Starting phenix.real_space_refine
on Tue Mar  3 15:55:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wp6_32676/03_2026/7wp6_32676.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wp6_32676/03_2026/7wp6_32676.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wp6_32676/03_2026/7wp6_32676.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wp6_32676/03_2026/7wp6_32676.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wp6_32676/03_2026/7wp6_32676.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wp6_32676/03_2026/7wp6_32676.map"
  }
  resolution = 3.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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      30      5.16       5
     C    4278      2.51       5
     N    1111      2.21       5
     O    1329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6748
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 924
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "C"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 805
          Classifications: {'peptide': 104}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 919
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "F"
      Number of atoms: 1462
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1462
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "H"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 930
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 113}
    Chain: "I"
      Number of atoms: 875
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 875
          Classifications: {'peptide': 113}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 107}
    Chain: "L"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 791
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 97}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.53, per 1000 atoms: 0.23
  Number of scatterers: 6748
  At special positions: 0
  Unit cell: (77.022, 109.698, 126.036, 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      30     16.00
     O    1329      8.00
     N    1111      7.00
     C    4278      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.72
    Simple disulfide: pdb=" SG  CYS F 480 " - pdb=" SG  CYS F 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS I  23 " - pdb=" SG  CYS I  94 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN F 343 "
      " NAG L 201 " - " ASN L  26 "
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 155.8 milliseconds
  

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1568

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 18 sheets defined
      1.6% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'F' and resid 405 through 410
      removed outlier: 4.893A  pdb=" N   ARG F 408 " --> pdb=" O   ASP F 405 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE F 410 " --> pdb=" O   VAL F 407 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'I' and resid 85 through 89
      removed outlier: 3.826A  pdb=" N   LEU I  89 " --> pdb=" O   ALA I  86 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 5
      removed outlier: 3.748A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   SER B  25 " --> pdb=" O   GLN B   3 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12
      removed outlier: 3.687A  pdb=" N   THR B 117 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   MET B  34 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   GLY B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   TRP B  36 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LYS B  38 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   GLU B  46 " --> pdb=" O   LYS B  38 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.108A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 19 through 24
      removed outlier: 3.617A  pdb=" N   THR C  63 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 54
      removed outlier: 3.618A  pdb=" N   THR C  53 " --> pdb=" O   SER C  49 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   LEU C  46 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLN C  37 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN C  38 " --> pdb=" O   ASP C  85 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   ASP C  85 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 11
      removed outlier: 3.711A  pdb=" N   THR D 117 " --> pdb=" O   GLU D  10 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   MET D  34 " --> pdb=" O   ALA D  50 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   ALA D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   TRP D  36 " --> pdb=" O   ILE D  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11
      removed outlier: 3.711A  pdb=" N   THR D 117 " --> pdb=" O   GLU D  10 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 22 through 23
      removed outlier: 3.722A  pdb=" N   THR D  78 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 354 through 358
      removed outlier: 3.507A  pdb=" N   ASN F 354 " --> pdb=" O   SER F 399 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL F 395 " --> pdb=" O   ILE F 358 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ASN F 394 " --> pdb=" O   GLU F 516 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 452 through 454
    Processing sheet with id=AB2, first strand: chain 'H' and resid 5 through 6
      removed outlier: 3.901A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.711A  pdb=" N   THR H 112 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE H  95 " --> pdb=" O   VAL H  37 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL H  37 " --> pdb=" O   PHE H  95 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   TRP H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.711A  pdb=" N   THR H 112 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   PHE H 107 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 6
      removed outlier: 3.813A  pdb=" N   SER I   5 " --> pdb=" O   LYS I  24 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   CYS I  23 " --> pdb=" O   PHE I  77 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP I  76 " --> pdb=" O   SER I  73 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'I' and resid 30 through 31
