Starting phenix.real_space_refine
on Sat May 10 22:35:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u4v_41899/05_2025/8u4v_41899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u4v_41899/05_2025/8u4v_41899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u4v_41899/05_2025/8u4v_41899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u4v_41899/05_2025/8u4v_41899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u4v_41899/05_2025/8u4v_41899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u4v_41899/05_2025/8u4v_41899.cif"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4212      2.51       5
     N    1102      2.21       5
     O    1292      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6637
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1324
          Classifications: {'peptide': 180}
          Link IDs: {'PTRANS': 4, 'TRANS': 175}
    Chain: "B"
      Number of atoms: 970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 970
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
          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: "L"
      Number of atoms: 1620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1620
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202}
    Chain: "H"
      Number of atoms: 1735
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 228, 1724
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215}
      Conformer: "B"
        Number of residues, atoms: 228, 1724
          Classifications: {'peptide': 228}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215}
          bond proxies already assigned to first conformer: 1761
    Chain: "K"
      Number of atoms: 916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 916
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "H"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'AV0': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 4.82, per 1000 atoms: 0.73
  Number of scatterers: 6637
  At special positions: 0
  Unit cell: (77.964, 96.12, 129.228, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1292      8.00
     N    1102      7.00
     C    4212      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  54 " - pdb=" SG  CYS A  64 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  48 " - pdb=" SG  CYS L 113 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 159 " - pdb=" SG  CYS L 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  48 " - pdb=" SG  CYS H 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 180 " - pdb=" SG  CYS H 236 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.44
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1588

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 17 sheets defined
      20.6% alpha, 38.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 27
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.600A  pdb=" N   LEU A  73 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.602A  pdb=" N   ALA A  79 " --> pdb=" O   GLN A  75 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ALA A  80 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 149
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 161 through 183
      removed outlier: 3.734A  pdb=" N   TYR A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 217
    Processing helix  chain 'B' and resid 267 through 270
      removed outlier: 3.666A  pdb=" N   ASN B 270 " --> pdb=" O   ASN B 267 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 267 through 270'
    Processing helix  chain 'L' and resid 104 through 108
      removed outlier: 4.109A  pdb=" N   PHE L 108 " --> pdb=" O   PRO L 105 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 146 through 153
    Processing helix  chain 'L' and resid 208 through 212
    Processing helix  chain 'H' and resid 54 through 57
      removed outlier: 3.636A  pdb=" N   SER H  57 " --> pdb=" O   ASN H  54 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 54 through 57'
    Processing helix  chain 'H' and resid 113 through 117
    Processing helix  chain 'H' and resid 130 through 137
      removed outlier: 3.588A  pdb=" N   LEU H 135 " --> pdb=" O   TRP H 131 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 196 through 198
      No H-bonds generated for 'chain 'H' and resid 196 through 198'
    Processing helix  chain 'H' and resid 225 through 229
      removed outlier: 3.531A  pdb=" N   LEU H 229 " --> pdb=" O   SER H 226 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 53 through 57
      removed outlier: 4.147A  pdb=" N   GLY K  57 " --> pdb=" O   SER K  54 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66
    Processing sheet with id=AA2, first strand: chain 'B' and resid 205 through 210
      removed outlier: 7.133A  pdb=" N   ALA B 205 " --> pdb=" O   ASN B 239 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   HIS B 241 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLU B 207 " --> pdb=" O   HIS B 241 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   THR B 243 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   LEU B 209 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   SER B 265 " --> pdb=" O   LYS B 273 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   LYS B 273 " --> pdb=" O   SER B 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 227
