Starting phenix.real_space_refine
on Fri Jun  6 01:42:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u4v_41899/06_2025/8u4v_41899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u4v_41899/06_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_41899/06_2025/8u4v_41899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u4v_41899/06_2025/8u4v_41899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u4v_41899/06_2025/8u4v_41899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u4v_41899/06_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.22, per 1000 atoms: 1.09
  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: 2.45
  Conformation dependent library (CDL) restraints added in 1.3 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: 0.90
  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: 2.23

  Time building geometry restraints manager: 2.14 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:             305.590
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     25.420
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:20.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  351.770
-------------------------------------------------------------------------------
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  : 0.815 
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: 1.3777
  time to fit residues: 215.2673
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  : 0.795 
-------------------------------------------------------------------------------
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 = 20684.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.2667 rms_B_bonded: 2.85
r_work: 0.2529 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2389 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2389
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2396
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2396 r_free = 0.2396    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2396 r_free = 0.2396    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2396
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
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  : 0.732 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8551 (tt0) cc_final: 0.8226 (mt0)
REVERT: A  130 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8825 (mm)
REVERT: B  250 LYS cc_start: 0.9121 (ttpt) cc_final: 0.8797 (tttp)
REVERT: L   49 ARG cc_start: 0.9086 (ttp-170) cc_final: 0.8642 (ttp-110)
REVERT: L   91 ARG cc_start: 0.9096 (ttt180) cc_final: 0.8862 (ttt180)
REVERT: L   95 ASP cc_start: 0.8977 (m-30) cc_final: 0.8450 (m-30)
REVERT: L  130 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8468 (mt-10)
REVERT: L  175 VAL cc_start: 0.9255 (m) cc_final: 0.8890 (t)
REVERT: H  178 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8814 (mp)
REVERT: H  239 ASN cc_start: 0.9327 (t0) cc_final: 0.9027 (t0)
REVERT: H  246 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8896 (mmmt)
REVERT: K   89 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8303 (pm20)
  outliers start: 25
  outliers final: 5
  residues processed: 124
  average time/residue: 1.2876
  time to fit residues: 167.6369
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  : 0.765 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 68 optimal weight:    0.4980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3124 r_free = 0.3124 target = 0.088580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.065723 restraints weight = 16627.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.2697 rms_B_bonded: 2.61
r_work: 0.2566 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2425 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2425
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2432 r_free = 0.2432    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 = 0.2432 r_free = 0.2432    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6791  Z= 0.168
  Angle     :  0.883  32.388   9243  Z= 0.367
  Chirality :  0.043   0.144   1056
  Planarity :  0.004   0.059   1153
  Dihedral  :  7.419  89.864   1055
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 21.33 %
    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:  1.18 (0.30), residues: 853
  helix:  2.47 (0.44), residues: 142
  sheet:  0.60 (0.28), residues: 349
  loop :  0.44 (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 241 
 PHE   0.011   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        0.03852 (  314)
  hydrogen bonds       : angle       5.16174 (  891)
  SS BOND              : bond        0.00209 (    6)
  SS BOND              : angle       1.07274 (   12)
  covalent geometry    : bond        0.00398 ( 6785)
  covalent geometry    : angle       0.88266 ( 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
  141 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A  130 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8782 (mm)
REVERT: B  250 LYS cc_start: 0.9124 (ttpt) cc_final: 0.8742 (tttp)
REVERT: L   49 ARG cc_start: 0.8988 (ttp-170) cc_final: 0.8477 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8957 (m-30) cc_final: 0.8214 (m-30)
REVERT: L  130 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8430 (mt-10)
REVERT: H  178 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8836 (mp)
REVERT: H  239 ASN cc_start: 0.9279 (t0) cc_final: 0.8977 (t0)
REVERT: H  246 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8893 (mmmt)
REVERT: K    4 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7780 (pp)
REVERT: K   44 GLU cc_start: 0.8723 (pm20) cc_final: 0.8498 (pm20)
  outliers start: 29
  outliers final: 9
  residues processed: 125
  average time/residue: 1.3275
  time to fit residues: 174.2304
Evaluate side-chains
  114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
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  178 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:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 3 optimal weight:    0.1980
   chunk 62 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 57 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3139 r_free = 0.3139 target = 0.089482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.066238 restraints weight = 17249.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.2709 rms_B_bonded: 2.68
r_work: 0.2573 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2432 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2432
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2439
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2439 r_free = 0.2439    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2439 r_free = 0.2439    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2439
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.2264

