Starting phenix.real_space_refine
on Tue Mar  3 15:14:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d73_46601/03_2026/9d73_46601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d73_46601/03_2026/9d73_46601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d73_46601/03_2026/9d73_46601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d73_46601/03_2026/9d73_46601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d73_46601/03_2026/9d73_46601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d73_46601/03_2026/9d73_46601.cif"
  }
  resolution = 3.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.012
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      26      5.16       5
     C    3965      2.51       5
     N    1080      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6311
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2202
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 15, 'TRANS': 257}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 821
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "P"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 8}
    Chain: "H"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1588
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 12, 'TRANS': 201}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1622
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 9, 'TRANS': 202}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 33
          Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 38
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   THR H 131 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  THR H 131 " occ=0.50
    residue:
      pdb=" N   GLY H 133 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY H 133 " occ=0.50
  Time building chain proxies: 1.52, per 1000 atoms: 0.24
  Number of scatterers: 6311
  At special positions: 0
  Unit cell: (71.38, 64.74, 146.91, 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      26     16.00
     O    1240      8.00
     N    1080      7.00
     C    3965      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 101 " - pdb=" SG  CYS A 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 259 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  80 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 133 " - pdb=" SG  CYS L 193 " 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: 0.49
  Conformation dependent library (CDL) restraints added in 339.3 milliseconds
  

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1506

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 17 sheets defined
      13.1% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 55
      removed outlier: 4.046A  pdb=" N   GLN A  54 " --> pdb=" O   TRP A  51 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU A  55 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 85
      removed outlier: 3.643A  pdb=" N   ARG A  79 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 149
      removed outlier: 3.711A  pdb=" N   THR A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LYS A 146 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 161
      removed outlier: 4.334A  pdb=" N   GLN A 155 " --> pdb=" O   ARG A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 175
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.828A  pdb=" N   LYS H  65 " --> pdb=" O   GLN H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.572A  pdb=" N   SER H  91 " --> pdb=" O   ASN H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 127 through 131
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'L' and resid 122 through 127
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 5.308A  pdb=" N   LEU A  32 " --> pdb=" O   VAL A  28 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   VAL A  28 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A  34 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   ASP A 114 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   TYR A 118 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   ASP A 122 " --> pdb=" O   TYR A 118 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 193
      removed outlier: 4.942A  pdb=" N   PHE A 241 " --> pdb=" O   GLY A 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193
      removed outlier: 4.942A  pdb=" N   PHE A 241 " --> pdb=" O   GLY A 207 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223
    Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11
      removed outlier: 6.101A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11
      removed outlier: 6.101A  pdb=" N   PHE B  62 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   SER B  55 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 6
    Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.401A  pdb=" N   MET H  34 " --> pdb=" O   ALA H  50 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ALA H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.337A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.337A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER H 177 " --> pdb=" O   VAL H 169 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL H 169 " --> pdb=" O   SER H 177 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 151 through 154
    Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.684A  pdb=" N   GLU L 104 " --> pdb=" O   MET L  11 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   TYR L  49 " --> pdb=" O   ARG L  53 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.684A  pdb=" N   GLU L 104 " --> pdb=" O   MET L  11 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 113 through 117
      removed outlier: 6.036A  pdb=" N   TYR L 172 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 152 through 153

    311 hydrogen bonds defined for protein.
    795 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: 0.84

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2060