      removed outlier: 3.912A  pdb=" N   GLN B 249 " --> pdb=" O   LEU B 291 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   HIS B 285 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 29 through 32
    Processing sheet with id=AA5, first strand: chain 'L' and resid 35 through 38
      removed outlier: 6.113A  pdb=" N   GLN L  62 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   LEU L  71 " --> pdb=" O   GLN L  62 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 35 through 38
    Processing sheet with id=AA7, first strand: chain 'L' and resid 139 through 143
      removed outlier: 5.495A  pdb=" N   TYR L 198 " --> pdb=" O   ASN L 163 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 169 through 174
    Processing sheet with id=AA9, first strand: chain 'H' and resid 29 through 33
    Processing sheet with id=AB1, first strand: chain 'H' and resid 37 through 38
      removed outlier: 4.214A  pdb=" N   TRP H 125 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
      removed outlier: 5.889A  pdb=" N   TYR H  59 " --> pdb=" O   TRP H 125 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   ARG H  64 " --> pdb=" O   TRP H  73 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   TRP H  73 " --> pdb=" O   ARG H  64 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 37 through 38
    Processing sheet with id=AB3, first strand: chain 'H' and resid 161 through 164
      removed outlier: 3.584A  pdb=" N   SER H 220 " --> pdb=" O   CYS H 180 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASP H 184 " --> pdb=" O   TYR H 216 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   TYR H 216 " --> pdb=" O   ASP H 184 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 161 through 164
      removed outlier: 3.584A  pdb=" N   SER H 220 " --> pdb=" O   CYS H 180 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASP H 184 " --> pdb=" O   TYR H 216 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   TYR H 216 " --> pdb=" O   ASP H 184 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 191 through 194
      removed outlier: 4.792A  pdb=" N   TYR H 234 " --> pdb=" O   VAL H 251 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'K' and resid 3 through 6
      removed outlier: 6.055A  pdb=" N   GLY K  16 " --> pdb=" O   SER K  85 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'K' and resid 59 through 60
      removed outlier: 5.532A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA K  33 " --> pdb=" O   ASP K  99 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'K' and resid 92 through 93

    335 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 1.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1464
        1.33 -     1.45: 1560
        1.45 -     1.57: 3717
        1.57 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 6785
  Sorted by residual:
  bond pdb=" N   GLY K  10 "
       pdb=" CA  GLY K  10 "
    ideal  model  delta    sigma   weight residual
    1.448  1.477 -0.029 9.20e-03 1.18e+04 9.94e+00
  bond pdb=" N   VAL K  50 "
       pdb=" CA  VAL K  50 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.15e-02 7.56e+03 9.27e+00
  bond pdb=" CCJ AV0 H 301 "
       pdb=" OBV AV0 H 301 "
    ideal  model  delta    sigma   weight residual
    1.374  1.431 -0.057 2.00e-02 2.50e+03 8.11e+00
  bond pdb=" CA  SER L  35 "
       pdb=" CB  SER L  35 "
    ideal  model  delta    sigma   weight residual
    1.533  1.489  0.044 1.66e-02 3.63e+03 7.10e+00
  bond pdb=" N   ILE K  29 "
       pdb=" CA  ILE K  29 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.35e-02 5.49e+03 7.09e+00
  ... (remaining 6780 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.71: 9215
        6.71 -    13.42: 9
       13.42 -    20.13: 2
       20.13 -    26.84: 3
       26.84 -    33.55: 2
  Bond angle restraints: 9231
  Sorted by residual:
  angle pdb=" CBR AV0 H 301 "
        pdb=" CCM AV0 H 301 "
        pdb=" CBT AV0 H 301 "
      ideal   model   delta    sigma   weight residual
     110.70   77.15   33.55 3.00e+00 1.11e-01 1.25e+02
  angle pdb=" CBQ AV0 H 301 "
        pdb=" CCM AV0 H 301 "
        pdb=" CBS AV0 H 301 "
      ideal   model   delta    sigma   weight residual
     110.52   81.56   28.96 3.00e+00 1.11e-01 9.32e+01
  angle pdb=" C   ARG K  38 "
        pdb=" CA  ARG K  38 "
        pdb=" CB  ARG K  38 "
      ideal   model   delta    sigma   weight residual
     109.38   92.93   16.45 1.80e+00 3.09e-01 8.35e+01
  angle pdb=" CBQ AV0 H 301 "
        pdb=" CCM AV0 H 301 "
        pdb=" CBR AV0 H 301 "
      ideal   model   delta    sigma   weight residual
     107.79   81.90   25.89 3.00e+00 1.11e-01 7.45e+01
  angle pdb=" CBS AV0 H 301 "
        pdb=" CCM AV0 H 301 "
        pdb=" CBT AV0 H 301 "
      ideal   model   delta    sigma   weight residual
     105.72   80.28   25.44 3.00e+00 1.11e-01 7.19e+01
  ... (remaining 9226 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.10: 3780
       23.10 -    46.19: 246
       46.19 -    69.29: 48
       69.29 -    92.38: 7
       92.38 -   115.48: 8
  Dihedral angle restraints: 4089
    sinusoidal: 1603
      harmonic: 2486
  Sorted by residual:
  dihedral pdb=" C   ARG K  38 "
           pdb=" N   ARG K  38 "
           pdb=" CA  ARG K  38 "
