Starting phenix.real_space_refine
on Thu May  1 03:10:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8q85_18247/05_2025/8q85_18247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8q85_18247/05_2025/8q85_18247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8q85_18247/05_2025/8q85_18247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8q85_18247/05_2025/8q85_18247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8q85_18247/05_2025/8q85_18247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8q85_18247/05_2025/8q85_18247.cif"
  }
  resolution = 3.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      41      5.16       5
     C    6366      2.51       5
     N    1836      2.21       5
     O    2056      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10299
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "F"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1145
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 221}
          Link IDs: {'PTRANS': 1, 'TRANS': 228}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 744
          Unresolved non-hydrogen angles: 925
          Unresolved non-hydrogen dihedrals: 593
          Unresolved non-hydrogen chiralities: 71
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 18, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 26, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 374
    Chain: "G"
      Number of atoms: 886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 886
          Classifications: {'peptide': 178}
          Incomplete info: {'truncation_to_alanine': 173}
          Link IDs: {'PTRANS': 1, 'TRANS': 176}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 588
          Unresolved non-hydrogen angles: 740
          Unresolved non-hydrogen dihedrals: 460
          Unresolved non-hydrogen chiralities: 64
          Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 13, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 292
    Chain: "U"
      Number of atoms: 757
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 757
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "V"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 935
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 1, 'TRANS': 115}
    Chain: "W"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 837
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 102}
          Chain breaks: 1
    Chain: "X"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 535
          Classifications: {'peptide': 68}
          Link IDs: {'TRANS': 67}
    Chain: "Y"
      Number of atoms: 571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 571
          Classifications: {'peptide': 72}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 68}
    Chain: "Z"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 761
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "a"
      Number of atoms: 1925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1925
          Classifications: {'peptide': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224}
          Chain breaks: 1
    Chain: "b"
      Number of atoms: 561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 561
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 1, 'TRANS': 68}
    Chain: "c"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 527
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
    Chain: "d"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 859
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 3, 'TRANS': 104}
  Time building chain proxies: 6.65, per 1000 atoms: 0.65
  Number of scatterers: 10299
  At special positions: 0
  Unit cell: (203.52, 142.04, 216.24, 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      41     16.00
     O    2056      8.00
     N    1836      7.00
     C    6366      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.07
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2776

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 4 sheets defined
      86.6% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'F' and resid 434 through 478
    Processing helix  chain 'F' and resid 484 through 489
      removed outlier: 3.688A  pdb=" N   LEU F 488 " --> pdb=" O   ASN F 484 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 506 through 511
      removed outlier: 3.776A  pdb=" N   LEU F 510 " --> pdb=" O   SER F 506 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 520 through 663
    Processing helix  chain 'G' and resid 271 through 307
    Processing helix  chain 'G' and resid 307 through 337
    Processing helix  chain 'G' and resid 339 through 386
    Processing helix  chain 'G' and resid 386 through 400
    Processing helix  chain 'G' and resid 405 through 446
    Processing helix  chain 'U' and resid 58 through 110
      Proline residue:  U  65  - end of helix
    Processing helix  chain 'U' and resid 120 through 151
    Processing helix  chain 'V' and resid 61 through 125
      removed outlier: 4.618A  pdb=" N   LEU V  89 " --> pdb=" O   LEU V  85 " (cutoff:3.500A)
      Proline residue:  V  90  - end of helix
    Processing helix  chain 'V' and resid 126 through 143
      removed outlier: 3.670A  pdb=" N   LEU V 130 " --> pdb=" O   ASP V 126 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 146 through 150
    Processing helix  chain 'V' and resid 151 through 176
    Processing helix  chain 'W' and resid 3 through 67
      removed outlier: 4.104A  pdb=" N   GLN W   7 " --> pdb=" O   SER W   3 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ASN W  55 " --> pdb=" O   GLN W  51 " (cutoff:3.500A)
      removed outlier: 5.307A  pdb=" N   TRP W  56 " --> pdb=" O   LEU W  52 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ASP W  57 " --> pdb=" O   MET W  53 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 68 through 73
    Processing helix  chain 'W' and resid 74 through 78
    Processing helix  chain 'W' and resid 80 through 84
    Processing helix  chain 'X' and resid 14 through 57
    Processing helix  chain 'X' and resid 58 through 67
      removed outlier: 3.897A  pdb=" N   VAL X  62 " --> pdb=" O   GLU X  58 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 72 through 80
      removed outlier: 4.066A  pdb=" N   ASP X  78 " --> pdb=" O   GLU X  74 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA X  80 " --> pdb=" O   LEU X  76 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 4 through 41
      removed outlier: 4.189A  pdb=" N   VAL Y   8 " --> pdb=" O   PRO Y   4 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 41 through 65
      removed outlier: 4.030A  pdb=" N   GLU Y  45 " --> pdb=" O   ASN Y  41 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ILE Y  46 " --> pdb=" O   LYS Y  42 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 6 through 35
    Processing helix  chain 'Z' and resid 53 through 65
      removed outlier: 3.523A  pdb=" N   ASP Z  59 " --> pdb=" O   GLN Z  55 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LYS Z  63 " --> pdb=" O   ASP Z  59 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 68 through 94
      removed outlier: 3.509A  pdb=" N   LYS Z  72 " --> pdb=" O   GLY Z  68 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL Z  75 " --> pdb=" O   LEU Z  71 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 4 through 22
    Processing helix  chain 'a' and resid 28 through 37
      removed outlier: 3.941A  pdb=" N   ASN a  32 " --> pdb=" O   GLY a  28 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 40 through 51
    Processing helix  chain 'a' and resid 56 through 63
    Processing helix  chain 'a' and resid 81 through 99
    Processing helix  chain 'a' and resid 111 through 125
      removed outlier: 3.570A  pdb=" N   TYR a 115 " --> pdb=" O   PRO a 111 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS a 118 " --> pdb=" O   VAL a 114 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   LEU a 121 " --> pdb=" O   ASN a 117 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 158 through 168
    Processing helix  chain 'a' and resid 171 through 183
    Processing helix  chain 'a' and resid 203 through 205
      No H-bonds generated for 'chain 'a' and resid 203 through 205'
    Processing helix  chain 'a' and resid 206 through 221
      removed outlier: 3.516A  pdb=" N   ILE a 210 " --> pdb=" O   PRO a 206 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 223 through 265
      removed outlier: 4.068A  pdb=" N   SER a 242 " --> pdb=" O   GLU a 238 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 3 through 38
    Processing helix  chain 'b' and resid 38 through 57
      removed outlier: 3.512A  pdb=" N   THR b  57 " --> pdb=" O   ILE b  53 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 57 through 69
      removed outlier: 3.532A  pdb=" N   GLY b  61 " --> pdb=" O   THR b  57 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   THR b  67 " --> pdb=" O   MET b  63 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 2 through 40
    Processing helix  chain 'c' and resid 44 through 63
    Processing helix  chain 'd' and resid 2 through 40
      Proline residue:  d  32  - end of helix
      removed outlier: 3.676A  pdb=" N   THR d  39 " --> pdb=" O   ASN d  35 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   MET d  40 " --> pdb=" O   LEU d  36 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 52 through 65
    Processing helix  chain 'd' and resid 65 through 108
    Processing sheet with id=AA1, first strand: chain 'U' and resid 112 through 113
    Processing sheet with id=AA2, first strand: chain 'a' and resid 52 through 54
    Processing sheet with id=AA3, first strand: chain 'a' and resid 64 through 67
    Processing sheet with id=AA4, first strand: chain 'a' and resid 185 through 189

    1042 hydrogen bonds defined for protein.