        1.34 -     1.46: 1636
        1.46 -     1.58: 2737
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 6471
  Sorted by residual:
  bond pdb=" CA  GLY A  26 "
       pdb=" C   GLY A  26 "
    ideal  model  delta    sigma   weight residual
    1.518  1.509  0.009 7.30e-03 1.88e+04 1.68e+00
  bond pdb=" CB  ASN L 144 "
       pdb=" CG  ASN L 144 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.40e-01
  bond pdb=" CB  LYS H 201 "
       pdb=" CG  LYS H 201 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.39e-01
  bond pdb=" CB  GLU B  74 "
       pdb=" CG  GLU B  74 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.12e-01
  bond pdb=" CA  VAL A 249 "
       pdb=" C   VAL A 249 "
    ideal  model  delta    sigma   weight residual
    1.516  1.525 -0.009 1.11e-02 8.12e+03 7.11e-01
  ... (remaining 6466 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 8522
        1.48 -     2.95: 216
        2.95 -     4.43: 38
        4.43 -     5.90: 21
        5.90 -     7.38: 4
  Bond angle restraints: 8801
  Sorted by residual:
  angle pdb=" CB  LYS H 201 "
        pdb=" CG  LYS H 201 "
        pdb=" CD  LYS H 201 "
      ideal   model   delta    sigma   weight residual
     111.30  118.68   -7.38 2.30e+00 1.89e-01 1.03e+01
  angle pdb=" CA  GLU L 184 "
        pdb=" CB  GLU L 184 "
        pdb=" CG  GLU L 184 "
      ideal   model   delta    sigma   weight residual
     114.10  119.98   -5.88 2.00e+00 2.50e-01 8.65e+00
  angle pdb=" CA  GLU L 194 "
        pdb=" CB  GLU L 194 "
        pdb=" CG  GLU L 194 "
      ideal   model   delta    sigma   weight residual
     114.10  119.73   -5.63 2.00e+00 2.50e-01 7.92e+00
  angle pdb=" N   ARG A 239 "
        pdb=" CA  ARG A 239 "
        pdb=" CB  ARG A 239 "
      ideal   model   delta    sigma   weight residual
     113.65  109.83    3.82 1.47e+00 4.63e-01 6.77e+00
  angle pdb=" CA  LYS H 201 "
        pdb=" CB  LYS H 201 "
        pdb=" CG  LYS H 201 "
      ideal   model   delta    sigma   weight residual
     114.10  119.07   -4.97 2.00e+00 2.50e-01 6.17e+00
  ... (remaining 8796 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3248
       17.92 -    35.85: 458
       35.85 -    53.77: 116
       53.77 -    71.70: 18
       71.70 -    89.62: 13
  Dihedral angle restraints: 3853
    sinusoidal: 1499
      harmonic: 2354
  Sorted by residual:
  dihedral pdb=" CB  CYS B  25 "
           pdb=" SG  CYS B  25 "
           pdb=" SG  CYS B  80 "
           pdb=" CB  CYS B  80 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   41.43   51.57     1      1.00e+01 1.00e-02 3.63e+01
  dihedral pdb=" CA  GLN L   6 "
           pdb=" C   GLN L   6 "
           pdb=" N   THR L   7 "
           pdb=" CA  THR L   7 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.63  -25.37     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  ILE B  35 "
           pdb=" C   ILE B  35 "
           pdb=" N   GLU B  36 "
           pdb=" CA  GLU B  36 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.51   20.49     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 3850 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 571
       0.029 -    0.058: 247
       0.058 -    0.087: 68
       0.087 -    0.116: 52
       0.116 -    0.145: 11
  Chirality restraints: 949
  Sorted by residual:
  chirality pdb=" CA  ILE L 149 "
            pdb=" N   ILE L 149 "
            pdb=" C   ILE L 149 "
            pdb=" CB  ILE L 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CA  HIS B  31 "
            pdb=" N   HIS B  31 "
            pdb=" C   HIS B  31 "
            pdb=" CB  HIS B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE L  21 "
            pdb=" N   ILE L  21 "
            pdb=" C   ILE L  21 "
            pdb=" CB  ILE L  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 946 not shown)

  Planarity restraints: 1141
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 184 "   -0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO H 185 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO H 185 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO H 185 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU L 184 "    0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" C   GLU L 184 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   GLU L 184 "    0.008 2.00e-02 2.50e+03
        pdb=" N   TYR L 185 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  19 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO A  20 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A  20 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  20 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1138 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 686
        2.75 -     3.29: 6138
        3.29 -     3.82: 10516
        3.82 -     4.36: 12485
        4.36 -     4.90: 21878
  Nonbonded interactions: 51703
  Sorted by model distance:
  nonbonded pdb=" N   GLN A 255 "
            pdb=" OE1 GLN A 255 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OG  SER L  63 "
            pdb=" OG1 THR L  74 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   PRO L   8 "
            pdb=" OG1 THR L 101 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU P   2 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   ARG H  13 "
            pdb=" OG  SER H  16 "
     model   vdw
     2.245 3.040
  ... (remaining 51698 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.730
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6478  Z= 0.127
  Angle     :  0.619   7.379   8815  Z= 0.322
  Chirality :  0.041   0.145    949
  Planarity :  0.003   0.036   1141
  Dihedral  : 17.873  89.619   2326
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 32.45 %
    Favored  : 62.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.31), residues: 797
  helix:  0.73 (0.60), residues: 87
  sheet:  0.56 (0.28), residues: 351
  loop : -0.98 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 239 