           pdb=" CB  ARG K  38 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -101.94  -20.66     0      2.50e+00 1.60e-01 6.83e+01
  dihedral pdb=" CB  CYS H 180 "
           pdb=" SG  CYS H 180 "
           pdb=" SG  CYS H 236 "
           pdb=" CB  CYS H 236 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -132.12   46.12     1      1.00e+01 1.00e-02 2.95e+01
  dihedral pdb=" C   ASN L 163 "
           pdb=" N   ASN L 163 "
           pdb=" CA  ASN L 163 "
           pdb=" CB  ASN L 163 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.49   11.89     0      2.50e+00 1.60e-01 2.26e+01
  ... (remaining 4086 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 985
       0.111 -    0.222: 65
       0.222 -    0.332: 4
       0.332 -    0.443: 1
       0.443 -    0.554: 1
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CA  ASN L 163 "
            pdb=" N   ASN L 163 "
            pdb=" C   ASN L 163 "
            pdb=" CB  ASN L 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.67e+00
  chirality pdb=" CA  ARG K  38 "
            pdb=" N   ARG K  38 "
            pdb=" C   ARG K  38 "
            pdb=" CB  ARG K  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.88   -0.37 2.00e-01 2.50e+01 3.44e+00
  chirality pdb=" CA  LYS A 157 "
            pdb=" N   LYS A 157 "
            pdb=" C   LYS A 157 "
            pdb=" CB  LYS A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 1053 not shown)

  Planarity restraints: 1153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  73 "   -0.039 5.00e-02 4.00e+02   5.99e-02 5.73e+00
        pdb=" N   PRO A  74 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 111 "    0.009 2.00e-02 2.50e+03   1.88e-02 3.52e+00
        pdb=" CD  GLU A 111 "   -0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 111 "    0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 111 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER L 184 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.48e+00
        pdb=" C   SER L 184 "    0.027 2.00e-02 2.50e+03
        pdb=" O   SER L 184 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLN L 185 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1150 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 108
        2.63 -     3.20: 5758
        3.20 -     3.77: 10273
        3.77 -     4.33: 14642
        4.33 -     4.90: 24696
  Nonbonded interactions: 55477
  Sorted by model distance:
  nonbonded pdb=" O   THR H 171 "
            pdb=" OG1 THR H 175 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" OG  SER L  51 "
            pdb=" OE1 GLN L  52 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ALA L 178 "
            pdb=" NE2 GLN L 180 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" CBS AV0 H 301 "
            pdb=" OBV AV0 H 301 "
     model   vdw
     2.334 2.752
  nonbonded pdb=" O   SER L 119 "
            pdb=" OG  SER H  85 "
     model   vdw
     2.354 3.040
  ... (remaining 55472 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.47 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.150
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:12.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   6791  Z= 0.377
  Angle     :  1.120  33.548   9243  Z= 0.618
  Chirality :  0.060   0.554   1056
  Planarity :  0.004   0.060   1153
  Dihedral  : 16.562 115.481   2483
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 21.47 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  0.66 (0.30), residues: 853
  helix:  2.16 (0.43), residues: 139
  sheet:  0.22 (0.29), residues: 344
  loop :  0.13 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  18 
 HIS   0.001   0.000   HIS B 285 
 PHE   0.013   0.001   PHE K  37 
 TYR   0.007   0.001   TYR H 121 
 ARG   0.003   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17811 (  314)
  hydrogen bonds       : angle       7.61977 (  891)
  SS BOND              : bond        0.00204 (    6)
  SS BOND              : angle       0.94701 (   12)
  covalent geometry    : bond        0.00567 ( 6785)
  covalent geometry    : angle       1.12051 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 145
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A   52 MET cc_start: 0.8997 (ptp) cc_final: 0.8581 (ptt)
REVERT: A   78 GLN cc_start: 0.7249 (tt0) cc_final: 0.6797 (mt0)
REVERT: B  250 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7697 (tttp)
REVERT: L   49 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7058 (ttp-110)
REVERT: L  130 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: L  147 ASP cc_start: 0.8481 (p0) cc_final: 0.8261 (m-30)
REVERT: L  210 ASP cc_start: 0.8229 (t0) cc_final: 0.7545 (t0)
REVERT: H  250 LYS cc_start: 0.8816 (tttm) cc_final: 0.8561 (tptt)
REVERT: H  252 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8906 (mt-10)
REVERT: K   89 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7310 (pm20)
REVERT: K  101 ASP cc_start: 0.8254 (t0) cc_final: 0.7948 (t0)
  outliers start: 6
  outliers final: 1
  residues processed: 149
  average time/residue: 1.2069
  time to fit residues: 188.9037
Evaluate side-chains
  114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain K residue   89 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0060
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    1.1800

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