      removed outlier: 3.506A  pdb=" N   LYS I  36 " --> pdb=" O   TYR I  31 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 51 through 52
      removed outlier: 4.011A  pdb=" N   CYS I  94 " --> pdb=" O   GLY I 105 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLY I 105 " --> pdb=" O   CYS I  94 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.772A  pdb=" N   SER L  69 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   SER L  66 " --> pdb=" O   SER L  69 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.683A  pdb=" N   TRP L  34 " --> pdb=" O   TRP L  46 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TRP L  46 " --> pdb=" O   TRP L  34 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    402 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.63

  Time building geometry restraints manager: 0.64 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: 2091
        1.34 -     1.46: 1794
        1.46 -     1.58: 2997
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 6922
  Sorted by residual:
  bond pdb=" C   TYR H  52 "
       pdb=" N   PRO H  53 "
    ideal  model  delta    sigma   weight residual
    1.337  1.307  0.030 1.06e-02 8.90e+03 7.91e+00
  bond pdb=" CA  CYS H  22 "
       pdb=" CB  CYS H  22 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.037 1.62e-02 3.81e+03 5.34e+00
  bond pdb=" CA  ALA L  25 "
       pdb=" C   ALA L  25 "
    ideal  model  delta    sigma   weight residual
    1.522  1.496  0.026 1.23e-02 6.61e+03 4.49e+00
  bond pdb=" C   VAL I  64 "
       pdb=" N   PRO I  65 "
    ideal  model  delta    sigma   weight residual
    1.331  1.356 -0.025 1.20e-02 6.94e+03 4.41e+00
  bond pdb=" CA  ALA F 344 "
       pdb=" C   ALA F 344 "
    ideal  model  delta    sigma   weight residual
    1.526  1.497  0.028 1.36e-02 5.41e+03 4.28e+00
  ... (remaining 6917 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.15: 9227
        3.15 -     6.30: 149
        6.30 -     9.44: 18
        9.44 -    12.59: 3
       12.59 -    15.74: 1
  Bond angle restraints: 9398
  Sorted by residual:
  angle pdb=" N   SER L  27 "
        pdb=" CA  SER L  27 "
        pdb=" C   SER L  27 "
      ideal   model   delta    sigma   weight residual
     110.80  120.85  -10.05 2.13e+00 2.20e-01 2.22e+01
  angle pdb=" C   GLN I  48 "
        pdb=" N   SER I  49 "
        pdb=" CA  SER I  49 "
      ideal   model   delta    sigma   weight residual
     121.27  137.01  -15.74 3.40e+00 8.65e-02 2.14e+01
  angle pdb=" C   TYR L  48 "
        pdb=" N   ALA L  49 "
        pdb=" CA  ALA L  49 "
      ideal   model   delta    sigma   weight residual
     121.19  128.35   -7.16 1.59e+00 3.96e-01 2.03e+01
  angle pdb=" N   PHE I 100 "
        pdb=" CA  PHE I 100 "
        pdb=" C   PHE I 100 "
      ideal   model   delta    sigma   weight residual
     109.81  119.75   -9.94 2.21e+00 2.05e-01 2.02e+01
  angle pdb=" C   SER B  40 "
        pdb=" N   HIS B  41 "
        pdb=" CA  HIS B  41 "
      ideal   model   delta    sigma   weight residual
     122.36  128.23   -5.87 1.42e+00 4.96e-01 1.71e+01
  ... (remaining 9393 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.61: 3544
       16.61 -    33.21: 450
       33.21 -    49.82: 75
       49.82 -    66.43: 12
       66.43 -    83.03: 9
  Dihedral angle restraints: 4090
    sinusoidal: 1608
      harmonic: 2482
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.57  -76.57     1      1.00e+01 1.00e-02 7.37e+01
  dihedral pdb=" CA  TRP C  50 "
           pdb=" C   TRP C  50 "
           pdb=" N   ALA C  51 "
           pdb=" CA  ALA C  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.27  -35.73     0      5.00e+00 4.00e-02 5.11e+01
  dihedral pdb=" CB  CYS F 480 "
           pdb=" SG  CYS F 480 "
           pdb=" SG  CYS F 488 "
           pdb=" CB  CYS F 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.21   47.21     1      1.00e+01 1.00e-02 3.08e+01
  ... (remaining 4087 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 859
       0.079 -    0.159: 126
       0.159 -    0.238: 14
       0.238 -    0.318: 3
       0.318 -    0.397: 4
  Chirality restraints: 1006
  Sorted by residual:
  chirality pdb=" CA  SER L  27 "
            pdb=" N   SER L  27 "
            pdb=" C   SER L  27 "
            pdb=" CB  SER L  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" CB  ILE H  51 "
            pdb=" CA  ILE H  51 "
            pdb=" CG1 ILE H  51 "
            pdb=" CG2 ILE H  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.38 2.00e-01 2.50e+01 3.59e+00
  chirality pdb=" CB  THR C 102 "
            pdb=" CA  THR C 102 "
            pdb=" OG1 THR C 102 "
            pdb=" CG2 THR C 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.21    0.34 2.00e-01 2.50e+01 2.89e+00
  ... (remaining 1003 not shown)

  Planarity restraints: 1201
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG L 201 "    0.328 2.00e-02 2.50e+03   2.84e-01 1.01e+03
        pdb=" C7  NAG L 201 "   -0.076 2.00e-02 2.50e+03
        pdb=" C8  NAG L 201 "    0.046 2.00e-02 2.50e+03
        pdb=" N2  NAG L 201 "   -0.499 2.00e-02 2.50e+03
        pdb=" O7  NAG L 201 "    0.200 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "    0.240 2.00e-02 2.50e+03   2.05e-01 5.26e+02
        pdb=" C7  NAG A   1 "   -0.052 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.030 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "   -0.341 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "    0.182 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "   -0.122 2.00e-02 2.50e+03   1.01e-01 1.27e+02
        pdb=" C7  NAG A   2 "    0.032 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "   -0.091 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "    0.162 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1198 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1243
        2.76 -     3.29: 5754
        3.29 -     3.83: 10868
        3.83 -     4.36: 11903
        4.36 -     4.90: 21382
  Nonbonded interactions: 51150
  Sorted by model distance:
  nonbonded pdb=" O   ASP C  30 "
            pdb=" OD1 ASP C  30 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG1 THR F 478 "
            pdb=" O   TYR I  98 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   SER F 438 "
