds       : bond        0.04025 (  641)
  hydrogen bonds       : angle       2.65051 ( 1628)
  covalent geometry    : bond        0.00410 (11312)
  covalent geometry    : angle       0.55123 (16289)

*********************** 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
  87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.913 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9325 (t) cc_final: 0.9018 (p)
REVERT: B   71 MET cc_start: 0.8709 (ttp) cc_final: 0.8440 (tmm)
REVERT: A  128 ASN cc_start: 0.7419 (t0) cc_final: 0.6945 (t0)
REVERT: C  118 GLN cc_start: 0.8708 (mt0) cc_final: 0.8298 (mt0)
REVERT: C  150 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: E  146 GLU cc_start: 0.8207 (tp30) cc_final: 0.7958 (tp30)
REVERT: E  172 MET cc_start: 0.8284 (ttm) cc_final: 0.8026 (ttp)
REVERT: H   31 ASP cc_start: 0.8528 (p0) cc_final: 0.8307 (p0)
REVERT: G  169 LYS cc_start: 0.6722 (mmtp) cc_final: 0.6377 (mtpt)
  outliers start: 12
  outliers final: 11
  residues processed: 82
  average time/residue: 0.2254
  time to fit residues: 26.8633
Evaluate side-chains
  84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
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  195 VAL
Chi-restraints excluded: chain G residue  197 SER
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 88 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 95 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 66 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3753 r_free = 0.3753 target = 0.124107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.089201 restraints weight = 18037.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.24
r_work: 0.3056 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.3749

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= 0.227
  Angle     :  0.610   7.345  16301  Z= 0.356
  Chirality :  0.037   0.182   1891
  Planarity :  0.004   0.041   1211
  Dihedral  : 29.809 170.326   3430
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.86 %
    Favored  : 82.64 %
  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:  1.95 (0.31), residues: 748
  helix:  2.33 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.85 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  55 
 PHE   0.049   0.003   PHE G 152 
 TYR   0.039   0.002   TYR H  81 
 ARG   0.004   0.001   ARG C 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00066 (    4)
  link_TRANS           : angle       0.17857 (   12)
  hydrogen bonds       : bond        0.04626 (  641)
  hydrogen bonds       : angle       2.88500 ( 1628)
  covalent geometry    : bond        0.00522 (11312)
  covalent geometry    : angle       0.60986 (16289)

*********************** 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
  88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.772 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9311 (t) cc_final: 0.8947 (p)
REVERT: B   71 MET cc_start: 0.8752 (ttp) cc_final: 0.8519 (tmm)
REVERT: A  128 ASN cc_start: 0.7396 (t0) cc_final: 0.7143 (t0)
REVERT: D   16 ASN cc_start: 0.6789 (OUTLIER) cc_final: 0.6544 (p0)
REVERT: F   89 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8373 (tm-30)
REVERT: E  172 MET cc_start: 0.8227 (ttm) cc_final: 0.7991 (ttp)
REVERT: H   16 ASN cc_start: 0.6088 (OUTLIER) cc_final: 0.5773 (p0)
REVERT: H   31 ASP cc_start: 0.8528 (p0) cc_final: 0.8318 (p0)
REVERT: G  169 LYS cc_start: 0.6850 (mmtp) cc_final: 0.6539 (mtpt)
  outliers start: 15
  outliers final: 12
  residues processed: 82
  average time/residue: 0.2347
  time to fit residues: 28.2825
Evaluate side-chains
  84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  100 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 E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
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  195 VAL
Chi-restraints excluded: chain G residue  197 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 82 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.1788

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.126165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.091394 restraints weight = 18090.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.25
r_work: 0.3092 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11316  Z= 0.168
  Angle     :  0.556   6.676  16301  Z= 0.331
  Chirality :  0.034   0.161   1891
  Planarity :  0.003   0.040   1211
  Dihedral  : 29.716 170.209   3430
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.03 %
    Favored  : 82.80 %
  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:  2.18 (0.31), residues: 748
  helix:  2.52 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.79 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  55 
 PHE   0.040   0.003   PHE G 152 
 TYR   0.028   0.002   TYR H  81 
 ARG   0.005   0.000   ARG C 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00055 (    4)
  link_TRANS           : angle       0.15801 (   12)
  hydrogen bonds       : bond        0.04071 (  641)
  hydrogen bonds       : angle       2.65795 ( 1628)
  covalent geometry    : bond        0.00373 (11312)
  covalent geometry    : angle       0.55650 (16289)