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= 0.151
  Angle     :  0.868  32.009   9243  Z= 0.360
  Chirality :  0.042   0.145   1056
  Planarity :  0.004   0.046   1153
  Dihedral  :  7.268  91.131   1052
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.88 %
    Favored  : 74.24 %
  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:  1.33 (0.31), residues: 853
  helix:  2.57 (0.44), residues: 142
  sheet:  0.78 (0.29), residues: 336
  loop :  0.44 (0.36), residues: 375

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        0.03539 (  314)
  hydrogen bonds       : angle       4.96811 (  891)
  SS BOND              : bond        0.00197 (    6)
  SS BOND              : angle       0.99029 (   12)
  covalent geometry    : bond        0.00361 ( 6785)
  covalent geometry    : angle       0.86800 ( 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
  137 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.738 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8482 (tt0) cc_final: 0.8111 (mt0)
REVERT: A  130 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8807 (mm)
REVERT: B  250 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8744 (tttp)
REVERT: L   49 ARG cc_start: 0.9035 (ttp-170) cc_final: 0.8545 (ttp-110)
REVERT: L   95 ASP cc_start: 0.8955 (m-30) cc_final: 0.8270 (m-30)
REVERT: L  120 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8802 (mp)
REVERT: H  239 ASN cc_start: 0.9286 (t0) cc_final: 0.8988 (t0)
REVERT: H  246 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8909 (mmmt)
REVERT: K    4 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7701 (pp)
  outliers start: 28
  outliers final: 14
  residues processed: 125
  average time/residue: 1.2168
  time to fit residues: 159.9177
Evaluate side-chains
  120 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3116 r_free = 0.3116 target = 0.088238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.066903 restraints weight = 11537.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 2.14
r_work: 0.2597 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2459 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2459
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2469 r_free = 0.2469    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2469 r_free = 0.2469    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   6791  Z= 0.193
  Angle     :  0.884  32.010   9243  Z= 0.369
  Chirality :  0.042   0.146   1056
  Planarity :  0.004   0.041   1153
  Dihedral  :  7.304  91.858   1052
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  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:  1.31 (0.31), residues: 853
  helix:  2.51 (0.44), residues: 142
  sheet:  0.78 (0.29), residues: 336
  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   0.001   HIS H  61 
 PHE   0.014   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        0.03694 (  314)
  hydrogen bonds       : angle       4.96121 (  891)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       1.14438 (   12)
  covalent geometry    : bond        0.00465 ( 6785)
  covalent geometry    : angle       0.88345 ( 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
  133 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8508 (tt0) cc_final: 0.8163 (mt0)
REVERT: A  130 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8787 (mm)
REVERT: A  157 LYS cc_start: 0.8562 (tptp) cc_final: 0.8331 (tptp)
REVERT: B  250 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8709 (tttp)
REVERT: L   49 ARG cc_start: 0.8946 (ttp-170) cc_final: 0.8708 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8814 (mp)
REVERT: L  190 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8489 (mm-30)
REVERT: H  239 ASN cc_start: 0.9198 (t0) cc_final: 0.8899 (t0)
REVERT: H  246 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8881 (mmmt)
REVERT: K    4 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7809 (pp)
  outliers start: 28
  outliers final: 15
  residues processed: 120
  average time/residue: 1.2326
  time to fit residues: 155.2775
Evaluate side-chains
  119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
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 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   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:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 12 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0670
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.3154 r_free = 0.3154 target = 0.090391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.066619 restraints weight = 20606.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.2713 rms_B_bonded: 2.89
r_work: 0.2578 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    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 = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6791  Z= 0.128
  Angle     :  0.864  31.603   9243  Z= 0.356
  Chirality :  0.041   0.145   1056
  Planarity :  0.004   0.039   1153
  Dihedral  :  7.210  91.949   1052
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 22.58 %
    Favored  : 74.10 %
  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:  1.43 (0.31), residues: 853
  helix:  2.65 (0.45), residues: 142
  sheet:  0.88 (0.29), residues: 336
  loop :  0.46 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  18 
 HIS   0.001   0.000   HIS H 127 
 PHE   0.010   0.001   PHE B 316 
 TYR   0.011   0.001   TYR L 217 
 ARG   0.003   0.000   ARG L 236 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  314)
  hydrogen bonds       : angle       4.79052 (  891)
  SS BOND              : bond        0.00148 (    6)
  SS BOND              : angle       0.83602 (   12)
  covalent geometry    : bond        0.00302 ( 6785)
  covalent geometry    : angle       0.86379 ( 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
  134 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A   78 GLN cc_start: 0.8403 (tt0) cc_final: 0.8060 (mt0)
REVERT: A  130 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8690 (mm)
REVERT: A  157 LYS cc_start: 0.8496 (tptp) cc_final: 0.8258 (tptp)
REVERT: B  250 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8679 (tttp)
REVERT: L   49 ARG cc_start: 0.8878 (ttp-170) cc_final: 0.8655 (ttp-170)
REVERT: H  239 ASN cc_start: 0.9106 (t0) cc_final: 0.8740 (t0)
REVERT: K    4 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7768 (pp)
  outliers start: 24
  outliers final: 10
  residues processed: 123
  average time/residue: 1.2563
  time to fit residues: 162.1800
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  : 0.795 
-------------------------------------------------------------------------------
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 B residue  254 LEU
Chi-restraints excluded: chain L residue   27 ILE
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  101 ASP
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:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0980
   chunk 7 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 239 ASN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.089678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.067386 restraints weight = 14001.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 2.41
r_work: 0.2603 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2462 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2462
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2467 r_free = 0.2467    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2467 r_free = 0.2467    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6791  Z= 0.151
  Angle     :  0.867  31.685   9243  Z= 0.358
  Chirality :  0.041   0.146   1056
  Planarity :  0.004   0.040   1153
  Dihedral  :  7.212  91.825   1052
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 22.16 %
    Favored  : 74.24 %
  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:  1.44 (0.31), residues: 853
  helix:  2.63 (0.45), residues: 142
  sheet:  0.90 (0.29), residues: 336
  loop :  0.47 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  18 
 HIS   0.001   0.000   HIS H  61 
 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        0.03374 (  314)
  hydrogen bonds       : angle       4.77450 (  891)
  SS BOND              : bond        0.00207 (    6)
  SS BOND              : angle       0.92624 (   12)
  covalent geometry    : bond        0.00361 ( 6785)
  covalent geometry    : angle       0.86739 ( 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
  132 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7033 (tm-30)
REVERT: A   78 GLN cc_start: 0.8515 (tt0) cc_final: 0.8184 (mt0)
REVERT: A  130 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8727 (mm)
REVERT: B  250 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8705 (tttp)
REVERT: L   49 ARG cc_start: 0.8966 (ttp-170) cc_final: 0.8721 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8786 (mp)
REVERT: H  239 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8817 (t0)
REVERT: K    4 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7810 (pp)
REVERT: K   89 GLU cc_start: 0.8946 (pm20) cc_final: 0.8732 (pm20)
  outliers start: 26
  outliers final: 13
  residues processed: 121
  average time/residue: 1.2338
  time to fit residues: 156.7728
Evaluate side-chains
  119 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
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  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  239 ASN
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   83 MET
Chi-restraints excluded: chain K residue  101 ASP
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:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
H 239 ASN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.089062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.066453 restraints weight = 14724.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 2.46
r_work: 0.2583 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2443 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2451
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2451 r_free = 0.2451    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 = 0.2451 r_free = 0.2451    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2451
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start:          0.2576