            pdb=" OG  SER F 438 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OD1 ASP F 442 "
            pdb=" OH  TYR F 451 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   THR D 114 "
            pdb=" OG1 THR D 114 "
     model   vdw
     2.321 3.040
  ... (remaining 51145 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=1.00 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:             5.930
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.480
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
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      :  0.011   0.684   6932  Z= 0.547
  Angle     :  1.138  32.640   9421  Z= 0.621
  Chirality :  0.062   0.397   1006
  Planarity :  0.013   0.284   1199
  Dihedral  : 14.824  83.035   2501
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.45 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 12.07 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.82 (0.24), residues: 847
  helix: -5.32 (0.38), residues: 8
  sheet: -1.64 (0.29), residues: 290
  loop : -3.20 (0.21), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 355 
 TYR   0.032   0.003   TYR I  55 
 PHE   0.029   0.003   PHE I 100 
 TRP   0.027   0.003   TRP I  56 
 HIS   0.006   0.003   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00768 ( 6922)
  covalent geometry    : angle       1.06603 ( 9398)
  SS BOND              : bond        0.25876 (    7)
  SS BOND              : angle       9.81092 (   14)
  hydrogen bonds       : bond        0.28652 (  154)
  hydrogen bonds       : angle      11.18493 (  402)
  link_BETA1-4         : bond        0.01095 (    1)
  link_BETA1-4         : angle       6.88447 (    3)
  link_NAG-ASN         : bond        0.00701 (    2)
  link_NAG-ASN         : angle       2.08832 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 242
  time to evaluate  : 0.190 
Fit side-chains
REVERT: B   10 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8433 (mp0)
REVERT: C   27 GLN cc_start: 0.7769 (mp10) cc_final: 0.7190 (mp10)
REVERT: C   54 ARG cc_start: 0.8072 (ptp90) cc_final: 0.7803 (ptp90)
REVERT: D   83 LEU cc_start: 0.9041 (mt) cc_final: 0.8733 (mp)
REVERT: F  414 GLN cc_start: 0.7616 (tt0) cc_final: 0.7164 (mp10)
REVERT: F  465 GLU cc_start: 0.8573 (tp30) cc_final: 0.8228 (tp30)
REVERT: H   73 ASP cc_start: 0.7839 (m-30) cc_final: 0.7029 (p0)
  outliers start: 5
  outliers final: 4
  residues processed: 245
  average time/residue: 0.0907
  time to fit residues: 28.4948
Evaluate side-chains
  194 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 190
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain I residue   42 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
C  79 GLN
C  90 GLN
D  62 GLN
F 487 ASN
F 493 GLN
I  96 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.141546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.108668 restraints weight = 12411.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.112362 restraints weight = 7798.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.114940 restraints weight = 5813.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.116720 restraints weight = 4782.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.117829 restraints weight = 4187.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6932  Z= 0.141
  Angle     :  0.683  12.367   9421  Z= 0.347
  Chirality :  0.045   0.214   1006
  Planarity :  0.005   0.059   1199
  Dihedral  :  6.211  41.566   1015
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 21.40 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.27), residues: 847
  helix: -5.23 (0.43), residues: 8
  sheet: -0.98 (0.28), residues: 350
  loop : -2.80 (0.24), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  61 
 TYR   0.020   0.002   TYR I  42 
 PHE   0.026   0.002   PHE I 100 
 TRP   0.025   0.002   TRP I  56 
 HIS   0.003   0.001   HIS L  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 6922)
  covalent geometry    : angle       0.67293 ( 9398)
  SS BOND              : bond        0.00616 (    7)
  SS BOND              : angle       1.43311 (   14)
  hydrogen bonds       : bond        0.04070 (  154)
  hydrogen bonds       : angle       7.68741 (  402)
  link_BETA1-4         : bond        0.00684 (    1)
  link_BETA1-4         : angle       5.57390 (    3)
  link_NAG-ASN         : bond        0.00189 (    2)
  link_NAG-ASN         : angle       1.95301 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 LYS cc_start: 0.7528 (tttt) cc_final: 0.7241 (ptmm)
REVERT: B   46 GLU cc_start: 0.6284 (pm20) cc_final: 0.6071 (pm20)
REVERT: B   80 TYR cc_start: 0.7737 (m-80) cc_final: 0.7390 (m-80)
REVERT: B   89 GLU cc_start: 0.7473 (mp0) cc_final: 0.7197 (mp0)
REVERT: C   18 ARG cc_start: 0.4520 (OUTLIER) cc_final: 0.3703 (ttp-110)
REVERT: C   54 ARG cc_start: 0.7694 (ptp90) cc_final: 0.7487 (ptp90)
REVERT: D   60 TYR cc_start: 0.8842 (m-10) cc_final: 0.8459 (m-80)
REVERT: D   80 TYR cc_start: 0.7913 (m-80) cc_final: 0.7615 (m-10)
REVERT: F  414 GLN cc_start: 0.7339 (tt0) cc_final: 0.7046 (mp10)
REVERT: H   38 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8375 (ttmm)
REVERT: H   46 GLU cc_start: 0.8225 (tp30) cc_final: 0.7980 (tp30)
REVERT: I   41 TRP cc_start: 0.8555 (m100) cc_final: 0.8210 (m100)
REVERT: L   38 LYS cc_start: 0.9172 (tppp) cc_final: 0.8653 (ttpt)
  outliers start: 24
  outliers final: 19
  residues processed: 222
  average time/residue: 0.0897
  time to fit residues: 25.6518
Evaluate side-chains
  204 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    5 GLN
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  103 LYS
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  113 THR
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   55 TYR
Chi-restraints excluded: chain I residue   67 ARG
Chi-restraints excluded: chain I residue   69 THR
Chi-restraints excluded: chain I residue  108 THR
Chi-restraints excluded: chain L residue    3 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0870
   chunk 0 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0040
   chunk 63 optimal weight:    9.9990
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.5372

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