Flipped N/Q/H residues before XYZ refinement:
B 295 GLN
L 115 GLN
** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 211 GLN
K   3 GLN
K  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.088024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.064239 restraints weight = 20684.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.2667 rms_B_bonded: 2.85
r_work: 0.2529 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2532 r_free = 0.2532    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2532 r_free = 0.2532    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8837
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   6791  Z= 0.248
  Angle     :  0.936  32.206   9243  Z= 0.399
  Chirality :  0.045   0.175   1056
  Planarity :  0.004   0.051   1153
  Dihedral  :  8.898  88.673   1056
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 20.36 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  0.99 (0.30), residues: 853
  helix:  2.30 (0.42), residues: 141
  sheet:  0.46 (0.28), residues: 353
  loop :  0.34 (0.36), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 125 
 HIS   0.003   0.001   HIS H 127 
 PHE   0.017   0.002   PHE B 261 
 TYR   0.016   0.002   TYR K 104 
 ARG   0.004   0.001   ARG K  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04379 (  314)
  hydrogen bonds       : angle       5.53770 (  891)
  SS BOND              : bond        0.00353 (    6)
  SS BOND              : angle       1.45737 (   12)
  covalent geometry    : bond        0.00594 ( 6785)
  covalent geometry    : angle       0.93529 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8448 (tt0) cc_final: 0.8125 (mt0)
REVERT: A  130 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8750 (mm)
REVERT: B  250 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8733 (tttp)
REVERT: L   49 ARG cc_start: 0.8919 (ttp-170) cc_final: 0.8481 (ttp-110)
REVERT: L   91 ARG cc_start: 0.8978 (ttt180) cc_final: 0.8744 (ttt180)
REVERT: L   95 ASP cc_start: 0.8889 (m-30) cc_final: 0.8267 (m-30)
REVERT: L  130 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8169 (mt-10)
REVERT: L  175 VAL cc_start: 0.9220 (m) cc_final: 0.8889 (t)
REVERT: H  178 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8777 (mp)
REVERT: H  239 ASN cc_start: 0.9201 (t0) cc_final: 0.8891 (t0)
REVERT: H  246 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8822 (mmmt)
REVERT: K   89 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8156 (pm20)
  outliers start: 25
  outliers final: 5
  residues processed: 124
  average time/residue: 1.2193
  time to fit residues: 158.6249
Evaluate side-chains
  110 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  130 GLU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  246 LYS
Chi-restraints excluded: chain K residue   89 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
L 185 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.088537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.065674 restraints weight = 16620.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2692 rms_B_bonded: 2.61
r_work: 0.2561 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2419 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2431
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2431 r_free = 0.2431    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2431 r_free = 0.2431    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6791  Z= 0.171
  Angle     :  0.886  32.393   9243  Z= 0.368
  Chirality :  0.043   0.144   1056
  Planarity :  0.004   0.058   1153
  Dihedral  :  7.437  89.882   1055
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 21.05 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.17 (0.30), residues: 853
  helix:  2.46 (0.44), residues: 142
  sheet:  0.59 (0.28), residues: 349
  loop :  0.43 (0.36), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 125 
 HIS   0.001   0.000   HIS B 285 
 PHE   0.012   0.001   PHE B 261 
 TYR   0.010   0.001   TYR B 264 
 ARG   0.003   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03871 (  314)
  hydrogen bonds       : angle       5.17768 (  891)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       1.09471 (   12)
  covalent geometry    : bond        0.00406 ( 6785)
  covalent geometry    : angle       0.88559 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A  130 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8782 (mm)
REVERT: B  250 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8737 (tttp)
REVERT: L   49 ARG cc_start: 0.8991 (ttp-170) cc_final: 0.8495 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8957 (m-30) cc_final: 0.8247 (m-30)
REVERT: L  130 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8436 (mt-10)
REVERT: L  175 VAL cc_start: 0.9203 (m) cc_final: 0.9002 (t)
REVERT: H  239 ASN cc_start: 0.9280 (t0) cc_final: 0.8977 (t0)
REVERT: H  246 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8895 (mmmt)
REVERT: K    4 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7780 (pp)
REVERT: K    5 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8492 (tm-30)
  outliers start: 29
  outliers final: 9
  residues processed: 124
  average time/residue: 1.2251
  time to fit residues: 159.5220
Evaluate side-chains
  115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue  201 SER