    3102 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: 3.55

  Time building geometry restraints manager: 3.55 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3628
        1.34 -     1.46: 1787
        1.46 -     1.58: 4905
        1.58 -     1.70: 1
        1.70 -     1.82: 73
  Bond restraints: 10394
  Sorted by residual:
  bond pdb=" CB  PRO Z   7 "
       pdb=" CG  PRO Z   7 "
    ideal  model  delta    sigma   weight residual
    1.492  1.620 -0.128 5.00e-02 4.00e+02 6.56e+00
  bond pdb=" CG  GLU b  16 "
       pdb=" CD  GLU b  16 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.30e+00
  bond pdb=" CB  ILE a 247 "
       pdb=" CG2 ILE a 247 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.30e+00
  bond pdb=" CB  ASP b  25 "
       pdb=" CG  ASP b  25 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.70e+00
  bond pdb=" CG  ASP Z  22 "
       pdb=" OD1 ASP Z  22 "
    ideal  model  delta    sigma   weight residual
    1.249  1.225  0.024 1.90e-02 2.77e+03 1.63e+00
  ... (remaining 10389 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.49: 13949
        3.49 -     6.99: 116
        6.99 -    10.48: 23
       10.48 -    13.98: 8
       13.98 -    17.47: 2
  Bond angle restraints: 14098
  Sorted by residual:
  angle pdb=" CA  PRO Z   7 "
        pdb=" N   PRO Z   7 "
        pdb=" CD  PRO Z   7 "
      ideal   model   delta    sigma   weight residual
     112.00  100.33   11.67 1.40e+00 5.10e-01 6.95e+01
  angle pdb=" CA  GLU Z  85 "
        pdb=" CB  GLU Z  85 "
        pdb=" CG  GLU Z  85 "
      ideal   model   delta    sigma   weight residual
     114.10  125.15  -11.05 2.00e+00 2.50e-01 3.05e+01
  angle pdb=" CA  LYS Z  17 "
        pdb=" CB  LYS Z  17 "
        pdb=" CG  LYS Z  17 "
      ideal   model   delta    sigma   weight residual
     114.10  124.41  -10.31 2.00e+00 2.50e-01 2.66e+01
  angle pdb=" CA  LEU Z  23 "
        pdb=" CB  LEU Z  23 "
        pdb=" CG  LEU Z  23 "
      ideal   model   delta    sigma   weight residual
     116.30  133.77  -17.47 3.50e+00 8.16e-02 2.49e+01
  angle pdb=" CA  MET V  77 "
        pdb=" CB  MET V  77 "
        pdb=" CG  MET V  77 "
      ideal   model   delta    sigma   weight residual
     114.10  123.75   -9.65 2.00e+00 2.50e-01 2.33e+01
  ... (remaining 14093 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 5609
       17.88 -    35.76: 618
       35.76 -    53.63: 142
       53.63 -    71.51: 38
       71.51 -    89.39: 20
  Dihedral angle restraints: 6427
    sinusoidal: 2201
      harmonic: 4226
  Sorted by residual:
  dihedral pdb=" CA  PHE a  64 "
           pdb=" C   PHE a  64 "
           pdb=" N   LYS a  65 "
           pdb=" CA  LYS a  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.02   25.98     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  ILE Z  53 "
           pdb=" C   ILE Z  53 "
           pdb=" N   LEU Z  54 "
           pdb=" CA  LEU Z  54 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.89  -21.11     0      5.00e+00 4.00e-02 1.78e+01
  dihedral pdb=" CA  PRO Z   7 "
           pdb=" C   PRO Z   7 "
           pdb=" N   LEU Z   8 "
           pdb=" CA  LEU Z   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.06   18.94     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 6424 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1640
       0.106 -    0.213: 54
       0.213 -    0.319: 1
       0.319 -    0.426: 1
       0.426 -    0.532: 1
  Chirality restraints: 1697
  Sorted by residual:
  chirality pdb=" CG  LEU Z  23 "
            pdb=" CB  LEU Z  23 "
            pdb=" CD1 LEU Z  23 "
            pdb=" CD2 LEU Z  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 7.07e+00
  chirality pdb=" CA  PRO Z   7 "
            pdb=" N   PRO Z   7 "
            pdb=" C   PRO Z   7 "
            pdb=" CB  PRO Z   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.40    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CB  THR V  82 "
            pdb=" CA  THR V  82 "
            pdb=" OG1 THR V  82 "
            pdb=" CG2 THR V  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 1694 not shown)

  Planarity restraints: 1868
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER Z   6 "    0.087 5.00e-02 4.00e+02   1.23e-01 2.43e+01
        pdb=" N   PRO Z   7 "   -0.213 5.00e-02 4.00e+02
        pdb=" CA  PRO Z   7 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO Z   7 "    0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP a 221 "    0.079 5.00e-02 4.00e+02   1.20e-01 2.29e+01
        pdb=" N   PRO a 222 "   -0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO a 222 "    0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO a 222 "    0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS Y  69 "   -0.047 5.00e-02 4.00e+02   6.97e-02 7.76e+00
        pdb=" N   PRO Y  70 "    0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO Y  70 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO Y  70 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1865 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 346
        2.70 -     3.25: 11884
        3.25 -     3.80: 18387
        3.80 -     4.35: 20876
        4.35 -     4.90: 33178
  Nonbonded interactions: 84671
  Sorted by model distance:
  nonbonded pdb=" OG  SER W   3 "
            pdb=" OD1 ASP W   5 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   ALA a  15 "
            pdb=" OG  SER a  18 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   LYS V  73 "
            pdb=" NZ  LYS V  73 "
     model   vdw
     2.170 3.120
  nonbonded pdb=" O   LEU G 336 "
            pdb=" N   MET G 341 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" O   LEU V  64 "
            pdb=" OG  SER V  68 "
     model   vdw
     2.192 3.040
  ... (remaining 84666 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     27.640
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
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      :  0.004   0.128  10394  Z= 0.188
  Angle     :  0.923  17.470  14098  Z= 0.491
  Chirality :  0.047   0.532   1697
  Planarity :  0.007   0.123   1868
  Dihedral  : 17.196  89.389   3651
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 18.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 31.30 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.22), residues: 1408
  helix:  1.67 (0.14), residues: 1181
  sheet: -2.04 (1.08), residues: 12
  loop : -0.54 (0.44), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP b  59 
 HIS   0.006   0.001   HIS a  31 
 PHE   0.026   0.002   PHE a  83 
 TYR   0.028   0.002   TYR a 230 
 ARG   0.007   0.001   ARG d  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09394 ( 1042)
  hydrogen bonds       : angle       5.53288 ( 3102)
  covalent geometry    : bond        0.00399 (10394)
  covalent geometry    : angle       0.92310 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 234
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: W   34 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8038 (mm-30)
REVERT: W   79 GLU cc_start: 0.8083 (mp0) cc_final: 0.7725 (pm20)
REVERT: Y    1 MET cc_start: 0.3898 (OUTLIER) cc_final: 0.3238 (mmt)
REVERT: Z   11 GLU cc_start: 0.9588 (tm-30) cc_final: 0.9220 (pp20)
REVERT: Z   38 HIS cc_start: 0.6533 (p-80) cc_final: 0.5048 (p-80)
REVERT: a  230 TYR cc_start: 0.8856 (t80) cc_final: 0.8228 (t80)
REVERT: d   67 GLU cc_start: 0.8602 (tp30) cc_final: 0.8346 (tp30)