Flipped N/Q/H residues before XYZ refinement:
** I  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.141624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.109331 restraints weight = 12123.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.113082 restraints weight = 7451.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.115603 restraints weight = 5482.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.117323 restraints weight = 4493.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.118341 restraints weight = 3930.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6932  Z= 0.127
  Angle     :  0.672  13.329   9421  Z= 0.334
  Chirality :  0.044   0.185   1006
  Planarity :  0.005   0.057   1199
  Dihedral  :  5.806  40.626   1015
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.02 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 20.99 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.27), residues: 847
  helix: -5.17 (0.46), residues: 8
  sheet: -0.57 (0.28), residues: 349
  loop : -2.63 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  76 
 TYR   0.021   0.002   TYR I  42 
 PHE   0.025   0.002   PHE I  77 
 TRP   0.017   0.001   TRP I  56 
 HIS   0.002   0.001   HIS L  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6922)
  covalent geometry    : angle       0.66250 ( 9398)
  SS BOND              : bond        0.00468 (    7)
  SS BOND              : angle       1.58808 (   14)
  hydrogen bonds       : bond        0.03795 (  154)
  hydrogen bonds       : angle       6.91931 (  402)
  link_BETA1-4         : bond        0.01189 (    1)
  link_BETA1-4         : angle       5.34044 (    3)
  link_NAG-ASN         : bond        0.00077 (    2)
  link_NAG-ASN         : angle       1.43724 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 198
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 LYS cc_start: 0.7561 (tttt) cc_final: 0.7281 (ptmm)
REVERT: B   89 GLU cc_start: 0.7507 (mp0) cc_final: 0.7216 (mp0)
REVERT: C   18 ARG cc_start: 0.4612 (OUTLIER) cc_final: 0.4268 (ttp80)
REVERT: C   54 ARG cc_start: 0.7694 (ptp90) cc_final: 0.7442 (ptp90)
REVERT: D   60 TYR cc_start: 0.8871 (m-10) cc_final: 0.8630 (m-80)
REVERT: F  414 GLN cc_start: 0.7263 (tt0) cc_final: 0.7046 (mp10)
REVERT: H   38 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8597 (ttmm)
REVERT: I   41 TRP cc_start: 0.8473 (m100) cc_final: 0.8225 (m100)
REVERT: I   73 SER cc_start: 0.7520 (t) cc_final: 0.7078 (m)
REVERT: L   38 LYS cc_start: 0.9187 (tppp) cc_final: 0.8646 (ttpt)
  outliers start: 39
  outliers final: 26
  residues processed: 217
  average time/residue: 0.0956
  time to fit residues: 26.7623
Evaluate side-chains
  215 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  114 THR
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue   23 CYS
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   55 TYR
Chi-restraints excluded: chain I residue   67 ARG
Chi-restraints excluded: chain I residue   68 PHE
Chi-restraints excluded: chain I residue   69 THR
Chi-restraints excluded: chain I residue  108 THR
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue  101 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0470
   chunk 37 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 15 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.1484

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

Flipped N/Q/H residues before XYZ refinement:
** I  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.139063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.106146 restraints weight = 12514.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.109712 restraints weight = 7924.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.112141 restraints weight = 5963.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.113744 restraints weight = 4955.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114876 restraints weight = 4373.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6932  Z= 0.181
  Angle     :  0.697  13.080   9421  Z= 0.348
  Chirality :  0.044   0.202   1006
  Planarity :  0.004   0.057   1199
  Dihedral  :  5.932  46.808   1015
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.20 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 21.67 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.46 (0.28), residues: 847
  helix: -5.09 (0.54), residues: 8
  sheet: -0.57 (0.28), residues: 353
  loop : -2.51 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG F 408 
 TYR   0.021   0.002   TYR I  42 
 PHE   0.026   0.002   PHE I  77 
 TRP   0.017   0.002   TRP I  56 
 HIS   0.003   0.001   HIS L  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6922)
  covalent geometry    : angle       0.68905 ( 9398)
  SS BOND              : bond        0.00564 (    7)
  SS BOND              : angle       1.49157 (   14)
  hydrogen bonds       : bond        0.03669 (  154)
  hydrogen bonds       : angle       6.61011 (  402)
  link_BETA1-4         : bond        0.01110 (    1)
  link_BETA1-4         : angle       5.11046 (    3)
  link_NAG-ASN         : bond        0.00035 (    2)
  link_NAG-ASN         : angle       1.33319 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 192
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   63 LYS cc_start: 0.9295 (tttm) cc_final: 0.8867 (tttp)
REVERT: B   89 GLU cc_start: 0.7550 (mp0) cc_final: 0.7234 (mp0)
REVERT: C   18 ARG cc_start: 0.4777 (OUTLIER) cc_final: 0.3880 (ttp-110)
REVERT: C   54 ARG cc_start: 0.7725 (ptp90) cc_final: 0.7476 (ptp90)
REVERT: D    6 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7413 (tm-30)
REVERT: D   60 TYR cc_start: 0.8878 (m-10) cc_final: 0.8619 (m-80)
REVERT: F  414 GLN cc_start: 0.7273 (tt0) cc_final: 0.7054 (mp10)
REVERT: F  472 ILE cc_start: 0.6286 (mm) cc_final: 0.6065 (mm)
REVERT: H   38 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8487 (ttmm)
REVERT: I   21 MET cc_start: 0.5757 (mmm) cc_final: 0.5430 (mmm)
REVERT: I   41 TRP cc_start: 0.8491 (m100) cc_final: 0.8222 (m100)
REVERT: I   73 SER cc_start: 0.7559 (t) cc_final: 0.7010 (m)
REVERT: L   38 LYS cc_start: 0.9186 (tppp) cc_final: 0.8654 (ttpt)
REVERT: L   78 GLU cc_start: 0.8482 (tt0) cc_final: 0.8100 (tt0)