Chi-restraints excluded: chain H residue  246 LYS
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   74 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 56 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.089243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.066055 restraints weight = 17302.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.2707 rms_B_bonded: 2.67
r_work: 0.2572 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2431 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2431
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2437 r_free = 0.2437    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2437 r_free = 0.2437    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8887
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6791  Z= 0.151
  Angle     :  0.868  32.059   9243  Z= 0.360
  Chirality :  0.042   0.145   1056
  Planarity :  0.004   0.045   1153
  Dihedral  :  7.264  91.013   1052
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 20.78 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.35 (0.31), residues: 853
  helix:  2.64 (0.44), residues: 141
  sheet:  0.69 (0.28), residues: 347
  loop :  0.54 (0.36), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  18 
 HIS   0.001   0.000   HIS B 285 
 PHE   0.011   0.001   PHE B 261 
 TYR   0.013   0.001   TYR A  67 
 ARG   0.003   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03556 (  314)
  hydrogen bonds       : angle       4.97201 (  891)
  SS BOND              : bond        0.00208 (    6)
  SS BOND              : angle       1.01720 (   12)
  covalent geometry    : bond        0.00357 ( 6785)
  covalent geometry    : angle       0.86768 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8472 (tt0) cc_final: 0.8096 (mt0)
REVERT: A  130 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8804 (mm)
REVERT: B  250 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8739 (tttp)
REVERT: L   49 ARG cc_start: 0.9034 (ttp-170) cc_final: 0.8546 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8975 (m-30) cc_final: 0.8286 (m-30)
REVERT: L  120 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8809 (mp)
REVERT: H  239 ASN cc_start: 0.9288 (t0) cc_final: 0.8980 (t0)
REVERT: H  246 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8907 (mmmt)
REVERT: K    4 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7794 (pp)
  outliers start: 30
  outliers final: 14
  residues processed: 126
  average time/residue: 1.2083
  time to fit residues: 160.4973
Evaluate side-chains
  121 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  120 LEU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain L residue  238 GLU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  201 SER
Chi-restraints excluded: chain H residue  246 LYS
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   74 ASP
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  109 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.088018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.066616 restraints weight = 11549.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.2715 rms_B_bonded: 2.16
r_work: 0.2590 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2450 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2459 r_free = 0.2459    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2459 r_free = 0.2459    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   6791  Z= 0.195
  Angle     :  0.885  32.028   9243  Z= 0.371
  Chirality :  0.042   0.146   1056
  Planarity :  0.004   0.040   1153
  Dihedral  :  7.304  91.836   1052
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 21.19 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.31 (0.31), residues: 853
  helix:  2.58 (0.44), residues: 141
  sheet:  0.75 (0.29), residues: 337
  loop :  0.44 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 125 
 HIS   0.001   0.000   HIS H  61 
 PHE   0.013   0.001   PHE B 261 
 TYR   0.012   0.001   TYR K 104 
 ARG   0.003   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03720 (  314)
  hydrogen bonds       : angle       4.97859 (  891)
  SS BOND              : bond        0.00283 (    6)
  SS BOND              : angle       1.12530 (   12)
  covalent geometry    : bond        0.00468 ( 6785)
  covalent geometry    : angle       0.88464 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8530 (tt0) cc_final: 0.8194 (mt0)
REVERT: A  130 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8794 (mm)
REVERT: B  250 LYS cc_start: 0.9093 (ttpt) cc_final: 0.8734 (tttp)
REVERT: L   49 ARG cc_start: 0.8969 (ttp-170) cc_final: 0.8511 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8952 (m-30) cc_final: 0.8209 (m-30)
REVERT: L  120 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8835 (mp)
REVERT: L  190 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8499 (mm-30)
REVERT: H  239 ASN cc_start: 0.9210 (t0) cc_final: 0.8908 (t0)
REVERT: H  246 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8890 (mmmt)
REVERT: K    4 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7827 (pp)
REVERT: K   34 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8892 (mmm)
  outliers start: 29
  outliers final: 17
  residues processed: 121
  average time/residue: 1.1989
  time to fit residues: 152.5833