*********************** 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
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 1.430 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9371 (t) cc_final: 0.9021 (p)
REVERT: B   71 MET cc_start: 0.8619 (ttp) cc_final: 0.8412 (tmm)
REVERT: A  128 ASN cc_start: 0.7259 (t0) cc_final: 0.6987 (t0)
REVERT: C  118 GLN cc_start: 0.8710 (mt0) cc_final: 0.8268 (mt0)
REVERT: F   89 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8387 (tm-30)
REVERT: E  172 MET cc_start: 0.8173 (ttm) cc_final: 0.7929 (ttp)
REVERT: H   31 ASP cc_start: 0.8486 (p0) cc_final: 0.8274 (p0)
REVERT: G  169 LYS cc_start: 0.6648 (mmtp) cc_final: 0.6262 (mtpt)
  outliers start: 13
  outliers final: 11
  residues processed: 82
  average time/residue: 0.2929
  time to fit residues: 34.9433
Evaluate side-chains
  84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 2.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain D residue   24 MET
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
Chi-restraints excluded: chain H residue   27 GLN
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  195 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
E 128 ASN
H  35 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.128815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.094350 restraints weight = 17954.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.26
r_work: 0.3139 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.3924

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= 0.150
  Angle     :  0.531   7.470  16301  Z= 0.317
  Chirality :  0.032   0.152   1891
  Planarity :  0.003   0.039   1211
  Dihedral  : 29.612 168.473   3430
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.86 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.39 (0.31), residues: 748
  helix:  2.72 (0.23), residues: 494
  sheet:  None (None), residues: 0
  loop : -0.81 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS D  55 
 PHE   0.036   0.002   PHE G 152 
 TYR   0.022   0.001   TYR H  81 
 ARG   0.004   0.000   ARG C 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00075 (    4)
  link_TRANS           : angle       0.17930 (   12)
  hydrogen bonds       : bond        0.03677 (  641)
  hydrogen bonds       : angle       2.50681 ( 1628)
  covalent geometry    : bond        0.00328 (11312)
  covalent geometry    : angle       0.53165 (16289)

********************** 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
  99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.848 
Fit side-chains
REVERT: B   41 SER cc_start: 0.9287 (t) cc_final: 0.8895 (p)
REVERT: A  128 ASN cc_start: 0.7248 (t0) cc_final: 0.6723 (t0)
REVERT: A  159 GLU cc_start: 0.7968 (mp0) cc_final: 0.7702 (mp0)
REVERT: C  118 GLN cc_start: 0.8693 (mt0) cc_final: 0.8287 (mt0)
REVERT: F  102 ASP cc_start: 0.8946 (t70) cc_final: 0.8509 (t0)
REVERT: E  172 MET cc_start: 0.8203 (ttm) cc_final: 0.7966 (ttp)
REVERT: G  169 LYS cc_start: 0.6482 (mmtp) cc_final: 0.6053 (mtpt)
  outliers start: 12
  outliers final: 9
  residues processed: 92
  average time/residue: 0.2370
  time to fit residues: 30.9718
Evaluate side-chains
  89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  100 THR
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain E residue  138 SER
Chi-restraints excluded: chain E residue  142 ILE
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  195 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 95 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.127856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.093283 restraints weight = 17963.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.26
r_work: 0.3133 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11316  Z= 0.158
  Angle     :  0.540   7.461  16301  Z= 0.320
  Chirality :  0.033   0.150   1891
  Planarity :  0.003   0.039   1211
  Dihedral  : 29.619 168.430   3430
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 16.36 %
    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:  2.36 (0.31), residues: 748
  helix:  2.65 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -0.75 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  55 
 PHE   0.038   0.002   PHE G 152 
 TYR   0.024   0.002   TYR H  81 
 ARG   0.004   0.000   ARG B  37 

Details of bonding type rmsd
  link_TRANS           : bond        0.00079 (    4)
  link_TRANS           : angle       0.17130 (   12)
  hydrogen bonds       : bond        0.03731 (  641)
  hydrogen bonds       : angle       2.50694 ( 1628)
  covalent geometry    : bond        0.00350 (11312)
  covalent geometry    : angle       0.54005 (16289)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4732.86 seconds
wall clock time: 83 minutes 43.45 seconds (5023.45 seconds total)