  outliers start: 42
  outliers final: 29
  residues processed: 216
  average time/residue: 0.0882
  time to fit residues: 24.6969
Evaluate side-chains
  219 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 188
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue  103 LYS
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  114 THR
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue   23 CYS
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   55 TYR
Chi-restraints excluded: chain I residue   64 VAL
Chi-restraints excluded: chain I residue   67 ARG
Chi-restraints excluded: chain I residue   68 PHE
Chi-restraints excluded: chain I residue   69 THR
Chi-restraints excluded: chain I residue  108 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue  101 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  41 HIS
H 101 HIS
I  27 GLN
** I  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.136776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.104012 restraints weight = 12625.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.107425 restraints weight = 8106.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.109777 restraints weight = 6124.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.111394 restraints weight = 5117.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.112305 restraints weight = 4517.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6932  Z= 0.225
  Angle     :  0.736  13.297   9421  Z= 0.369
  Chirality :  0.044   0.218   1006
  Planarity :  0.005   0.056   1199
  Dihedral  :  6.116  53.850   1015
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.15 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 22.22 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.28), residues: 847
  helix: -4.96 (0.65), residues: 8
  sheet: -0.55 (0.28), residues: 352
  loop : -2.46 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  98 
 TYR   0.024   0.002   TYR I  97 
 PHE   0.024   0.002   PHE I 100 
 TRP   0.020   0.002   TRP I  56 
 HIS   0.004   0.001   HIS L  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 6922)
  covalent geometry    : angle       0.72693 ( 9398)
  SS BOND              : bond        0.01277 (    7)
  SS BOND              : angle       1.87598 (   14)
  hydrogen bonds       : bond        0.03691 (  154)
  hydrogen bonds       : angle       6.48003 (  402)
  link_BETA1-4         : bond        0.01097 (    1)
  link_BETA1-4         : angle       4.88653 (    3)
  link_NAG-ASN         : bond        0.00101 (    2)
  link_NAG-ASN         : angle       1.43427 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 194
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   17 SER cc_start: 0.8141 (m) cc_final: 0.7774 (p)
REVERT: B   63 LYS cc_start: 0.9332 (tttm) cc_final: 0.8881 (tttp)
REVERT: B   89 GLU cc_start: 0.7601 (mp0) cc_final: 0.7238 (mp0)
REVERT: C   18 ARG cc_start: 0.4876 (OUTLIER) cc_final: 0.3970 (ttp-110)
REVERT: C   47 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8206 (mp)
REVERT: D   60 TYR cc_start: 0.8890 (m-10) cc_final: 0.8311 (m-10)
REVERT: F  472 ILE cc_start: 0.6377 (mm) cc_final: 0.6173 (mm)
REVERT: H   38 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8352 (ttmm)
REVERT: H   63 LYS cc_start: 0.8902 (mttt) cc_final: 0.8678 (mttt)
REVERT: I   97 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8121 (p90)
REVERT: L   38 LYS cc_start: 0.9194 (tppp) cc_final: 0.8667 (ttpt)
  outliers start: 51
  outliers final: 39
  residues processed: 220
  average time/residue: 0.0887
  time to fit residues: 25.1625
Evaluate side-chains
  228 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 185
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  114 THR
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue   23 CYS
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue   39 LEU
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   64 VAL
Chi-restraints excluded: chain I residue   67 ARG
Chi-restraints excluded: chain I residue   68 PHE
Chi-restraints excluded: chain I residue   69 THR
Chi-restraints excluded: chain I residue   97 TYR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   32 MET
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   57 VAL
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  101 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 42 optimal weight:    0.1980
   chunk 72 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:    0.3980
   chunk 79 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 14 optimal weight:    0.3980
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
I  95 GLN
L  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.139132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.106251 restraints weight = 12481.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.109961 restraints weight = 7788.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.112487 restraints weight = 5764.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.114146 restraints weight = 4765.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.115307 restraints weight = 4196.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6932  Z= 0.127
  Angle     :  0.685  12.999   9421  Z= 0.338
  Chirality :  0.043   0.181   1006
  Planarity :  0.004   0.053   1199
  Dihedral  :  5.843  47.404   1015
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.38 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 23.73 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.28), residues: 847
  helix: -4.74 (0.86), residues: 8
  sheet: -0.46 (0.28), residues: 350
  loop : -2.28 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F 457 
 TYR   0.027   0.002   TYR F 380 
 PHE   0.034   0.002   PHE F 456 
 TRP   0.011   0.001   TRP H  50 
 HIS   0.002   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6922)
  covalent geometry    : angle       0.67845 ( 9398)
  SS BOND              : bond        0.00769 (    7)
  SS BOND              : angle       0.91322 (   14)
  hydrogen bonds       : bond        0.03306 (  154)
  hydrogen bonds       : angle       6.21498 (  402)
  link_BETA1-4         : bond        0.01155 (    1)
  link_BETA1-4         : angle       4.98990 (    3)