Evaluate side-chains
  122 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  120 LEU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain L residue  238 GLU
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  201 SER
Chi-restraints excluded: chain H residue  246 LYS
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   34 MET
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   74 ASP
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  109 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0770
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.088753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.065061 restraints weight = 20567.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.2682 rms_B_bonded: 2.87
r_work: 0.2547 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2556 r_free = 0.2556    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8821
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6791  Z= 0.159
  Angle     :  0.877  31.833   9243  Z= 0.365
  Chirality :  0.042   0.146   1056
  Planarity :  0.004   0.039   1153
  Dihedral  :  7.286  91.949   1052
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.47 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.36 (0.31), residues: 853
  helix:  2.58 (0.45), residues: 143
  sheet:  0.80 (0.29), residues: 336
  loop :  0.45 (0.36), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  18 
 HIS   0.001   0.000   HIS B 285 
 PHE   0.011   0.001   PHE B 261 
 TYR   0.010   0.001   TYR A  67 
 ARG   0.002   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03496 (  314)
  hydrogen bonds       : angle       4.91245 (  891)
  SS BOND              : bond        0.00215 (    6)
  SS BOND              : angle       0.96775 (   12)
  covalent geometry    : bond        0.00382 ( 6785)
  covalent geometry    : angle       0.87722 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 0.778 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8434 (tt0) cc_final: 0.8071 (mt0)
REVERT: A  130 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: B  250 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8695 (tttp)
REVERT: L   49 ARG cc_start: 0.8867 (ttp-170) cc_final: 0.8652 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8783 (mp)
REVERT: L  190 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8374 (mm-30)
REVERT: K    4 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7806 (pp)
REVERT: K   34 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8801 (mmm)
  outliers start: 28
  outliers final: 14
  residues processed: 121
  average time/residue: 1.2172
  time to fit residues: 154.9254
Evaluate side-chains
  121 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  120 LEU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   34 MET
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  109 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.088479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.065987 restraints weight = 14117.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2704 rms_B_bonded: 2.42
r_work: 0.2576 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2433 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2440
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2440 r_free = 0.2440    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2440 r_free = 0.2440    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2440
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6791  Z= 0.182
  Angle     :  0.885  31.818   9243  Z= 0.370
  Chirality :  0.042   0.147   1056
  Planarity :  0.004   0.040   1153
  Dihedral  :  7.308  92.069   1052
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.75 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.35 (0.31), residues: 853
  helix:  2.58 (0.44), residues: 142
  sheet:  0.77 (0.29), residues: 337
  loop :  0.48 (0.36), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 125 
 HIS   0.001   0.000   HIS H  61 
 PHE   0.013   0.001   PHE B 261 
 TYR   0.014   0.001   TYR L 217 
 ARG   0.003   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03605 (  314)
  hydrogen bonds       : angle       4.89755 (  891)
  SS BOND              : bond        0.00265 (    6)
  SS BOND              : angle       1.06653 (   12)
  covalent geometry    : bond        0.00438 ( 6785)
  covalent geometry    : angle       0.88492 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   61 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8662 (tt0)
REVERT: A   75 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7033 (tm-30)
REVERT: A   78 GLN cc_start: 0.8537 (tt0) cc_final: 0.8200 (mt0)
REVERT: A  130 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8778 (mm)
REVERT: B  250 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8692 (tttp)
REVERT: L   49 ARG cc_start: 0.9004 (ttp-170) cc_final: 0.8753 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8778 (mp)
REVERT: K    4 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7827 (pp)
REVERT: K   34 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8989 (mmm)
  outliers start: 28
  outliers final: 16
  residues processed: 114
  average time/residue: 1.2166
  time to fit residues: 145.8222
Evaluate side-chains
  118 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   61 GLN