 TYR   0.022   0.001   TYR L 185 
 PHE   0.008   0.001   PHE B  56 
 TRP   0.006   0.001   TRP H  36 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6471)
  covalent geometry    : angle       0.61850 ( 8801)
  SS BOND              : bond        0.00354 (    7)
  SS BOND              : angle       1.01744 (   14)
  hydrogen bonds       : bond        0.15440 (  267)
  hydrogen bonds       : angle       6.49661 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8516 (tmm) cc_final: 0.8201 (tmm)
REVERT: A  181 ARG cc_start: 0.8578 (tmm160) cc_final: 0.8225 (ttp80)
REVERT: A  260 HIS cc_start: 0.8341 (m-70) cc_final: 0.8103 (t-90)
REVERT: B   36 GLU cc_start: 0.8358 (pt0) cc_final: 0.8094 (pm20)
REVERT: B   89 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8549 (mm-40)
REVERT: H   11 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8341 (mp)
REVERT: H   13 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7685 (mmm-85)
REVERT: H   69 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7510 (mppt)
REVERT: H   96 CYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7628 (p)
REVERT: H  102 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.6745 (mp10)
REVERT: H  148 GLU cc_start: 0.8548 (tp30) cc_final: 0.7803 (tp30)
REVERT: L   38 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8605 (tt)
REVERT: L   79 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8313 (mm-30)
REVERT: L  104 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8127 (mt-10)
REVERT: L  123 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8418 (tp-100)
  outliers start: 33
  outliers final: 26
  residues processed: 126
  average time/residue: 0.0848
  time to fit residues: 13.9811
Evaluate side-chains
  129 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   42 ASN
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue   69 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  197 ASN
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue   38 LEU
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   43 SER
Chi-restraints excluded: chain L residue   46 THR
Chi-restraints excluded: chain L residue   55 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  104 GLU
Chi-restraints excluded: chain L residue  143 ILE
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
A  93 HIS
A 144 GLN
** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  21 ASN
B  83 ASN
H   6 GLN
H  35 HIS
H 164 HIS
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 209 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.110753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.074803 restraints weight = 13208.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 3.02
r_work: 0.3093 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3103 r_free = 0.3103    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6478  Z= 0.210
  Angle     :  0.635   6.741   8815  Z= 0.330
  Chirality :  0.044   0.157    949
  Planarity :  0.004   0.034   1141
  Dihedral  :  8.000  59.158    944
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  8.52 %
    Allowed  : 26.28 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.31), residues: 797
  helix:  0.24 (0.57), residues: 88
  sheet:  0.57 (0.29), residues: 345
  loop : -0.95 (0.35), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 157 
 TYR   0.022   0.002   TYR B  78 
 PHE   0.008   0.001   PHE H 146 
 TRP   0.006   0.001   TRP H  36 
 HIS   0.007   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 6471)
  covalent geometry    : angle       0.63310 ( 8801)
  SS BOND              : bond        0.00411 (    7)
  SS BOND              : angle       1.32309 (   14)
  hydrogen bonds       : bond        0.03837 (  267)
  hydrogen bonds       : angle       5.31821 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 98
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7530 (ptt-90)
REVERT: A  181 ARG cc_start: 0.8446 (tmm160) cc_final: 0.8044 (ttp80)
REVERT: A  260 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8009 (t-90)
REVERT: B   36 GLU cc_start: 0.8388 (pt0) cc_final: 0.8079 (pm20)
REVERT: B   41 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9280 (mmmm)
REVERT: B   89 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8577 (mm-40)
REVERT: H   13 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.8011 (mmm-85)
REVERT: H   46 GLU cc_start: 0.8388 (tt0) cc_final: 0.8153 (tt0)
REVERT: H   65 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8126 (mptm)
REVERT: H   96 CYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7664 (p)
REVERT: H  102 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7034 (mp10)
REVERT: H  148 GLU cc_start: 0.8670 (tp30) cc_final: 0.7979 (tp30)
REVERT: L   79 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8367 (mm-30)
REVERT: L  104 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8243 (mt-10)
REVERT: L  123 GLN cc_start: 0.8891 (tp-100) cc_final: 0.8623 (tp-100)
REVERT: L  139 TYR cc_start: 0.8095 (t80) cc_final: 0.7721 (t80)
  outliers start: 58
  outliers final: 33
  residues processed: 144
  average time/residue: 0.0843
  time to fit residues: 15.9184
Evaluate side-chains
  134 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 96
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  186 LYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  260 HIS
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   42 ASN
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  197 ASN
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  163 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 30 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.109799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.080206 restraints weight = 12915.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.90
r_work: 0.3216 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6478  Z= 0.122
  Angle     :  0.585   6.505   8815  Z= 0.303