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= 0.181
  Angle     :  0.884  31.710   9243  Z= 0.369
  Chirality :  0.042   0.146   1056
  Planarity :  0.004   0.041   1153
  Dihedral  :  7.251  91.901   1052
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 22.85 %
    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:  2.59 (0.44), residues: 142
  sheet:  0.88 (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 A  18 
 HIS   0.002   0.001   HIS H 240 
 PHE   0.013   0.001   PHE B 261 
 TYR   0.012   0.001   TYR L 217 
 ARG   0.003   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03534 (  314)
  hydrogen bonds       : angle       4.80021 (  891)
  SS BOND              : bond        0.00260 (    6)
  SS BOND              : angle       1.01961 (   12)
  covalent geometry    : bond        0.00437 ( 6785)
  covalent geometry    : angle       0.88356 ( 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
  124 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.777 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7521 (tm-30) cc_final: 0.6998 (tm-30)
REVERT: A   78 GLN cc_start: 0.8528 (tt0) cc_final: 0.8207 (mt0)
REVERT: A  130 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8785 (mm)
REVERT: B  250 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8726 (tttp)
REVERT: L   49 ARG cc_start: 0.9004 (ttp-170) cc_final: 0.8764 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8780 (mp)
REVERT: H  239 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.9110 (t0)
REVERT: K    4 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7836 (pp)
  outliers start: 20
  outliers final: 13
  residues processed: 113
  average time/residue: 1.2131
  time to fit residues: 144.0705
Evaluate side-chains
  118 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
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 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  239 ASN
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   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:    0.0040
   chunk 14 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
B 295 GLN
H  39 GLN
H 239 ASN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.089555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.066592 restraints weight = 16558.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.2707 rms_B_bonded: 2.59
r_work: 0.2579 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2442 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2457
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2457 r_free = 0.2457    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 = 0.2457 r_free = 0.2457    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2457
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8892
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6791  Z= 0.146
  Angle     :  0.881  31.618   9243  Z= 0.367
  Chirality :  0.041   0.146   1056
  Planarity :  0.004   0.041   1153
  Dihedral  :  7.234  91.734   1052
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.85 %
    Favored  : 74.24 %
  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:  2.68 (0.45), residues: 141
  sheet:  0.92 (0.29), residues: 336
  loop :  0.47 (0.36), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  18 
 HIS   0.004   0.001   HIS H 240 
 PHE   0.011   0.001   PHE B 261 
 TYR   0.011   0.001   TYR A  67 
 ARG   0.003   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  314)
  hydrogen bonds       : angle       4.75992 (  891)
  SS BOND              : bond        0.00193 (    6)
  SS BOND              : angle       0.89294 (   12)
  covalent geometry    : bond        0.00350 ( 6785)
  covalent geometry    : angle       0.88128 ( 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
  125 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7071 (tm-30)
REVERT: A   78 GLN cc_start: 0.8527 (tt0) cc_final: 0.8221 (mt0)
REVERT: A  130 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8741 (mm)
REVERT: B  250 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8750 (tttp)
REVERT: L   49 ARG cc_start: 0.9002 (ttp-170) cc_final: 0.8774 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8826 (mp)
REVERT: H  239 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.9032 (t0)
REVERT: K    4 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7882 (pp)
  outliers start: 21
  outliers final: 12
  residues processed: 116
  average time/residue: 1.2146
  time to fit residues: 147.9511
Evaluate side-chains
  117 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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 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  239 ASN
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  109 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0870
   chunk 48 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0000
   chunk 74 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.4362