  outliers start: 5
  outliers final: 1
  residues processed: 235
  average time/residue: 0.2743
  time to fit residues: 88.4855
Evaluate side-chains
  223 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 221
  time to evaluate  : 2.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain Y residue    1 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 35 optimal weight:   50.0000
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 108 optimal weight:   30.0000
   chunk 41 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 80 optimal weight:    0.5980
   chunk 125 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
U 108 ASN
** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  31 ASN
Z  41 GLN
a 239 GLN
c  63 GLN
d  30 ASN
d  92 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.146233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.105520 restraints weight = 32663.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.108138 restraints weight = 19040.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.109801 restraints weight = 13315.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10394  Z= 0.145
  Angle     :  0.686  12.345  14098  Z= 0.350
  Chirality :  0.042   0.475   1697
  Planarity :  0.004   0.079   1868
  Dihedral  :  4.735  55.294   1503
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 23.63 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.05 (0.22), residues: 1408
  helix:  2.48 (0.14), residues: 1184
  sheet: -2.00 (1.03), residues: 12
  loop : -0.45 (0.45), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP b  59 
 HIS   0.006   0.001   HIS a  31 
 PHE   0.021   0.002   PHE X  20 
 TYR   0.020   0.002   TYR a 230 
 ARG   0.004   0.001   ARG d  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04274 ( 1042)
  hydrogen bonds       : angle       4.02788 ( 3102)
  covalent geometry    : bond        0.00305 (10394)
  covalent geometry    : angle       0.68575 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 246
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   89 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8014 (tm-30)
REVERT: U   93 ASP cc_start: 0.8079 (m-30) cc_final: 0.7821 (m-30)
REVERT: U  120 ASP cc_start: 0.7929 (p0) cc_final: 0.7722 (p0)
REVERT: W   11 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8193 (mtpt)
REVERT: W   34 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8190 (mm-30)
REVERT: W   72 GLN cc_start: 0.8291 (tp40) cc_final: 0.8012 (tp-100)
REVERT: W   75 GLU cc_start: 0.8429 (tp30) cc_final: 0.8226 (tm-30)
REVERT: W   79 GLU cc_start: 0.8116 (mp0) cc_final: 0.7758 (pm20)
REVERT: Z   16 TYR cc_start: 0.7888 (m-80) cc_final: 0.6696 (m-80)
REVERT: Z   17 LYS cc_start: 0.9553 (mmtt) cc_final: 0.9176 (mmtt)
REVERT: Z   38 HIS cc_start: 0.5678 (p-80) cc_final: 0.4353 (p-80)
REVERT: a   93 MET cc_start: 0.7453 (mmt) cc_final: 0.6989 (mmm)
REVERT: a  168 PHE cc_start: 0.7607 (m-80) cc_final: 0.6410 (m-80)
REVERT: a  227 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8960 (mmmt)
REVERT: b    1 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6746 (ppp)
REVERT: b   48 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: d   63 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8942 (tp)
REVERT: d   67 GLU cc_start: 0.8492 (tp30) cc_final: 0.8108 (tp30)
  outliers start: 42
  outliers final: 15
  residues processed: 271
  average time/residue: 0.2571
  time to fit residues: 95.9514
Evaluate side-chains
  244 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 227
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain W residue  122 GLU
Chi-restraints excluded: chain W residue  123 THR
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Y residue   51 CYS
Chi-restraints excluded: chain Z residue   29 THR
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue  186 VAL
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   63 MET
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain d residue   63 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9990
   chunk 127 optimal weight:    4.9990
   chunk 129 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 16 optimal weight:   60.0000
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.145740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.103001 restraints weight = 33619.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.105490 restraints weight = 20131.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.107043 restraints weight = 14332.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10394  Z= 0.152
  Angle     :  0.673  12.707  14098  Z= 0.339
  Chirality :  0.041   0.246   1697
  Planarity :  0.004   0.061   1868
  Dihedral  :  4.555  56.628   1500
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 23.63 %
    Favored  : 72.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.32 (0.22), residues: 1408
  helix:  2.69 (0.14), residues: 1177
  sheet: -2.08 (1.03), residues: 12
  loop : -0.47 (0.44), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP b  59 
 HIS   0.006   0.001   HIS a  31 
 PHE   0.018   0.002   PHE X  20 
 TYR   0.024   0.002   TYR a 230 
 ARG   0.007   0.001   ARG d  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04153 ( 1042)
  hydrogen bonds       : angle       3.85597 ( 3102)
  covalent geometry    : bond        0.00328 (10394)
  covalent geometry    : angle       0.67285 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 236
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   89 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7959 (tm-30)
REVERT: U   93 ASP cc_start: 0.8050 (m-30) cc_final: 0.7707 (m-30)
REVERT: U   98 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8521 (mm)
REVERT: U  120 ASP cc_start: 0.7888 (p0) cc_final: 0.7684 (p0)
REVERT: W    6 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7847 (pt0)
REVERT: W   34 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8197 (mm-30)
REVERT: W   72 GLN cc_start: 0.8290 (tp40) cc_final: 0.8078 (tp-100)
REVERT: W   79 GLU cc_start: 0.8125 (mp0) cc_final: 0.7723 (pm20)
REVERT: X   47 ILE cc_start: 0.7625 (mt) cc_final: 0.7414 (mm)
REVERT: Z   16 TYR cc_start: 0.7758 (m-80) cc_final: 0.6536 (m-80)
REVERT: Z   17 LYS cc_start: 0.9628 (mmtt) cc_final: 0.9291 (mmtt)
REVERT: Z   22 ASP cc_start: 0.8240 (t0) cc_final: 0.7745 (p0)
REVERT: Z   38 HIS cc_start: 0.5903 (p-80) cc_final: 0.4336 (p-80)
REVERT: a  188 MET cc_start: 0.3976 (ppp) cc_final: 0.3756 (ppp)
REVERT: a  227 LYS cc_start: 0.9136 (mmmt) cc_final: 0.8898 (mmmt)
REVERT: a  230 TYR cc_start: 0.8744 (t80) cc_final: 0.8053 (t80)
REVERT: a  259 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9110 (mtmm)
REVERT: b    1 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6856 (ppp)
REVERT: b   48 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8194 (tm-30)
REVERT: d   63 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9003 (tp)
REVERT: d   67 GLU cc_start: 0.8538 (tp30) cc_final: 0.8150 (tp30)
  outliers start: 33
  outliers final: 20
  residues processed: 255
  average time/residue: 0.2446
  time to fit residues: 85.9664
Evaluate side-chains
  251 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 228
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   81 PHE
Chi-restraints excluded: chain U residue   98 LEU
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  113 ILE