  Chirality :  0.042   0.151    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  6.553  58.786    914
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 28.19 %
    Favored  : 65.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.31), residues: 797
  helix:  0.21 (0.57), residues: 89
  sheet:  0.70 (0.29), residues: 351
  loop : -1.03 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 157 
 TYR   0.012   0.001   TYR L 185 
 PHE   0.007   0.001   PHE B  22 
 TRP   0.006   0.001   TRP A 244 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6471)
  covalent geometry    : angle       0.58446 ( 8801)
  SS BOND              : bond        0.00308 (    7)
  SS BOND              : angle       1.03478 (   14)
  hydrogen bonds       : bond        0.03310 (  267)
  hydrogen bonds       : angle       4.90768 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 108
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8542 (tmm) cc_final: 0.8098 (tmm)
REVERT: A  181 ARG cc_start: 0.8362 (tmm160) cc_final: 0.8007 (ttp80)
REVERT: A  197 HIS cc_start: 0.8558 (t70) cc_final: 0.8344 (t70)
REVERT: A  219 ARG cc_start: 0.8907 (ttm170) cc_final: 0.8658 (ttm170)
REVERT: A  260 HIS cc_start: 0.8468 (m-70) cc_final: 0.8136 (t-90)
REVERT: B   36 GLU cc_start: 0.8300 (pt0) cc_final: 0.8028 (pm20)
REVERT: B   41 LYS cc_start: 0.9474 (mmmm) cc_final: 0.9160 (mmmm)
REVERT: B   77 GLU cc_start: 0.8169 (tp30) cc_final: 0.7947 (tp30)
REVERT: B   89 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8563 (mm-40)
REVERT: H   65 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8157 (mptm)
REVERT: H   67 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7159 (tptt)
REVERT: H   96 CYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7467 (p)
REVERT: H  148 GLU cc_start: 0.8601 (tp30) cc_final: 0.7848 (tp30)
REVERT: L  104 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8306 (mt-10)
REVERT: L  139 TYR cc_start: 0.8068 (t80) cc_final: 0.7678 (t80)
  outliers start: 42
  outliers final: 27
  residues processed: 138
  average time/residue: 0.0776
  time to fit residues: 13.9830
Evaluate side-chains
  130 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  163 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 69 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 49 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 209 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.108296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.078279 restraints weight = 12985.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.87
r_work: 0.3183 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6478  Z= 0.185
  Angle     :  0.612   6.557   8815  Z= 0.318
  Chirality :  0.043   0.148    949
  Planarity :  0.004   0.037   1141
  Dihedral  :  6.057  53.079    903
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  7.78 %
    Allowed  : 27.17 %
    Favored  : 65.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.31), residues: 797
  helix:  0.16 (0.56), residues: 88
  sheet:  0.66 (0.29), residues: 348
  loop : -1.03 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  13 
 TYR   0.012   0.001   TYR B  63 
 PHE   0.007   0.001   PHE B  56 
 TRP   0.007   0.001   TRP H  33 
 HIS   0.007   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 6471)
  covalent geometry    : angle       0.61111 ( 8801)
  SS BOND              : bond        0.00344 (    7)
  SS BOND              : angle       1.18093 (   14)
  hydrogen bonds       : bond        0.03398 (  267)
  hydrogen bonds       : angle       4.89204 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 101
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7619 (ptt-90)
REVERT: A   92 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.8977 (t)
REVERT: A  181 ARG cc_start: 0.8455 (tmm160) cc_final: 0.8053 (ttp80)
REVERT: A  219 ARG cc_start: 0.8900 (ttm170) cc_final: 0.8623 (ttm170)
REVERT: A  260 HIS cc_start: 0.8444 (OUTLIER) cc_final: 0.8035 (t-90)
REVERT: B   36 GLU cc_start: 0.8372 (pt0) cc_final: 0.8080 (pm20)
REVERT: B   41 LYS cc_start: 0.9466 (mmmm) cc_final: 0.9218 (mmmm)
REVERT: B   69 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8822 (mm-30)
REVERT: B   77 GLU cc_start: 0.8183 (tp30) cc_final: 0.7896 (tp30)
REVERT: B   89 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8567 (mm-40)
REVERT: H   39 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8108 (tt0)
REVERT: H   96 CYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7615 (p)
REVERT: H  102 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7394 (mp10)
REVERT: H  148 GLU cc_start: 0.8678 (tp30) cc_final: 0.7977 (tp30)
REVERT: L   83 MET cc_start: 0.8788 (mmt) cc_final: 0.8562 (mmt)
REVERT: L  139 TYR cc_start: 0.8061 (t80) cc_final: 0.7210 (t80)
REVERT: L  209 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8121 (t0)
  outliers start: 53
  outliers final: 32
  residues processed: 141
  average time/residue: 0.0901
  time to fit residues: 16.4774
Evaluate side-chains
  136 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 98
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   92 SER
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  186 LYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  260 HIS
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  197 ASN
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  163 THR
Chi-restraints excluded: chain L residue  205 VAL
Chi-restraints excluded: chain L residue  209 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.2980
   chunk 19 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 54 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0980
   chunk 7 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 209 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.108003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.077978 restraints weight = 13030.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.96