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 239 ASN
H 244 ASN
K  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.090310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.066105 restraints weight = 22567.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 3.03
r_work: 0.2566 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2569
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6791  Z= 0.133
  Angle     :  0.887  31.532   9243  Z= 0.371
  Chirality :  0.041   0.146   1056
  Planarity :  0.004   0.041   1153
  Dihedral  :  7.197  91.420   1052
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 23.41 %
    Favored  : 74.24 %
  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:  2.73 (0.45), residues: 141
  sheet:  1.00 (0.29), residues: 327
  loop :  0.45 (0.35), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  18 
 HIS   0.005   0.001   HIS H 240 
 PHE   0.009   0.001   PHE B 316 
 TYR   0.011   0.001   TYR A  67 
 ARG   0.002   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03283 (  314)
  hydrogen bonds       : angle       4.70606 (  891)
  SS BOND              : bond        0.00168 (    6)
  SS BOND              : angle       0.80729 (   12)
  covalent geometry    : bond        0.00319 ( 6785)
  covalent geometry    : angle       0.88711 ( 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
  120 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.759 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7011 (tm-30)
REVERT: A   78 GLN cc_start: 0.8427 (tt0) cc_final: 0.8123 (mt0)
REVERT: A  130 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8676 (mm)
REVERT: B  250 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8686 (tttp)
REVERT: L   49 ARG cc_start: 0.8917 (ttp-170) cc_final: 0.8682 (ttp-170)
REVERT: L  120 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8743 (mp)
REVERT: H  239 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8891 (t0)
REVERT: K    4 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7794 (pp)
  outliers start: 17
  outliers final: 12
  residues processed: 113
  average time/residue: 1.2423
  time to fit residues: 147.4180
Evaluate side-chains
  117 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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 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  239 ASN
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  101 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    0.0370
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0970
   chunk 32 optimal weight:    0.4980
   chunk 56 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.3856

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H 239 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 = 0.3153 r_free = 0.3153 target = 0.090494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.068471 restraints weight = 14115.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 2.35
r_work: 0.2626 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2489 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2496 r_free = 0.2496    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2496 r_free = 0.2496    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.2643

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= 0.125
  Angle     :  0.879  31.495   9243  Z= 0.365
  Chirality :  0.041   0.146   1056
  Planarity :  0.003   0.040   1153
  Dihedral  :  7.173  91.164   1052
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 23.27 %
    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:  1.52 (0.31), residues: 853
  helix:  2.73 (0.45), residues: 141
  sheet:  1.01 (0.29), residues: 327
  loop :  0.46 (0.35), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  18 
 HIS   0.003   0.001   HIS H 240 
 PHE   0.010   0.001   PHE K 103 
 TYR   0.011   0.001   TYR A  67 
 ARG   0.003   0.000   ARG K  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03233 (  314)
  hydrogen bonds       : angle       4.67098 (  891)
  SS BOND              : bond        0.00142 (    6)
  SS BOND              : angle       0.79471 (   12)
  covalent geometry    : bond        0.00298 ( 6785)
  covalent geometry    : angle       0.87944 ( 9231)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6596.06 seconds
wall clock time: 114 minutes 44.02 seconds (6884.02 seconds total)