  link_NAG-ASN         : bond        0.00077 (    2)
  link_NAG-ASN         : angle       1.28883 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 196
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 SER cc_start: 0.8094 (m) cc_final: 0.7823 (p)
REVERT: B   63 LYS cc_start: 0.9327 (tttm) cc_final: 0.8973 (tttm)
REVERT: B   89 GLU cc_start: 0.7529 (mp0) cc_final: 0.7214 (mp0)
REVERT: C   18 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.3998 (ttp-110)
REVERT: C   54 ARG cc_start: 0.7749 (ptp90) cc_final: 0.7458 (ptp90)
REVERT: D   23 LYS cc_start: 0.8321 (tttm) cc_final: 0.7855 (ttmm)
REVERT: F  472 ILE cc_start: 0.6293 (mm) cc_final: 0.6092 (mm)
REVERT: H    3 GLN cc_start: 0.8342 (tt0) cc_final: 0.7964 (tm-30)
REVERT: H   38 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8369 (ttmm)
REVERT: I   34 ASN cc_start: 0.8517 (p0) cc_final: 0.8059 (p0)
REVERT: L   38 LYS cc_start: 0.9183 (tppp) cc_final: 0.8681 (ttpt)
  outliers start: 43
  outliers final: 30
  residues processed: 219
  average time/residue: 0.0901
  time to fit residues: 25.6010
Evaluate side-chains
  218 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 186
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain D residue  114 THR
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue  101 HIS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue   23 CYS
Chi-restraints excluded: chain I residue   36 LYS
Chi-restraints excluded: chain I residue   39 LEU
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   64 VAL
Chi-restraints excluded: chain I residue   67 ARG
Chi-restraints excluded: chain I residue   68 PHE
Chi-restraints excluded: chain I residue   91 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   50 THR
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  101 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0770
   chunk 59 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.7742

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

Flipped N/Q/H residues before XYZ refinement:
C  20 ASN
** I  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.141016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.109037 restraints weight = 12370.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.112548 restraints weight = 7908.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114890 restraints weight = 5958.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.116437 restraints weight = 4968.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.117608 restraints weight = 4387.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6932  Z= 0.145
  Angle     :  0.691  12.303   9421  Z= 0.342
  Chirality :  0.043   0.177   1006
  Planarity :  0.004   0.054   1199
  Dihedral  :  5.770  47.062   1015
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.73 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 24.28 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.28), residues: 847
  helix: -4.58 (1.03), residues: 8
  sheet: -0.18 (0.29), residues: 333
  loop : -2.19 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG L  24 
 TYR   0.024   0.002   TYR F 380 
 PHE   0.033   0.002   PHE I  77 
 TRP   0.011   0.001   TRP F 436 
 HIS   0.002   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6922)
  covalent geometry    : angle       0.68373 ( 9398)
  SS BOND              : bond        0.00509 (    7)
  SS BOND              : angle       1.19967 (   14)
  hydrogen bonds       : bond        0.03233 (  154)
  hydrogen bonds       : angle       6.14623 (  402)
  link_BETA1-4         : bond        0.01044 (    1)
  link_BETA1-4         : angle       4.78559 (    3)
  link_NAG-ASN         : bond        0.00042 (    2)
  link_NAG-ASN         : angle       1.31233 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 197
  time to evaluate  : 0.304 
Fit side-chains
REVERT: B   17 SER cc_start: 0.8169 (m) cc_final: 0.7914 (p)
REVERT: B   63 LYS cc_start: 0.9312 (tttm) cc_final: 0.9026 (tttm)
REVERT: B   89 GLU cc_start: 0.7598 (mp0) cc_final: 0.7258 (mp0)
REVERT: D   10 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6348 (tm-30)
REVERT: D   23 LYS cc_start: 0.8257 (tttm) cc_final: 0.7840 (ttmm)
REVERT: D   60 TYR cc_start: 0.8902 (m-10) cc_final: 0.8584 (m-10)
REVERT: H    3 GLN cc_start: 0.8318 (tt0) cc_final: 0.8018 (tm-30)
REVERT: H   38 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8548 (ttmm)
REVERT: H   69 THR cc_start: 0.8995 (m) cc_final: 0.8598 (p)
REVERT: H   80 TYR cc_start: 0.7917 (m-80) cc_final: 0.7683 (m-80)
REVERT: I   21 MET cc_start: 0.5669 (mmm) cc_final: 0.5221 (mmm)
REVERT: I   31 TYR cc_start: 0.7585 (t80) cc_final: 0.7321 (t80)
REVERT: I   34 ASN cc_start: 0.8481 (p0) cc_final: 0.7972 (p0)
REVERT: I   56 TRP cc_start: 0.7727 (m-10) cc_final: 0.7480 (m-10)
REVERT: I   67 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5625 (ptt180)
REVERT: L   38 LYS cc_start: 0.9191 (tppp) cc_final: 0.8680 (ttpt)
  outliers start: 42
  outliers final: 34
  residues processed: 214
  average time/residue: 0.0848
  time to fit residues: 23.7114
Evaluate side-chains
  225 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 189
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  114 THR
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  380 TYR
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue  101 HIS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue   23 CYS
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue   39 LEU
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   64 VAL
Chi-restraints excluded: chain I residue   67 ARG
Chi-restraints excluded: chain I residue   68 PHE
Chi-restraints excluded: chain I residue   69 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   68 THR
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue  101 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   chunk 68 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  35 HIS
C  20 ASN