r_work: 0.3164 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6478  Z= 0.127
  Angle     :  0.591   6.501   8815  Z= 0.307
  Chirality :  0.043   0.197    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  5.910  53.188    903
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 27.90 %
    Favored  : 65.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.31), residues: 797
  helix:  0.22 (0.56), residues: 89
  sheet:  0.78 (0.29), residues: 348
  loop : -1.04 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  13 
 TYR   0.013   0.001   TYR L 185 
 PHE   0.007   0.001   PHE B  56 
 TRP   0.006   0.001   TRP A 244 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6471)
  covalent geometry    : angle       0.58978 ( 8801)
  SS BOND              : bond        0.00293 (    7)
  SS BOND              : angle       1.10307 (   14)
  hydrogen bonds       : bond        0.03136 (  267)
  hydrogen bonds       : angle       4.81005 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 110
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7588 (ptt-90)
REVERT: A   98 MET cc_start: 0.8550 (tmm) cc_final: 0.8036 (tmm)
REVERT: A  122 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8413 (m-30)
REVERT: A  181 ARG cc_start: 0.8503 (tmm160) cc_final: 0.8027 (ttp80)
REVERT: A  219 ARG cc_start: 0.8921 (ttm170) cc_final: 0.8615 (ttm170)
REVERT: A  260 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7998 (t-90)
REVERT: B   19 LYS cc_start: 0.8370 (pttm) cc_final: 0.8122 (pttm)
REVERT: B   21 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8343 (t0)
REVERT: B   36 GLU cc_start: 0.8318 (pt0) cc_final: 0.7997 (pm20)
REVERT: B   70 PHE cc_start: 0.8448 (p90) cc_final: 0.7143 (p90)
REVERT: B   77 GLU cc_start: 0.8174 (tp30) cc_final: 0.7838 (tp30)
REVERT: B   89 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8551 (mm-40)
REVERT: H   39 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8149 (tt0)
REVERT: H   67 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7097 (tptt)
REVERT: H   96 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7560 (p)
REVERT: H  102 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7334 (mp10)
REVERT: H  122 PHE cc_start: 0.8453 (m-80) cc_final: 0.7957 (m-80)
REVERT: H  148 GLU cc_start: 0.8648 (tp30) cc_final: 0.7927 (tp30)
REVERT: L   83 MET cc_start: 0.8765 (mmt) cc_final: 0.8531 (mmt)
REVERT: L  139 TYR cc_start: 0.8042 (t80) cc_final: 0.7040 (t80)
  outliers start: 45
  outliers final: 29
  residues processed: 144
  average time/residue: 0.0846
  time to fit residues: 15.8518
Evaluate side-chains
  136 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  260 HIS
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   21 ASN
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  197 ASN
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 32 optimal weight:    0.0670
   chunk 55 optimal weight:    6.9990
   chunk 73 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:   10.0000
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.107604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.077130 restraints weight = 12949.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.96
r_work: 0.3160 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6478  Z= 0.129
  Angle     :  0.595   6.511   8815  Z= 0.308
  Chirality :  0.042   0.147    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  5.800  54.004    903
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 27.02 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.11 (0.31), residues: 797
  helix:  0.23 (0.56), residues: 87
  sheet:  0.81 (0.29), residues: 346
  loop : -1.02 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  13 
 TYR   0.010   0.001   TYR A 113 
 PHE   0.008   0.001   PHE H 166 
 TRP   0.007   0.001   TRP A 244 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6471)
  covalent geometry    : angle       0.59360 ( 8801)
  SS BOND              : bond        0.00305 (    7)
  SS BOND              : angle       1.12209 (   14)
  hydrogen bonds       : bond        0.03046 (  267)
  hydrogen bonds       : angle       4.69024 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 108
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7657 (ptt-90)
REVERT: A   98 MET cc_start: 0.8589 (tmm) cc_final: 0.8112 (tmm)
REVERT: A  122 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8416 (m-30)
REVERT: A  181 ARG cc_start: 0.8469 (tmm160) cc_final: 0.8030 (ttp80)
REVERT: A  219 ARG cc_start: 0.8881 (ttm170) cc_final: 0.8557 (ttm170)
REVERT: B   19 LYS cc_start: 0.8176 (pttm) cc_final: 0.7901 (pttm)
REVERT: B   36 GLU cc_start: 0.8337 (pt0) cc_final: 0.8064 (pm20)
REVERT: B   77 GLU cc_start: 0.8153 (tp30) cc_final: 0.7809 (tp30)
REVERT: B   89 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8493 (mm-40)
REVERT: H   39 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8225 (tt0)
REVERT: H   67 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7221 (tptt)
REVERT: H   96 CYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7494 (p)
REVERT: H  102 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7335 (mp10)
REVERT: H  122 PHE cc_start: 0.8581 (m-80) cc_final: 0.8086 (m-80)
REVERT: H  148 GLU cc_start: 0.8673 (tp30) cc_final: 0.7960 (tp30)
REVERT: H  199 ASN cc_start: 0.8002 (t0) cc_final: 0.7772 (t0)
REVERT: L  139 TYR cc_start: 0.7917 (t80) cc_final: 0.7031 (t80)
  outliers start: 49
  outliers final: 36
  residues processed: 147
  average time/residue: 0.0876
  time to fit residues: 16.7973
Evaluate side-chains
  142 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 101
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   86 ASN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  197 ASN
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   46 THR