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain W residue   67 SER
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain X residue   28 LEU
Chi-restraints excluded: chain X residue   58 GLU
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Z residue   62 VAL
Chi-restraints excluded: chain Z residue   74 SER
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue   16 GLU
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   39 ILE
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain d residue   38 SER
Chi-restraints excluded: chain d residue   63 ILE
Chi-restraints excluded: chain d residue   73 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 126 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 125 optimal weight:    5.9990
   chunk 113 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 132 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0070
   chunk 92 optimal weight:    2.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 109 HIS
** a 239 GLN ** 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 = 0.4327 r_free = 0.4327 target = 0.146267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.106060 restraints weight = 31849.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.108646 restraints weight = 18469.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.110254 restraints weight = 12872.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10394  Z= 0.134
  Angle     :  0.663  13.463  14098  Z= 0.332
  Chirality :  0.040   0.413   1697
  Planarity :  0.004   0.050   1868
  Dihedral  :  4.498  56.506   1500
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 25.32 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.48 (0.22), residues: 1408
  helix:  2.82 (0.14), residues: 1176
  sheet: -2.00 (1.06), residues: 12
  loop : -0.52 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP b  59 
 HIS   0.006   0.001   HIS a  31 
 PHE   0.024   0.002   PHE a 168 
 TYR   0.019   0.001   TYR a 230 
 ARG   0.007   0.001   ARG d  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04026 ( 1042)
  hydrogen bonds       : angle       3.74975 ( 3102)
  covalent geometry    : bond        0.00280 (10394)
  covalent geometry    : angle       0.66316 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 257
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   78 ASP cc_start: 0.7622 (t0) cc_final: 0.7362 (t0)
REVERT: U   83 ARG cc_start: 0.7655 (ptp-170) cc_final: 0.7383 (ptp-170)
REVERT: U   89 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: U   93 ASP cc_start: 0.8151 (m-30) cc_final: 0.7821 (m-30)
REVERT: U   94 LEU cc_start: 0.8979 (tp) cc_final: 0.8731 (tt)
REVERT: U   98 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8389 (mm)
REVERT: U  136 ASP cc_start: 0.9424 (m-30) cc_final: 0.9171 (p0)
REVERT: V   77 MET cc_start: 0.9109 (ppp) cc_final: 0.8853 (ppp)
REVERT: W    6 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7812 (pt0)
REVERT: W   34 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8190 (mm-30)
REVERT: W   72 GLN cc_start: 0.8277 (tp40) cc_final: 0.8073 (tp-100)
REVERT: W   79 GLU cc_start: 0.8028 (mp0) cc_final: 0.7714 (pm20)
REVERT: X   47 ILE cc_start: 0.7618 (mt) cc_final: 0.7417 (mm)
REVERT: Z   16 TYR cc_start: 0.7702 (m-80) cc_final: 0.6311 (m-80)
REVERT: Z   17 LYS cc_start: 0.9616 (mmtt) cc_final: 0.9290 (mmtt)
REVERT: Z   35 TYR cc_start: 0.5925 (t80) cc_final: 0.5697 (t80)
REVERT: Z   38 HIS cc_start: 0.5816 (p-80) cc_final: 0.4692 (p-80)
REVERT: a  168 PHE cc_start: 0.7323 (m-80) cc_final: 0.6282 (m-80)
REVERT: a  188 MET cc_start: 0.4259 (ppp) cc_final: 0.3465 (ppp)
REVERT: a  227 LYS cc_start: 0.9247 (mmmt) cc_final: 0.9004 (mmmt)
REVERT: a  230 TYR cc_start: 0.8646 (t80) cc_final: 0.8142 (t80)
REVERT: b    1 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6553 (ppp)
REVERT: b   48 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: c    1 MET cc_start: 0.7730 (tmm) cc_final: 0.7453 (tmm)
REVERT: c    6 GLN cc_start: 0.7959 (tm130) cc_final: 0.7505 (tm-30)
REVERT: c   61 MET cc_start: 0.8039 (mmt) cc_final: 0.7822 (mmt)
REVERT: c   64 MET cc_start: 0.8827 (pmm) cc_final: 0.8396 (pmm)
REVERT: d   67 GLU cc_start: 0.8487 (tp30) cc_final: 0.8100 (tp30)
REVERT: d   89 ASP cc_start: 0.9146 (t0) cc_final: 0.8850 (m-30)
  outliers start: 37
  outliers final: 24
  residues processed: 277
  average time/residue: 0.2365
  time to fit residues: 89.5201
Evaluate side-chains
  256 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 230
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   81 PHE
Chi-restraints excluded: chain U residue   98 LEU
Chi-restraints excluded: chain U residue  100 SER
Chi-restraints excluded: chain U residue  105 ILE
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain W residue   67 SER
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Y residue   51 CYS
Chi-restraints excluded: chain Z residue   29 THR
Chi-restraints excluded: chain Z residue   33 LEU
Chi-restraints excluded: chain Z residue   74 SER
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue  202 VAL
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue    6 LYS
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain c residue   11 GLN
Chi-restraints excluded: chain c residue   44 GLN
Chi-restraints excluded: chain d residue    2 THR
Chi-restraints excluded: chain d residue   38 SER
Chi-restraints excluded: chain d residue   73 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 75 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   chunk 28 optimal weight:   50.0000
   chunk 9 optimal weight:   50.0000
   chunk 65 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0770
   chunk 40 optimal weight:    0.5980
   chunk 136 optimal weight:    4.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** V 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  61 ASN
** Z  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  49 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.147086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.105525 restraints weight = 32165.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.108148 restraints weight = 18856.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.109795 restraints weight = 13225.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10394  Z= 0.132
  Angle     :  0.674  13.304  14098  Z= 0.338
  Chirality :  0.041   0.353   1697
  Planarity :  0.004   0.050   1868
  Dihedral  :  4.454  56.521   1500
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.47 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.52 (0.22), residues: 1408
  helix:  2.81 (0.14), residues: 1182
  sheet: -2.10 (1.12), residues: 12
  loop : -0.35 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP b  59 
 HIS   0.006   0.001   HIS a  31 
 PHE   0.019   0.002   PHE a 168 
 TYR   0.017   0.001   TYR a 230 
 ARG   0.006   0.001   ARG a  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 ( 1042)
  hydrogen bonds       : angle       3.70242 ( 3102)
  covalent geometry    : bond        0.00275 (10394)
  covalent geometry    : angle       0.67358 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 252
  time to evaluate  : 1.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   89 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8135 (tm-30)
REVERT: U   93 ASP cc_start: 0.8186 (m-30) cc_final: 0.7816 (m-30)
REVERT: U   94 LEU cc_start: 0.8971 (tp) cc_final: 0.8735 (tt)