** I  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.133748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.101279 restraints weight = 12744.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.104587 restraints weight = 8178.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.106817 restraints weight = 6225.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.108320 restraints weight = 5226.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.109169 restraints weight = 4651.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069   6932  Z= 0.302
  Angle     :  0.812  12.799   9421  Z= 0.408
  Chirality :  0.046   0.232   1006
  Planarity :  0.005   0.057   1199
  Dihedral  :  6.534  59.072   1015
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  9.80 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 24.55 %
    Favored  : 69.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.28), residues: 847
  helix: -4.60 (0.99), residues: 8
  sheet: -0.56 (0.28), residues: 344
  loop : -2.29 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  99 
 TYR   0.035   0.003   TYR I  97 
 PHE   0.037   0.003   PHE I  77 
 TRP   0.013   0.002   TRP F 353 
 HIS   0.006   0.002   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 ( 6922)
  covalent geometry    : angle       0.80532 ( 9398)
  SS BOND              : bond        0.00612 (    7)
  SS BOND              : angle       1.68132 (   14)
  hydrogen bonds       : bond        0.03994 (  154)
  hydrogen bonds       : angle       6.50949 (  402)
  link_BETA1-4         : bond        0.00941 (    1)
  link_BETA1-4         : angle       4.53441 (    3)
  link_NAG-ASN         : bond        0.00100 (    2)
  link_NAG-ASN         : angle       1.54890 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 184
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 GLU cc_start: 0.7645 (mp0) cc_final: 0.7309 (mp0)
REVERT: D   10 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6373 (tm-30)
REVERT: D   60 TYR cc_start: 0.8853 (m-10) cc_final: 0.8358 (m-80)
REVERT: H    3 GLN cc_start: 0.8376 (tt0) cc_final: 0.8039 (tm-30)
REVERT: H   38 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8368 (ttmm)
REVERT: I   34 ASN cc_start: 0.8433 (p0) cc_final: 0.8219 (p0)
REVERT: I   51 LYS cc_start: 0.9125 (tptt) cc_final: 0.8867 (tptt)
REVERT: I   97 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.8098 (p90)
REVERT: L   38 LYS cc_start: 0.9195 (tppp) cc_final: 0.8641 (ttpt)
  outliers start: 45
  outliers final: 39
  residues processed: 211
  average time/residue: 0.0869
  time to fit residues: 23.9755
Evaluate side-chains
  215 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 175
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue    3 VAL
Chi-restraints excluded: chain C residue   19 VAL
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  114 THR
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  380 TYR
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue   23 CYS
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue   36 LYS
Chi-restraints excluded: chain I residue   39 LEU
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   64 VAL
Chi-restraints excluded: chain I residue   68 PHE
Chi-restraints excluded: chain I residue   69 THR
Chi-restraints excluded: chain I residue   97 TYR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   68 THR
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue   77 VAL
Chi-restraints excluded: chain L residue  101 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C  20 ASN
I  95 GLN
L  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.139077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.106727 restraints weight = 12430.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.110329 restraints weight = 7771.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.112817 restraints weight = 5776.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.114479 restraints weight = 4766.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115631 restraints weight = 4188.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6932  Z= 0.146
  Angle     :  0.738  12.106   9421  Z= 0.368
  Chirality :  0.044   0.181   1006
  Planarity :  0.004   0.053   1199
  Dihedral  :  6.155  57.649   1015
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 26.47 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.28), residues: 847
  helix: -4.41 (1.17), residues: 8
  sheet: -0.26 (0.29), residues: 329
  loop : -2.21 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 408 
 TYR   0.026   0.002   TYR F 473 
 PHE   0.035   0.002   PHE I  77 
 TRP   0.015   0.002   TRP I  56 
 HIS   0.002   0.001   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6922)
  covalent geometry    : angle       0.73260 ( 9398)
  SS BOND              : bond        0.00487 (    7)
  SS BOND              : angle       1.04670 (   14)
  hydrogen bonds       : bond        0.03351 (  154)
  hydrogen bonds       : angle       6.05856 (  402)
  link_BETA1-4         : bond        0.00999 (    1)
  link_BETA1-4         : angle       4.77842 (    3)
  link_NAG-ASN         : bond        0.00081 (    2)
  link_NAG-ASN         : angle       1.26496 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 192
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 GLU cc_start: 0.7638 (mp0) cc_final: 0.7290 (mp0)
REVERT: D   10 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6371 (tm-30)
REVERT: D   23 LYS cc_start: 0.8283 (tttm) cc_final: 0.7827 (ttmm)
REVERT: D   60 TYR cc_start: 0.8867 (m-10) cc_final: 0.8388 (m-80)
REVERT: H   38 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8347 (ttmm)
REVERT: H   69 THR cc_start: 0.8976 (m) cc_final: 0.8544 (p)
REVERT: I   34 ASN cc_start: 0.8464 (p0) cc_final: 0.8084 (p0)
REVERT: I   51 LYS cc_start: 0.9133 (tptt) cc_final: 0.8920 (tptt)
REVERT: I   95 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.6372 (tm-30)
REVERT: L   38 LYS cc_start: 0.9197 (tppp) cc_final: 0.8648 (ttpt)
  outliers start: 40
  outliers final: 32
  residues processed: 214
  average time/residue: 0.0847
  time to fit residues: 23.6000
Evaluate side-chains
  218 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 184
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  114 THR
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  380 TYR
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue  101 HIS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue   36 LYS
Chi-restraints excluded: chain I residue   39 LEU
