Starting phenix.real_space_refine
on Tue Mar  3 16:00:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wp8_32678/03_2026/7wp8_32678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wp8_32678/03_2026/7wp8_32678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wp8_32678/03_2026/7wp8_32678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wp8_32678/03_2026/7wp8_32678.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wp8_32678/03_2026/7wp8_32678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wp8_32678/03_2026/7wp8_32678.map"
  }
  resolution = 3.88
  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      31      5.16       5
     C    4313      2.51       5
     N    1123      2.21       5
     O    1330      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 6797
  Number of models: 1
  Model: ""
    Number of chains: 9
    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: "E"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 966
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
    Chain: "F"
      Number of atoms: 1470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1470
          Classifications: {'peptide': 183}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "G"
      Number of atoms: 874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 874
          Classifications: {'peptide': 113}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107}
    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: "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: 1.45, per 1000 atoms: 0.21
  Number of scatterers: 6797
  At special positions: 0
  Unit cell: (89.47, 112.032, 112.032, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1330      8.00
     N    1123      7.00
     C    4313      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    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 E  22 " - pdb=" SG  CYS E  96 " distance=2.15
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 480 " - pdb=" SG  CYS F 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03

  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: 0.67
  Conformation dependent library (CDL) restraints added in 186.9 milliseconds
  

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  VAL F 503 "
  Number of C-beta restraints generated:  1574

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 21 sheets defined
      3.6% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.850A  pdb=" N   ARG D  31 " --> pdb=" O   THR D  28 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.866A  pdb=" N   SER D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.703A  pdb=" N   ASP E  90 " --> pdb=" O   THR E  87 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing helix  chain 'F' and resid 403 through 410
      removed outlier: 3.524A  pdb=" N   GLU F 406 " --> pdb=" O   ARG F 403 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   ARG F 408 " --> pdb=" O   ASP F 405 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.893A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 6
      removed outlier: 4.160A  pdb=" N   ASP C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.158A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C  47 " --> pdb=" O   TRP C  35 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.697A  pdb=" N   LEU D   4 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   SER D  25 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   THR D  78 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 18 through 19
    Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 60
      removed outlier: 6.289A  pdb=" N   TRP D  47 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LYS D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ARG D  98 " --> pdb=" O   ALA D 108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 59 through 60
      removed outlier: 6.289A  pdb=" N   TRP D  47 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LYS D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 5
      removed outlier: 3.511A  pdb=" N   THR E  71 " --> pdb=" O   TYR E  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 12
    Processing sheet with id=AA9, first strand: chain 'E' and resid 59 through 60
      removed outlier: 3.565A  pdb=" N   HIS E  59 " --> pdb=" O   ARG E  50 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   TRP E  36 " --> pdb=" O   ILE E  48 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ARG E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   MET E  34 " --> pdb=" O   ARG E  50 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL E  37 " --> pdb=" O   TYR E  95 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   TYR E 108 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 357 through 358
      removed outlier: 3.737A  pdb=" N   ASP F 398 " --> pdb=" O   VAL F 512 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL F 433 " --> pdb=" O   LYS F 378 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS F 378 " --> pdb=" O   VAL F 433 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 452 through 454
    Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 13
      removed outlier: 3.502A  pdb=" N   MET G  13 " --> pdb=" O   GLU G 111 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 19 through 20
    Processing sheet with id=AB5, first strand: chain 'G' and resid 50 through 52
    Processing sheet with id=AB6, first strand: chain 'G' and resid 54 through 55
      removed outlier: 3.783A  pdb=" N   THR G  59 " --> pdb=" O   TYR G  55 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.590A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR H 112 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TYR H  94 " --> pdb=" O   THR H 112 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU H 114 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.518A  pdb=" N   ILE H  59 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ILE H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY H  98 " --> pdb=" O   PHE H 107 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 12
    Processing sheet with id=AC2, first strand: chain 'L' and resid 19 through 24
      removed outlier: 3.727A  pdb=" N   TYR L  70 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER L  69 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 43 through 47
      removed outlier: 6.722A  pdb=" N   TRP L  34 " --> pdb=" O   TRP L  46 " (cutoff:3.500A)

    143 hydrogen bonds defined for protein.
    321 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: 0.82