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  120 LEU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue   37 LEU
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain H residue  201 SER
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   11 LEU
Chi-restraints excluded: chain K residue   34 MET
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  109 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0980
   chunk 36 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
K  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.089009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.066612 restraints weight = 14658.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 2.43
r_work: 0.2585 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2448 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2448
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2460
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2460 r_free = 0.2460    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2460 r_free = 0.2460    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2460
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6791  Z= 0.156
  Angle     :  0.878  31.625   9243  Z= 0.365
  Chirality :  0.042   0.147   1056
  Planarity :  0.004   0.040   1153
  Dihedral  :  7.255  91.968   1052
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.88 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.42 (0.31), residues: 853
  helix:  2.62 (0.45), residues: 142
  sheet:  0.85 (0.29), residues: 336
  loop :  0.50 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  18 
 HIS   0.002   0.000   HIS H 127 
 PHE   0.011   0.001   PHE B 261 
 TYR   0.011   0.001   TYR L 217 
 ARG   0.002   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03434 (  314)
  hydrogen bonds       : angle       4.81127 (  891)
  SS BOND              : bond        0.00216 (    6)
  SS BOND              : angle       0.95012 (   12)
  covalent geometry    : bond        0.00374 ( 6785)
  covalent geometry    : angle       0.87740 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7548 (tm-30) cc_final: 0.7036 (tm-30)
REVERT: A   78 GLN cc_start: 0.8533 (tt0) cc_final: 0.8264 (mt0)
REVERT: A  130 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8801 (mm)
REVERT: B  250 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8717 (tttp)
REVERT: L   49 ARG cc_start: 0.8968 (ttp-170) cc_final: 0.8732 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8812 (mp)
REVERT: K    4 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7851 (pp)
  outliers start: 27
  outliers final: 15
  residues processed: 118
  average time/residue: 1.1907
  time to fit residues: 147.6966
Evaluate side-chains
  118 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  120 LEU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain H residue  201 SER
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   43 LYS
Chi-restraints excluded: chain K residue   62 ASP
Chi-restraints excluded: chain K residue   83 MET
Chi-restraints excluded: chain K residue  109 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    0.0870
   chunk 14 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 65 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
K  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.089353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.066484 restraints weight = 16588.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 2.58
r_work: 0.2581 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2441 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2441
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2452 r_free = 0.2452    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2452 r_free = 0.2452    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6791  Z= 0.145
  Angle     :  0.879  31.599   9243  Z= 0.365
  Chirality :  0.042   0.147   1056
  Planarity :  0.004   0.039   1153
  Dihedral  :  7.247  91.648   1052
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.16 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.41 (0.31), residues: 853
  helix:  2.62 (0.45), residues: 142
  sheet:  0.81 (0.29), residues: 338
  loop :  0.51 (0.36), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  18 
 HIS   0.001   0.000   HIS H  61 
 PHE   0.011   0.001   PHE B 316 
 TYR   0.012   0.001   TYR K 110 
 ARG   0.002   0.000   ARG K  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 (  314)
  hydrogen bonds       : angle       4.77181 (  891)
  SS BOND              : bond        0.00217 (    6)
  SS BOND              : angle       0.89432 (   12)
  covalent geometry    : bond        0.00347 ( 6785)
  covalent geometry    : angle       0.87884 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7142 (tm-30)
REVERT: A   78 GLN cc_start: 0.8517 (tt0) cc_final: 0.8220 (mt0)
REVERT: A  130 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8765 (mm)
REVERT: B  250 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8746 (tttp)
REVERT: L   49 ARG cc_start: 0.8991 (ttp-170) cc_final: 0.8762 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8820 (mp)
REVERT: K    4 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7881 (pp)
REVERT: K   89 GLU cc_start: 0.8974 (pm20) cc_final: 0.8751 (pm20)
  outliers start: 19