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   64 VAL
Chi-restraints excluded: chain I residue   68 PHE
Chi-restraints excluded: chain I residue   69 THR
Chi-restraints excluded: chain I residue   95 GLN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue  101 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0570
   chunk 70 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   chunk 78 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
I  95 GLN
L  37 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.139033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.106715 restraints weight = 12505.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.110264 restraints weight = 7934.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.112660 restraints weight = 5948.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.114292 restraints weight = 4936.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.115452 restraints weight = 4353.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6932  Z= 0.155
  Angle     :  0.747  11.880   9421  Z= 0.370
  Chirality :  0.044   0.175   1006
  Planarity :  0.004   0.053   1199
  Dihedral  :  6.068  57.805   1015
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.56 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 27.57 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.04 (0.28), residues: 847
  helix: -4.73 (0.80), residues: 14
  sheet: -0.31 (0.29), residues: 332
  loop : -2.09 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 408 
 TYR   0.027   0.002   TYR F 473 
 PHE   0.021   0.002   PHE I 100 
 TRP   0.020   0.002   TRP I  56 
 HIS   0.002   0.001   HIS L  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6922)
  covalent geometry    : angle       0.74119 ( 9398)
  SS BOND              : bond        0.00464 (    7)
  SS BOND              : angle       1.16866 (   14)
  hydrogen bonds       : bond        0.03238 (  154)
  hydrogen bonds       : angle       6.00485 (  402)
  link_BETA1-4         : bond        0.00915 (    1)
  link_BETA1-4         : angle       4.62706 (    3)
  link_NAG-ASN         : bond        0.00049 (    2)
  link_NAG-ASN         : angle       1.23631 (    6)

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 185
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: B   89 GLU cc_start: 0.7653 (mp0) cc_final: 0.7322 (mp0)
REVERT: D   10 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6389 (tm-30)
REVERT: D   23 LYS cc_start: 0.8263 (tttm) cc_final: 0.7827 (ttmm)
REVERT: D   60 TYR cc_start: 0.8861 (m-10) cc_final: 0.8386 (m-80)
REVERT: F  386 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8434 (tttm)
REVERT: H   38 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8520 (ttmm)
REVERT: I   34 ASN cc_start: 0.8416 (p0) cc_final: 0.8068 (p0)
REVERT: I   51 LYS cc_start: 0.9102 (tptt) cc_final: 0.8897 (tptt)
REVERT: L   38 LYS cc_start: 0.9234 (tppp) cc_final: 0.8697 (ttpt)
  outliers start: 36
  outliers final: 32
  residues processed: 203
  average time/residue: 0.0823
  time to fit residues: 21.6125
Evaluate side-chains
  215 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 182
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain C residue   27 GLN
Chi-restraints excluded: chain C residue   75 ILE
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   81 GLU
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   74 LYS
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  114 THR
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  380 TYR
Chi-restraints excluded: chain F residue  391 CYS
Chi-restraints excluded: chain F residue  478 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue  101 HIS
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain I residue   29 LEU
Chi-restraints excluded: chain I residue   36 LYS
Chi-restraints excluded: chain I residue   39 LEU
Chi-restraints excluded: chain I residue   42 TYR
Chi-restraints excluded: chain I residue   64 VAL
Chi-restraints excluded: chain I residue   68 PHE
Chi-restraints excluded: chain I residue   69 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   72 LEU
Chi-restraints excluded: chain L residue  101 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0070
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
C  20 ASN
H   3 GLN
I  95 GLN
L  37 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.140213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.107627 restraints weight = 12489.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.111204 restraints weight = 7932.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.113657 restraints weight = 5977.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.115184 restraints weight = 4954.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.116359 restraints weight = 4393.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.4335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6932  Z= 0.146
  Angle     :  0.732  11.638   9421  Z= 0.367
  Chirality :  0.044   0.316   1006
  Planarity :  0.004   0.054   1199
  Dihedral  :  5.949  55.105   1015
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.97 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 27.43 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.28), residues: 847
  helix: -4.68 (0.85), residues: 14
  sheet: -0.28 (0.29), residues: 332
  loop : -2.05 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F 408 
 TYR   0.026   0.002   TYR F 473 
 PHE   0.030   0.002   PHE I  77 
 TRP   0.017   0.002   TRP I  56 
 HIS   0.002   0.001   HIS C  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6922)
  covalent geometry    : angle       0.72676 ( 9398)
  SS BOND              : bond        0.00476 (    7)
  SS BOND              : angle       1.10574 (   14)
  hydrogen bonds       : bond        0.03259 (  154)
  hydrogen bonds       : angle       5.84719 (  402)
  link_BETA1-4         : bond        0.01011 (    1)
  link_BETA1-4         : angle       4.57558 (    3)
  link_NAG-ASN         : bond        0.00087 (    2)
  link_NAG-ASN         : angle       1.19956 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1386.36 seconds
wall clock time: 24 minutes 37.20 seconds (1477.20 seconds total)