REVERT: U   98 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8409 (mm)
REVERT: V   79 LYS cc_start: 0.9362 (mmmt) cc_final: 0.9118 (mmmt)
REVERT: W    6 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7800 (pt0)
REVERT: W   34 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: W   72 GLN cc_start: 0.8245 (tp40) cc_final: 0.8035 (tp-100)
REVERT: W   79 GLU cc_start: 0.7968 (mp0) cc_final: 0.7563 (pm20)
REVERT: Z   16 TYR cc_start: 0.7694 (m-80) cc_final: 0.6346 (m-80)
REVERT: Z   17 LYS cc_start: 0.9611 (mmtt) cc_final: 0.9291 (mmtt)
REVERT: Z   22 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7100 (m-30)
REVERT: Z   24 LYS cc_start: 0.8737 (mttp) cc_final: 0.8327 (mttp)
REVERT: Z   38 HIS cc_start: 0.5767 (p-80) cc_final: 0.4617 (p-80)
REVERT: a  168 PHE cc_start: 0.7523 (m-80) cc_final: 0.7205 (m-80)
REVERT: a  216 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7950 (pt0)
REVERT: a  222 PRO cc_start: 0.8147 (Cg_exo) cc_final: 0.7806 (Cg_exo)
REVERT: a  227 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8986 (mmmt)
REVERT: a  230 TYR cc_start: 0.8609 (t80) cc_final: 0.8219 (t80)
REVERT: b    1 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6481 (ppp)
REVERT: b   48 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: c    1 MET cc_start: 0.7586 (tmm) cc_final: 0.7338 (tmm)
REVERT: c    6 GLN cc_start: 0.7923 (tm130) cc_final: 0.7433 (tm-30)
REVERT: c   64 MET cc_start: 0.8847 (pmm) cc_final: 0.8422 (pmm)
REVERT: d   67 GLU cc_start: 0.8514 (tp30) cc_final: 0.8043 (tp30)
REVERT: d   89 ASP cc_start: 0.9161 (t0) cc_final: 0.8919 (m-30)
  outliers start: 39
  outliers final: 24
  residues processed: 279
  average time/residue: 0.2543
  time to fit residues: 96.9764
Evaluate side-chains
  263 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 235
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   81 PHE
Chi-restraints excluded: chain U residue   98 LEU
Chi-restraints excluded: chain U residue  100 SER
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain W residue   67 SER
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain X residue   28 LEU
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Y residue   44 LEU
Chi-restraints excluded: chain Y residue   51 CYS
Chi-restraints excluded: chain Z residue   22 ASP
Chi-restraints excluded: chain Z residue   29 THR
Chi-restraints excluded: chain Z residue   33 LEU
Chi-restraints excluded: chain Z residue   74 SER
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue  202 VAL
Chi-restraints excluded: chain a residue  216 GLU
Chi-restraints excluded: chain a residue  264 TYR
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue    6 LYS
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain c residue   11 GLN
Chi-restraints excluded: chain d residue   38 SER
Chi-restraints excluded: chain d residue   73 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 29 optimal weight:   40.0000
   chunk 107 optimal weight:    0.0020
   chunk 67 optimal weight:    0.6980
   chunk 82 optimal weight:   30.0000
   chunk 93 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 37 optimal weight:   50.0000
   chunk 131 optimal weight:    0.3980
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
V 134 ASN
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  61 ASN
** Z  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.146659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.104924 restraints weight = 32418.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.107522 restraints weight = 19167.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.109130 restraints weight = 13431.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10394  Z= 0.138
  Angle     :  0.690  14.144  14098  Z= 0.347
  Chirality :  0.040   0.252   1697
  Planarity :  0.004   0.050   1868
  Dihedral  :  4.458  56.963   1500
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 27.84 %
    Favored  : 68.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.58 (0.21), residues: 1408
  helix:  2.88 (0.14), residues: 1175
  sheet: -1.06 (1.39), residues: 12
  loop : -0.46 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP b  59 
 HIS   0.006   0.001   HIS a  31 
 PHE   0.015   0.002   PHE a 168 
 TYR   0.014   0.001   TYR Z  35 
 ARG   0.005   0.000   ARG a  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 ( 1042)
  hydrogen bonds       : angle       3.68686 ( 3102)
  covalent geometry    : bond        0.00290 (10394)
  covalent geometry    : angle       0.68991 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 250
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   89 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: U   93 ASP cc_start: 0.8176 (m-30) cc_final: 0.7824 (m-30)
REVERT: U   94 LEU cc_start: 0.8977 (tp) cc_final: 0.8748 (tt)
REVERT: U   98 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8414 (mm)
REVERT: V   79 LYS cc_start: 0.9398 (mmmt) cc_final: 0.9168 (mmmt)
REVERT: V  105 SER cc_start: 0.8564 (t) cc_final: 0.8088 (p)
REVERT: W   34 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8187 (mm-30)
REVERT: W   72 GLN cc_start: 0.8259 (tp40) cc_final: 0.8049 (tp-100)
REVERT: W   79 GLU cc_start: 0.7933 (mp0) cc_final: 0.7540 (pm20)
REVERT: Z   16 TYR cc_start: 0.7660 (m-80) cc_final: 0.6320 (m-80)
REVERT: Z   17 LYS cc_start: 0.9611 (mmtt) cc_final: 0.9307 (mmtt)
REVERT: Z   21 LEU cc_start: 0.9104 (pp) cc_final: 0.8757 (pp)
REVERT: Z   22 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7025 (m-30)
REVERT: Z   24 LYS cc_start: 0.8765 (mttp) cc_final: 0.8316 (mttp)
REVERT: Z   33 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7956 (mm)
REVERT: Z   38 HIS cc_start: 0.5513 (p-80) cc_final: 0.4232 (p-80)
REVERT: a  168 PHE cc_start: 0.7457 (m-80) cc_final: 0.7215 (m-80)
REVERT: a  216 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7913 (pt0)
REVERT: a  227 LYS cc_start: 0.9270 (mmmt) cc_final: 0.9018 (mmmt)
REVERT: b    1 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6411 (ppp)
REVERT: b   48 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8151 (tm-30)
REVERT: c    6 GLN cc_start: 0.7931 (tm130) cc_final: 0.7464 (tm-30)
REVERT: c   64 MET cc_start: 0.8991 (pmm) cc_final: 0.8678 (pmm)
REVERT: d   63 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8992 (tp)
REVERT: d   71 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8329 (mmm160)
REVERT: d   95 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.8189 (m-80)
  outliers start: 36
  outliers final: 24
  residues processed: 272
  average time/residue: 0.2440
  time to fit residues: 91.0074
Evaluate side-chains
  265 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 234
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   81 PHE
Chi-restraints excluded: chain U residue   98 LEU
Chi-restraints excluded: chain U residue  100 SER
Chi-restraints excluded: chain U residue  105 ILE
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain V residue  134 ASN
Chi-restraints excluded: chain W residue   67 SER
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Y residue   44 LEU
Chi-restraints excluded: chain Y residue   51 CYS
Chi-restraints excluded: chain Z residue   22 ASP
Chi-restraints excluded: chain Z residue   29 THR
Chi-restraints excluded: chain Z residue   33 LEU
Chi-restraints excluded: chain Z residue   35 TYR
Chi-restraints excluded: chain Z residue   74 SER