Chi-restraints excluded: chain L residue   55 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.109294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.078984 restraints weight = 13106.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.08
r_work: 0.3199 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3211
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6478  Z= 0.131
  Angle     :  0.603   6.414   8815  Z= 0.310
  Chirality :  0.042   0.139    949
  Planarity :  0.003   0.036   1141
  Dihedral  :  5.755  54.364    901
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 27.75 %
    Favored  : 65.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.31), residues: 797
  helix:  0.23 (0.56), residues: 87
  sheet:  0.87 (0.29), residues: 346
  loop : -1.03 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  13 
 TYR   0.016   0.001   TYR B  78 
 PHE   0.007   0.001   PHE B  56 
 TRP   0.007   0.001   TRP A 244 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6471)
  covalent geometry    : angle       0.60193 ( 8801)
  SS BOND              : bond        0.00310 (    7)
  SS BOND              : angle       1.10792 (   14)
  hydrogen bonds       : bond        0.03052 (  267)
  hydrogen bonds       : angle       4.68368 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 103
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7656 (ptt-90)
REVERT: A   89 GLU cc_start: 0.8741 (pm20) cc_final: 0.8394 (mm-30)
REVERT: A   98 MET cc_start: 0.8580 (tmm) cc_final: 0.8142 (tmm)
REVERT: A  122 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8402 (m-30)
REVERT: A  181 ARG cc_start: 0.8504 (tmm160) cc_final: 0.8005 (ttp80)
REVERT: A  191 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.7863 (p90)
REVERT: A  219 ARG cc_start: 0.8890 (ttm170) cc_final: 0.8507 (ttm170)
REVERT: B   19 LYS cc_start: 0.8129 (pttm) cc_final: 0.7908 (pttm)
REVERT: B   36 GLU cc_start: 0.8340 (pt0) cc_final: 0.8026 (pm20)
REVERT: B   77 GLU cc_start: 0.8181 (tp30) cc_final: 0.7783 (tp30)
REVERT: B   89 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8510 (mm-40)
REVERT: H   39 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8234 (tt0)
REVERT: H   67 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7177 (tptt)
REVERT: H  102 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7312 (mp10)
REVERT: H  122 PHE cc_start: 0.8568 (m-80) cc_final: 0.8037 (m-80)
REVERT: H  148 GLU cc_start: 0.8672 (tp30) cc_final: 0.7957 (tp30)
REVERT: L   83 MET cc_start: 0.8664 (mmt) cc_final: 0.8404 (mmt)
REVERT: L  139 TYR cc_start: 0.7913 (t80) cc_final: 0.7042 (t80)
REVERT: L  194 GLU cc_start: 0.8296 (pm20) cc_final: 0.8011 (pm20)
REVERT: L  209 ASN cc_start: 0.8266 (m-40) cc_final: 0.7825 (t0)
  outliers start: 49
  outliers final: 40
  residues processed: 141
  average time/residue: 0.0824
  time to fit residues: 15.3782
Evaluate side-chains
  146 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 101
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   86 ASN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  191 HIS
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  197 ASN
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   46 THR
Chi-restraints excluded: chain L residue   55 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 73 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
** B  21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.108728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.078399 restraints weight = 13109.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 3.03
r_work: 0.3204 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6478  Z= 0.142
  Angle     :  0.613   6.378   8815  Z= 0.316
  Chirality :  0.042   0.136    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  5.790  55.057    901
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 27.61 %
    Favored  : 64.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.31), residues: 797
  helix:  0.21 (0.56), residues: 87
  sheet:  0.94 (0.29), residues: 340
  loop : -1.05 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  13 
 TYR   0.020   0.001   TYR B  78 
 PHE   0.007   0.001   PHE B  56 
 TRP   0.006   0.001   TRP A 244 
 HIS   0.005   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6471)
  covalent geometry    : angle       0.61203 ( 8801)
  SS BOND              : bond        0.00316 (    7)
  SS BOND              : angle       1.14066 (   14)
  hydrogen bonds       : bond        0.03052 (  267)
  hydrogen bonds       : angle       4.69002 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 105
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7624 (ptt-90)
REVERT: A   98 MET cc_start: 0.8578 (tmm) cc_final: 0.8144 (tmm)
REVERT: A  122 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8419 (m-30)
REVERT: A  181 ARG cc_start: 0.8534 (tmm160) cc_final: 0.7996 (ttp80)
REVERT: A  191 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.7858 (p90)
REVERT: A  219 ARG cc_start: 0.8878 (ttm170) cc_final: 0.8570 (ttm170)
REVERT: A  260 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7896 (t-90)
REVERT: B   36 GLU cc_start: 0.8370 (pt0) cc_final: 0.8062 (pm20)
REVERT: B   77 GLU cc_start: 0.8156 (tp30) cc_final: 0.7755 (tp30)
REVERT: B   89 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8493 (mm-40)
REVERT: H   39 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8224 (tt0)
REVERT: H   67 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7165 (tptt)
REVERT: H   96 CYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7597 (p)
REVERT: H  102 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7285 (mp10)
REVERT: H  122 PHE cc_start: 0.8589 (m-80) cc_final: 0.8039 (m-80)
REVERT: H  148 GLU cc_start: 0.8695 (tp30) cc_final: 0.7984 (tp30)
REVERT: L  139 TYR cc_start: 0.7926 (t80) cc_final: 0.7054 (t80)
REVERT: L  184 GLU cc_start: 0.8831 (tp30) cc_final: 0.8567 (tp30)
REVERT: L  194 GLU cc_start: 0.8284 (pm20) cc_final: 0.7951 (pm20)
REVERT: L  209 ASN cc_start: 0.8295 (m-40) cc_final: 0.7819 (t0)