  outliers final: 12
  residues processed: 115
  average time/residue: 1.1879
  time to fit residues: 143.6230
Evaluate side-chains
  116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain B residue  235 THR
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  120 LEU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain H residue  201 SER
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   43 LYS
Chi-restraints excluded: chain K residue   83 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 3 optimal weight:    0.2980
   chunk 48 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 71 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0870
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.090434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.066669 restraints weight = 22538.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 2.93
r_work: 0.2576 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6791  Z= 0.126
  Angle     :  0.872  31.469   9243  Z= 0.360
  Chirality :  0.041   0.147   1056
  Planarity :  0.003   0.039   1153
  Dihedral  :  7.181  91.129   1052
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.58 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.47 (0.31), residues: 853
  helix:  2.71 (0.45), residues: 141
  sheet:  0.91 (0.29), residues: 329
  loop :  0.49 (0.35), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  18 
 HIS   0.001   0.000   HIS B 285 
 PHE   0.009   0.001   PHE B 261 
 TYR   0.011   0.001   TYR K  60 
 ARG   0.002   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03184 (  314)
  hydrogen bonds       : angle       4.67693 (  891)
  SS BOND              : bond        0.00148 (    6)
  SS BOND              : angle       0.79483 (   12)
  covalent geometry    : bond        0.00299 ( 6785)
  covalent geometry    : angle       0.87195 ( 9231)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.795 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7049 (tm-30)
REVERT: A   78 GLN cc_start: 0.8417 (tt0) cc_final: 0.8158 (mt0)
REVERT: A  130 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8671 (mm)
REVERT: B  250 LYS cc_start: 0.9015 (ttpt) cc_final: 0.8696 (tttp)
REVERT: L   49 ARG cc_start: 0.8907 (ttp-170) cc_final: 0.8702 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8772 (mp)
REVERT: K    4 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7779 (pp)
REVERT: K   62 ASP cc_start: 0.8662 (m-30) cc_final: 0.8415 (t0)
REVERT: K   89 GLU cc_start: 0.8633 (pm20) cc_final: 0.7940 (pp20)
  outliers start: 19
  outliers final: 11
  residues processed: 116
  average time/residue: 1.1445
  time to fit residues: 139.5480
Evaluate side-chains
  115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain L residue   27 ILE
Chi-restraints excluded: chain L residue  120 LEU
Chi-restraints excluded: chain L residue  204 LEU
Chi-restraints excluded: chain L residue  230 VAL
Chi-restraints excluded: chain H residue   38 VAL
Chi-restraints excluded: chain H residue  109 MET
Chi-restraints excluded: chain H residue  201 SER
Chi-restraints excluded: chain H residue  249 LYS
Chi-restraints excluded: chain K residue    2 VAL
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   43 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    0.0970
   chunk 70 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0370
   chunk 32 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 29 optimal weight:    0.2980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.3256

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
K  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.091182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.069081 restraints weight = 14171.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 2.40
r_work: 0.2635 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2494 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2494
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2501
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2501 r_free = 0.2501    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2501 r_free = 0.2501    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.2669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6791  Z= 0.116
  Angle     :  0.870  31.396   9243  Z= 0.359
  Chirality :  0.041   0.146   1056
  Planarity :  0.004   0.040   1153
  Dihedral  :  7.134  90.549   1052
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.41 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    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:  1.51 (0.31), residues: 853
  helix:  2.74 (0.45), residues: 141
  sheet:  0.96 (0.29), residues: 330
  loop :  0.50 (0.35), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  18 
 HIS   0.001   0.000   HIS L 214 
 PHE   0.009   0.001   PHE B 316 
 TYR   0.009   0.001   TYR A  67 
 ARG   0.002   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  314)
  hydrogen bonds       : angle       4.58872 (  891)
  SS BOND              : bond        0.00134 (    6)
  SS BOND              : angle       0.72076 (   12)
  covalent geometry    : bond        0.00272 ( 6785)
  covalent geometry    : angle       0.86997 ( 9231)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5505.82 seconds
wall clock time: 95 minutes 35.07 seconds (5735.07 seconds total)