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue  216 GLU
Chi-restraints excluded: chain a residue  264 TYR
Chi-restraints excluded: chain b residue    1 MET
Chi-restraints excluded: chain b residue    6 LYS
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain c residue   11 GLN
Chi-restraints excluded: chain d residue   63 ILE
Chi-restraints excluded: chain d residue   69 LEU
Chi-restraints excluded: chain d residue   73 LEU
Chi-restraints excluded: chain d residue   95 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 120 optimal weight:    0.4980
   chunk 123 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 9 optimal weight:   50.0000
   chunk 50 optimal weight:    3.9990
   chunk 121 optimal weight:    0.6980
   chunk 137 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 10 optimal weight:   50.0000
   chunk 48 optimal weight:    6.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  61 ASN
** Z  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 239 GLN ** 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 = 0.4314 r_free = 0.4314 target = 0.145363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.104925 restraints weight = 32365.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.107482 restraints weight = 18915.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.109108 restraints weight = 13265.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10394  Z= 0.142
  Angle     :  0.716  13.726  14098  Z= 0.359
  Chirality :  0.041   0.370   1697
  Planarity :  0.004   0.049   1868
  Dihedral  :  4.463  58.226   1500
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 28.47 %
    Favored  : 67.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.63 (0.21), residues: 1408
  helix:  2.91 (0.14), residues: 1175
  sheet: -0.51 (1.46), residues: 12
  loop : -0.43 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP b  59 
 HIS   0.016   0.002   HIS a 109 
 PHE   0.012   0.002   PHE X  20 
 TYR   0.024   0.002   TYR a 230 
 ARG   0.006   0.000   ARG a  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 ( 1042)
  hydrogen bonds       : angle       3.69626 ( 3102)
  covalent geometry    : bond        0.00301 (10394)
  covalent geometry    : angle       0.71645 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 249
  time to evaluate  : 1.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   89 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8152 (tm-30)
REVERT: U   93 ASP cc_start: 0.8220 (m-30) cc_final: 0.7806 (m-30)
REVERT: U   94 LEU cc_start: 0.8996 (tp) cc_final: 0.8641 (tt)
REVERT: U   98 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8428 (mm)
REVERT: U  135 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8600 (pp20)
REVERT: V   77 MET cc_start: 0.9196 (ppp) cc_final: 0.8843 (ppp)
REVERT: W   34 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8220 (mm-30)
REVERT: W   72 GLN cc_start: 0.8272 (tp40) cc_final: 0.8051 (tp-100)
REVERT: W   79 GLU cc_start: 0.7942 (mp0) cc_final: 0.7621 (pm20)
REVERT: Z   16 TYR cc_start: 0.7677 (m-80) cc_final: 0.6351 (m-80)
REVERT: Z   17 LYS cc_start: 0.9631 (mmtt) cc_final: 0.9392 (mmtt)
REVERT: Z   21 LEU cc_start: 0.9064 (pp) cc_final: 0.8693 (pp)
REVERT: Z   22 ASP cc_start: 0.8022 (t0) cc_final: 0.7441 (m-30)
REVERT: Z   24 LYS cc_start: 0.8772 (mttp) cc_final: 0.8337 (mttp)
REVERT: Z   33 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7991 (mt)
REVERT: Z   38 HIS cc_start: 0.5462 (p-80) cc_final: 0.4029 (p-80)
REVERT: b   48 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: c    6 GLN cc_start: 0.7992 (tm130) cc_final: 0.7594 (tm-30)
REVERT: c   35 LYS cc_start: 0.9293 (ttmm) cc_final: 0.9038 (ttmm)
REVERT: d   24 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7212 (tm-30)
REVERT: d   63 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.7667 (tp)
REVERT: d   67 GLU cc_start: 0.8619 (tp30) cc_final: 0.8191 (tp30)
REVERT: d   71 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8256 (mmm160)
REVERT: d   95 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.8104 (m-80)
  outliers start: 40
  outliers final: 28
  residues processed: 276
  average time/residue: 0.2463
  time to fit residues: 92.9372
Evaluate side-chains
  263 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 231
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   81 PHE
Chi-restraints excluded: chain U residue   98 LEU
Chi-restraints excluded: chain U residue  100 SER
Chi-restraints excluded: chain U residue  105 ILE
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain W residue   67 SER
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain X residue   28 LEU
Chi-restraints excluded: chain X residue   58 GLU
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Y residue   13 LEU
Chi-restraints excluded: chain Y residue   44 LEU
Chi-restraints excluded: chain Y residue   51 CYS
Chi-restraints excluded: chain Z residue   33 LEU
Chi-restraints excluded: chain Z residue   74 SER
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue  202 VAL
Chi-restraints excluded: chain a residue  264 TYR
Chi-restraints excluded: chain b residue    6 LYS
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   39 ILE
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain c residue    4 ASN
Chi-restraints excluded: chain c residue   11 GLN
Chi-restraints excluded: chain d residue   38 SER
Chi-restraints excluded: chain d residue   63 ILE
Chi-restraints excluded: chain d residue   73 LEU
Chi-restraints excluded: chain d residue   95 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 29 optimal weight:   30.0000
   chunk 43 optimal weight:    0.6980
   chunk 2 optimal weight:   30.0000
   chunk 21 optimal weight:   20.0000
   chunk 87 optimal weight:    7.9990
   chunk 104 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 30 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  61 ASN
Y   5 HIS
** Z  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z  34 ASN
** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.145715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.105204 restraints weight = 32362.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.107764 restraints weight = 19019.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.109372 restraints weight = 13330.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10394  Z= 0.147
  Angle     :  0.759  15.593  14098  Z= 0.384
  Chirality :  0.043   0.361   1697
  Planarity :  0.004   0.050   1868
  Dihedral  :  4.519  59.093   1500
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 29.94 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.59 (0.21), residues: 1408
  helix:  2.86 (0.14), residues: 1175
  sheet: -0.33 (1.38), residues: 12
  loop : -0.33 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP b  59 
 HIS   0.017   0.002   HIS a 109 
 PHE   0.017   0.002   PHE a 168 
 TYR   0.034   0.002   TYR a 230 
 ARG   0.005   0.000   ARG a  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04035 ( 1042)
  hydrogen bonds       : angle       3.73905 ( 3102)
  covalent geometry    : bond        0.00313 (10394)
  covalent geometry    : angle       0.75869 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 248
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   89 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8141 (tm-30)
REVERT: U   93 ASP cc_start: 0.8188 (m-30) cc_final: 0.7786 (m-30)