  outliers start: 52
  outliers final: 40
  residues processed: 145
  average time/residue: 0.0788
  time to fit residues: 15.0606
Evaluate side-chains
  148 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 101
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   86 ASN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  156 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  191 HIS
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  260 HIS
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   67 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  197 ASN
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   46 THR
Chi-restraints excluded: chain L residue   55 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0670
   chunk 52 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 25 optimal weight:    8.9990
   chunk 41 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.108305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.078410 restraints weight = 12898.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.93
r_work: 0.3189 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3210
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6478  Z= 0.123
  Angle     :  0.621   6.807   8815  Z= 0.320
  Chirality :  0.042   0.139    949
  Planarity :  0.003   0.036   1141
  Dihedral  :  5.731  55.158    901
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  6.90 %
    Allowed  : 28.34 %
    Favored  : 64.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.31), residues: 797
  helix:  0.30 (0.56), residues: 87
  sheet:  0.94 (0.29), residues: 341
  loop : -1.06 (0.34), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L 187 
 TYR   0.017   0.001   TYR B  78 
 PHE   0.007   0.001   PHE H 166 
 TRP   0.007   0.001   TRP A 244 
 HIS   0.004   0.000   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6471)
  covalent geometry    : angle       0.61982 ( 8801)
  SS BOND              : bond        0.00305 (    7)
  SS BOND              : angle       1.07036 (   14)
  hydrogen bonds       : bond        0.02972 (  267)
  hydrogen bonds       : angle       4.61113 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 110
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7683 (ptt-90)
REVERT: A   89 GLU cc_start: 0.8729 (pm20) cc_final: 0.8519 (mm-30)
REVERT: A   98 MET cc_start: 0.8592 (tmm) cc_final: 0.8054 (tmm)
REVERT: A  122 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8365 (m-30)
REVERT: A  181 ARG cc_start: 0.8464 (tmm160) cc_final: 0.7963 (ttp80)
REVERT: A  191 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.7775 (p90)
REVERT: A  204 TRP cc_start: 0.8835 (m100) cc_final: 0.8527 (m100)
REVERT: A  219 ARG cc_start: 0.8858 (ttm170) cc_final: 0.8553 (ttm170)
REVERT: A  260 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7974 (t-90)
REVERT: B   36 GLU cc_start: 0.8319 (pt0) cc_final: 0.8081 (pm20)
REVERT: B   77 GLU cc_start: 0.8126 (tp30) cc_final: 0.7740 (tp30)
REVERT: P    5 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7367 (mmm160)
REVERT: H   39 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8288 (tt0)
REVERT: H  102 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7330 (mp10)
REVERT: H  122 PHE cc_start: 0.8647 (m-80) cc_final: 0.8149 (m-80)
REVERT: H  148 GLU cc_start: 0.8682 (tp30) cc_final: 0.7981 (tp30)
REVERT: L  105 MET cc_start: 0.8289 (mmm) cc_final: 0.7342 (mmm)
REVERT: L  139 TYR cc_start: 0.7797 (t80) cc_final: 0.7559 (t80)
REVERT: L  194 GLU cc_start: 0.8225 (pm20) cc_final: 0.7848 (pm20)
REVERT: L  209 ASN cc_start: 0.8301 (m-40) cc_final: 0.7810 (t0)
  outliers start: 47
  outliers final: 37
  residues processed: 148
  average time/residue: 0.0765
  time to fit residues: 15.0430
Evaluate side-chains
  152 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 109
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   86 ASN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  191 HIS
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  260 HIS
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  197 ASN
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   46 THR
Chi-restraints excluded: chain L residue   55 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 THR
Chi-restraints excluded: chain L residue  205 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.0370
   chunk 26 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0170
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0870
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.3674

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.109184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.079395 restraints weight = 12719.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.92
r_work: 0.3208 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6478  Z= 0.117
  Angle     :  0.622   7.220   8815  Z= 0.320
  Chirality :  0.042   0.142    949
  Planarity :  0.003   0.036   1141
  Dihedral  :  5.580  55.108    901
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 29.22 %
    Favored  : 64.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.31), residues: 797
  helix:  0.38 (0.55), residues: 87
  sheet:  0.92 (0.29), residues: 348
  loop : -0.95 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  13 
 TYR   0.019   0.001   TYR B  78 
 PHE   0.007   0.001   PHE L 138 
 TRP   0.007   0.001   TRP A 244 
 HIS   0.003   0.000   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6471)
  covalent geometry    : angle       0.62109 ( 8801)
  SS BOND              : bond        0.00287 (    7)
  SS BOND              : angle       1.05376 (   14)
  hydrogen bonds       : bond        0.02899 (  267)
  hydrogen bonds       : angle       4.55949 (  795)

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

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

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1594 Ramachandran restraints generated.
    797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 111
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7682 (ptt-90)
REVERT: A   67 SER cc_start: 0.8316 (p) cc_final: 0.8017 (p)
REVERT: A   89 GLU cc_start: 0.8719 (pm20) cc_final: 0.8476 (mm-30)
REVERT: A   98 MET cc_start: 0.8569 (tmm) cc_final: 0.8066 (tmm)
REVERT: A  122 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8330 (m-30)
REVERT: A  181 ARG cc_start: 0.8481 (tmm160) cc_final: 0.7997 (ttp80)
REVERT: A  191 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7805 (p90)
REVERT: A  204 TRP cc_start: 0.8794 (m100) cc_final: 0.8522 (m100)
REVERT: A  219 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8547 (ttm170)
REVERT: A  260 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7991 (t-90)
REVERT: B   36 GLU cc_start: 0.8305 (pt0) cc_final: 0.8098 (pm20)
REVERT: B   77 GLU cc_start: 0.8138 (tp30) cc_final: 0.7741 (tp30)
REVERT: P    5 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7324 (mmm160)
REVERT: H  102 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7322 (mp10)
REVERT: H  122 PHE cc_start: 0.8661 (m-80) cc_final: 0.8171 (m-80)
REVERT: H  148 GLU cc_start: 0.8688 (tp30) cc_final: 0.7971 (tp30)
REVERT: L   11 MET cc_start: 0.8349 (ppp) cc_final: 0.7545 (ppp)
REVERT: L  194 GLU cc_start: 0.8243 (pm20) cc_final: 0.7851 (pm20)
REVERT: L  209 ASN cc_start: 0.8205 (m-40) cc_final: 0.7714 (t0)
  outliers start: 42
  outliers final: 33
  residues processed: 146
  average time/residue: 0.0776
  time to fit residues: 15.0273
Evaluate side-chains
  145 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 106
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ARG
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   86 ASN
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  172 LEU
Chi-restraints excluded: chain A residue  176 LYS
Chi-restraints excluded: chain A residue  191 HIS
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  260 HIS
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   80 CYS
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain P residue    5 ARG
Chi-restraints excluded: chain P residue    7 PHE
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue    9 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  102 GLN
Chi-restraints excluded: chain H residue  163 VAL
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue   39 LYS
Chi-restraints excluded: chain L residue   46 THR
Chi-restraints excluded: chain L residue   55 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   70 ASP
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue   96 THR
Chi-restraints excluded: chain L residue  120 SER
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.109815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.079504 restraints weight = 13058.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 3.00
r_work: 0.3211 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3236
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3236 r_free = 0.3236    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3236
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6478  Z= 0.143
  Angle     :  0.637   6.869   8815  Z= 0.329
  Chirality :  0.042   0.180    949
  Planarity :  0.004   0.036   1141
  Dihedral  :  5.677  55.715    901
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 29.52 %
    Favored  : 64.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.31), residues: 797
  helix:  0.39 (0.55), residues: 87
  sheet:  0.94 (0.29), residues: 348
  loop : -0.90 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 107 
 TYR   0.021   0.001   TYR B  78 
 PHE   0.031   0.001   PHE H 146 
 TRP   0.007   0.001   TRP A 244 
 HIS   0.004   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6471)
  covalent geometry    : angle       0.63593 ( 8801)
  SS BOND              : bond        0.00318 (    7)
  SS BOND              : angle       1.19972 (   14)
  hydrogen bonds       : bond        0.02958 (  267)
  hydrogen bonds       : angle       4.61429 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1660.65 seconds
wall clock time: 29 minutes 9.67 seconds (1749.67 seconds total)