REVERT: U   94 LEU cc_start: 0.8988 (tp) cc_final: 0.8634 (tt)
REVERT: U   98 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8438 (mm)
REVERT: U  135 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8669 (pp20)
REVERT: W   34 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8204 (mm-30)
REVERT: W   79 GLU cc_start: 0.7954 (mp0) cc_final: 0.7644 (pm20)
REVERT: Z   16 TYR cc_start: 0.7599 (m-80) cc_final: 0.6367 (m-80)
REVERT: Z   17 LYS cc_start: 0.9661 (mmtt) cc_final: 0.9440 (mmtt)
REVERT: Z   21 LEU cc_start: 0.9070 (pp) cc_final: 0.8699 (pp)
REVERT: Z   22 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7522 (m-30)
REVERT: Z   24 LYS cc_start: 0.8756 (mttp) cc_final: 0.8325 (mttp)
REVERT: Z   33 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7992 (mt)
REVERT: Z   34 ASN cc_start: 0.8497 (t0) cc_final: 0.8076 (p0)
REVERT: Z   38 HIS cc_start: 0.5394 (p-80) cc_final: 0.4154 (p-80)
REVERT: a  168 PHE cc_start: 0.7512 (m-80) cc_final: 0.7206 (m-80)
REVERT: a  256 ASP cc_start: 0.9527 (m-30) cc_final: 0.9185 (p0)
REVERT: b   16 GLU cc_start: 0.6541 (mp0) cc_final: 0.6319 (mp0)
REVERT: b   48 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: c    1 MET cc_start: 0.7407 (tmm) cc_final: 0.7148 (tpt)
REVERT: c    6 GLN cc_start: 0.7990 (tm130) cc_final: 0.7587 (tm-30)
REVERT: c   15 GLU cc_start: 0.8325 (tp30) cc_final: 0.7873 (mm-30)
REVERT: c   35 LYS cc_start: 0.9249 (ttmm) cc_final: 0.9005 (ttmm)
REVERT: d   24 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7214 (tm-30)
REVERT: d   86 ARG cc_start: 0.8158 (ptt180) cc_final: 0.7870 (ptm160)
REVERT: d   95 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.8119 (m-80)
  outliers start: 37
  outliers final: 25
  residues processed: 274
  average time/residue: 0.2417
  time to fit residues: 90.3295
Evaluate side-chains
  263 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 234
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   81 PHE
Chi-restraints excluded: chain U residue   98 LEU
Chi-restraints excluded: chain U residue  100 SER
Chi-restraints excluded: chain U residue  105 ILE
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain U residue  119 HIS
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain W residue   67 SER
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain X residue   28 LEU
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Y residue   13 LEU
Chi-restraints excluded: chain Y residue   44 LEU
Chi-restraints excluded: chain Y residue   51 CYS
Chi-restraints excluded: chain Z residue   22 ASP
Chi-restraints excluded: chain Z residue   33 LEU
Chi-restraints excluded: chain Z residue   74 SER
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue  264 TYR
Chi-restraints excluded: chain b residue    6 LYS
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   39 ILE
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain c residue   11 GLN
Chi-restraints excluded: chain d residue   73 LEU
Chi-restraints excluded: chain d residue   95 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 33 optimal weight:   50.0000
   chunk 1 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 92 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 133 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  61 ASN
** Z  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c   8 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.145122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.104328 restraints weight = 32702.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.106878 restraints weight = 19342.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.108453 restraints weight = 13611.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10394  Z= 0.151
  Angle     :  0.769  15.618  14098  Z= 0.385
  Chirality :  0.043   0.348   1697
  Planarity :  0.004   0.069   1868
  Dihedral  :  4.520  59.246   1500
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 30.57 %
    Favored  : 65.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.58 (0.22), residues: 1408
  helix:  2.84 (0.14), residues: 1176
  sheet: -0.35 (1.30), residues: 12
  loop : -0.27 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP b  59 
 HIS   0.016   0.001   HIS a 109 
 PHE   0.017   0.002   PHE a 205 
 TYR   0.030   0.002   TYR a 230 
 ARG   0.006   0.000   ARG a  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 ( 1042)
  hydrogen bonds       : angle       3.74261 ( 3102)
  covalent geometry    : bond        0.00326 (10394)
  covalent geometry    : angle       0.76886 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 239
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   83 ARG cc_start: 0.7685 (ptp-170) cc_final: 0.7483 (ptp-170)
REVERT: U   89 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: U   93 ASP cc_start: 0.8187 (m-30) cc_final: 0.7753 (m-30)
REVERT: U   94 LEU cc_start: 0.8994 (tp) cc_final: 0.8628 (tt)
REVERT: U   98 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8468 (mm)
REVERT: U  135 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8771 (pp20)
REVERT: W   34 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8154 (mm-30)
REVERT: W   79 GLU cc_start: 0.8002 (mp0) cc_final: 0.7681 (pm20)
REVERT: Z   11 GLU cc_start: 0.9579 (tm-30) cc_final: 0.9263 (pp20)
REVERT: Z   16 TYR cc_start: 0.7587 (m-80) cc_final: 0.6370 (m-80)
REVERT: Z   17 LYS cc_start: 0.9676 (mmtt) cc_final: 0.9437 (mmtt)
REVERT: Z   21 LEU cc_start: 0.9069 (pp) cc_final: 0.8678 (pp)
REVERT: Z   22 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7526 (m-30)
REVERT: Z   24 LYS cc_start: 0.8730 (mttp) cc_final: 0.8288 (mttp)
REVERT: Z   33 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8028 (mt)
REVERT: Z   34 ASN cc_start: 0.8563 (t0) cc_final: 0.8186 (p0)
REVERT: Z   38 HIS cc_start: 0.5507 (p-80) cc_final: 0.4196 (p-80)
REVERT: a  168 PHE cc_start: 0.7411 (m-80) cc_final: 0.7180 (m-80)
REVERT: b    1 MET cc_start: 0.6726 (ppp) cc_final: 0.5475 (ppp)
REVERT: b   48 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: c    1 MET cc_start: 0.7391 (tmm) cc_final: 0.7168 (tpt)
REVERT: c    6 GLN cc_start: 0.8022 (tm130) cc_final: 0.7655 (tm-30)
REVERT: c   15 GLU cc_start: 0.8348 (tp30) cc_final: 0.7880 (mm-30)
REVERT: c   35 LYS cc_start: 0.9229 (ttmm) cc_final: 0.9001 (ttmm)
REVERT: c   64 MET cc_start: 0.8815 (pmm) cc_final: 0.8165 (pmm)
REVERT: d   57 ARG cc_start: 0.8877 (tpp80) cc_final: 0.8470 (tpp80)
REVERT: d   67 GLU cc_start: 0.8493 (tp30) cc_final: 0.8145 (tp30)
REVERT: d   95 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.8136 (m-80)
  outliers start: 33
  outliers final: 25
  residues processed: 262
  average time/residue: 0.2377
  time to fit residues: 85.5068
Evaluate side-chains
  261 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 232
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   81 PHE
Chi-restraints excluded: chain U residue   98 LEU
Chi-restraints excluded: chain U residue  100 SER
Chi-restraints excluded: chain U residue  105 ILE
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain W residue   61 ASN
Chi-restraints excluded: chain W residue   67 SER
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain X residue   28 LEU
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Y residue   44 LEU
Chi-restraints excluded: chain Y residue   51 CYS
Chi-restraints excluded: chain Z residue   22 ASP
Chi-restraints excluded: chain Z residue   33 LEU
Chi-restraints excluded: chain Z residue   74 SER
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue  197 ARG
Chi-restraints excluded: chain a residue  264 TYR
Chi-restraints excluded: chain b residue    6 LYS
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   39 ILE
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain c residue   11 GLN
Chi-restraints excluded: chain d residue   73 LEU
Chi-restraints excluded: chain d residue   95 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0060
   chunk 0 optimal weight:   30.0000
   chunk 64 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 137 optimal weight:    5.9990
   chunk 117 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 129 optimal weight:    4.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  61 ASN
** Z  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 239 GLN ** 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 = 0.4319 r_free = 0.4319 target = 0.145560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.105078 restraints weight = 32370.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.107582 restraints weight = 19070.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.109225 restraints weight = 13450.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10394  Z= 0.151
  Angle     :  0.804  15.491  14098  Z= 0.404
  Chirality :  0.044   0.375   1697
  Planarity :  0.004   0.068   1868
  Dihedral  :  4.515  56.177   1500
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 31.41 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.52 (0.22), residues: 1408
  helix:  2.81 (0.14), residues: 1175
  sheet: -0.23 (1.29), residues: 12
  loop : -0.32 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP b  59 
 HIS   0.016   0.002   HIS a 109 
 PHE   0.018   0.002   PHE X  20 
 TYR   0.022   0.001   TYR a 230 
 ARG   0.007   0.001   ARG d  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04084 ( 1042)
  hydrogen bonds       : angle       3.76738 ( 3102)
  covalent geometry    : bond        0.00323 (10394)
  covalent geometry    : angle       0.80402 (14098)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 242
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: U   83 ARG cc_start: 0.7672 (ptp-170) cc_final: 0.7470 (ptp-170)
REVERT: U   89 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8137 (tm-30)
REVERT: U   93 ASP cc_start: 0.8191 (m-30) cc_final: 0.7783 (m-30)
REVERT: U   94 LEU cc_start: 0.8973 (tp) cc_final: 0.8637 (tt)
REVERT: U   98 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8452 (mm)
REVERT: U  135 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8783 (pp20)
REVERT: W   13 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8466 (ptpp)
REVERT: W   34 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8143 (mm-30)
REVERT: W   79 GLU cc_start: 0.7879 (mp0) cc_final: 0.7607 (pm20)
REVERT: X   24 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8363 (mtt180)
REVERT: Z   16 TYR cc_start: 0.7574 (m-80) cc_final: 0.6305 (m-80)
REVERT: Z   21 LEU cc_start: 0.9029 (pp) cc_final: 0.8646 (pp)
REVERT: Z   22 ASP cc_start: 0.8034 (t0) cc_final: 0.7525 (m-30)
REVERT: Z   24 LYS cc_start: 0.8700 (mttp) cc_final: 0.8267 (mttp)
REVERT: Z   33 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8051 (mt)
REVERT: Z   34 ASN cc_start: 0.8534 (t0) cc_final: 0.8168 (p0)
REVERT: Z   38 HIS cc_start: 0.5336 (p-80) cc_final: 0.4003 (p-80)
REVERT: a  197 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6206 (ptm-80)
REVERT: b    1 MET cc_start: 0.6748 (ppp) cc_final: 0.5467 (ppp)
REVERT: b   48 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8047 (tm-30)
REVERT: c    1 MET cc_start: 0.7395 (tmm) cc_final: 0.7174 (tpt)
REVERT: c    6 GLN cc_start: 0.8033 (tm130) cc_final: 0.7675 (tm-30)
REVERT: c   15 GLU cc_start: 0.8405 (tp30) cc_final: 0.7908 (mm-30)
REVERT: d   57 ARG cc_start: 0.8839 (tpp80) cc_final: 0.8609 (tpp80)
REVERT: d   86 ARG cc_start: 0.8186 (ptt180) cc_final: 0.7907 (ptm160)
REVERT: d   95 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.8131 (m-80)
  outliers start: 28
  outliers final: 22
  residues processed: 261
  average time/residue: 0.2364
  time to fit residues: 84.7270
Evaluate side-chains
  257 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 231
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain U residue   81 PHE
Chi-restraints excluded: chain U residue   98 LEU
Chi-restraints excluded: chain U residue  100 SER
Chi-restraints excluded: chain U residue  105 ILE
Chi-restraints excluded: chain U residue  106 MET
Chi-restraints excluded: chain V residue  102 SER
Chi-restraints excluded: chain V residue  114 HIS
Chi-restraints excluded: chain W residue   67 SER
Chi-restraints excluded: chain W residue  118 VAL
Chi-restraints excluded: chain X residue   28 LEU
Chi-restraints excluded: chain Y residue    8 VAL
Chi-restraints excluded: chain Y residue    9 GLN
Chi-restraints excluded: chain Y residue   44 LEU
Chi-restraints excluded: chain Y residue   51 CYS
Chi-restraints excluded: chain Z residue   33 LEU
Chi-restraints excluded: chain Z residue   74 SER
Chi-restraints excluded: chain Z residue   85 GLU
Chi-restraints excluded: chain a residue   66 VAL
Chi-restraints excluded: chain a residue  197 ARG
Chi-restraints excluded: chain a residue  264 TYR
Chi-restraints excluded: chain b residue    6 LYS
Chi-restraints excluded: chain b residue   38 ASP
Chi-restraints excluded: chain b residue   67 THR
Chi-restraints excluded: chain c residue   11 GLN
Chi-restraints excluded: chain d residue   73 LEU
Chi-restraints excluded: chain d residue   95 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 119 optimal weight:    0.7980
   chunk 27 optimal weight:   90.0000
   chunk 48 optimal weight:    6.9990
   chunk 17 optimal weight:   40.0000
   chunk 135 optimal weight:    3.9990
   chunk 20 optimal weight:   40.0000
   chunk 51 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
V 134 ASN
** W  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  61 ASN
** Z  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.144153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.103531 restraints weight = 32088.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.105919 restraints weight = 19066.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.107453 restraints weight = 13511.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10394  Z= 0.173
  Angle     :  0.818  16.348  14098  Z= 0.412
  Chirality :  0.045   0.369   1697
  Planarity :  0.004   0.066   1868
  Dihedral  :  4.496  56.087   1500
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 15.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 31.51 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.44 (0.22), residues: 1408
  helix:  2.75 (0.14), residues: 1177
  sheet: -0.27 (1.30), residues: 12
  loop : -0.36 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP b  59 
 HIS   0.017   0.002   HIS a 109 
 PHE   0.020   0.002   PHE b  30 
 TYR   0.012   0.002   TYR Z  35 
 ARG   0.014   0.001   ARG a  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 ( 1042)
  hydrogen bonds       : angle       3.82160 ( 3102)
  covalent geometry    : bond        0.00385 (10394)
  covalent geometry    : angle       0.81785 (14098)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5762.97 seconds
wall clock time: 102 minutes 1.19 seconds (6121.19 seconds total)