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 1092
        1.25 -     1.39: 1865
        1.39 -     1.54: 3785
        1.54 -     1.68: 193
        1.68 -     1.82: 42
  Bond restraints: 6977
  Sorted by residual:
  bond pdb=" CA  VAL F 503 "
       pdb=" C   VAL F 503 "
    ideal  model  delta    sigma   weight residual
    1.523  1.336  0.188 1.27e-02 6.20e+03 2.18e+02
  bond pdb=" C   GLN F 498 "
       pdb=" N   PRO F 499 "
    ideal  model  delta    sigma   weight residual
    1.337  1.206  0.131 1.11e-02 8.12e+03 1.39e+02
  bond pdb=" CA  VAL F 503 "
       pdb=" CB  VAL F 503 "
    ideal  model  delta    sigma   weight residual
    1.540  1.400  0.141 1.25e-02 6.40e+03 1.26e+02
  bond pdb=" CA  GLN F 498 "
       pdb=" C   GLN F 498 "
    ideal  model  delta    sigma   weight residual
    1.524  1.390  0.134 1.28e-02 6.10e+03 1.09e+02
  bond pdb=" C   VAL F 503 "
       pdb=" O   VAL F 503 "
    ideal  model  delta    sigma   weight residual
    1.237  1.121  0.116 1.17e-02 7.31e+03 9.88e+01
  ... (remaining 6972 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 9196
        2.50 -     5.01: 214
        5.01 -     7.51: 44
        7.51 -    10.02: 14
       10.02 -    12.52: 7
  Bond angle restraints: 9475
  Sorted by residual:
  angle pdb=" N   VAL F 503 "
        pdb=" CA  VAL F 503 "
        pdb=" CB  VAL F 503 "
      ideal   model   delta    sigma   weight residual
     110.54  123.06  -12.52 1.36e+00 5.41e-01 8.48e+01
  angle pdb=" CA  GLY F 504 "
        pdb=" C   GLY F 504 "
        pdb=" O   GLY F 504 "
      ideal   model   delta    sigma   weight residual
     120.75  111.28    9.47 1.03e+00 9.43e-01 8.46e+01
  angle pdb=" C   GLN F 498 "
        pdb=" N   PRO F 499 "
        pdb=" CA  PRO F 499 "
      ideal   model   delta    sigma   weight residual
     119.87  129.27   -9.40 1.04e+00 9.25e-01 8.17e+01
  angle pdb=" CA  PRO F 499 "
        pdb=" C   PRO F 499 "
        pdb=" O   PRO F 499 "
      ideal   model   delta    sigma   weight residual
     118.86  108.34   10.52 1.38e+00 5.25e-01 5.82e+01
  angle pdb=" N   THR E 113 "
        pdb=" CA  THR E 113 "
        pdb=" C   THR E 113 "
      ideal   model   delta    sigma   weight residual
     108.52  120.80  -12.28 1.63e+00 3.76e-01 5.68e+01
  ... (remaining 9470 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 3692
       17.87 -    35.74: 352
       35.74 -    53.61: 54
       53.61 -    71.48: 9
       71.48 -    89.35: 12
  Dihedral angle restraints: 4119
    sinusoidal: 1633
      harmonic: 2486
  Sorted by residual:
  dihedral pdb=" CA  TYR G  55 "
           pdb=" C   TYR G  55 "
           pdb=" N   PHE G  56 "
           pdb=" CA  PHE G  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -132.22  -47.78     0      5.00e+00 4.00e-02 9.13e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.81  -86.81     1      1.00e+01 1.00e-02 9.07e+01
  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  157.16  -64.16     1      1.00e+01 1.00e-02 5.42e+01
  ... (remaining 4116 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.531: 1006
       0.531 -    1.062: 0
       1.062 -    1.593: 0
       1.593 -    2.124: 0
       2.124 -    2.655: 1
  Chirality restraints: 1007
  Sorted by residual:
  chirality pdb=" CA  VAL F 503 "
            pdb=" N   VAL F 503 "
            pdb=" C   VAL F 503 "
            pdb=" CB  VAL F 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44   -0.21    2.66 2.00e-01 2.50e+01 1.76e+02
  chirality pdb=" CA  PRO F 499 "
            pdb=" N   PRO F 499 "
            pdb=" C   PRO F 499 "
            pdb=" CB  PRO F 499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.40 2.00e-01 2.50e+01 4.10e+00
  chirality pdb=" CA  ASN F 343 "
            pdb=" N   ASN F 343 "
            pdb=" C   ASN F 343 "
            pdb=" CB  ASN F 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.74e+00
  ... (remaining 1004 not shown)

  Planarity restraints: 1214
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "    0.310 2.00e-02 2.50e+03   2.59e-01 8.41e+02
        pdb=" C7  NAG A   1 "   -0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "    0.191 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "   -0.444 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG L 201 "   -0.201 2.00e-02 2.50e+03   1.65e-01 3.39e+02
        pdb=" C7  NAG L 201 "    0.059 2.00e-02 2.50e+03
        pdb=" C8  NAG L 201 "   -0.148 2.00e-02 2.50e+03
        pdb=" N2  NAG L 201 "    0.263 2.00e-02 2.50e+03
        pdb=" O7  NAG L 201 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "    0.151 2.00e-02 2.50e+03   1.24e-01 1.93e+02
        pdb=" C7  NAG A   2 "   -0.043 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "    0.113 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "   -0.199 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1211 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1556
        2.78 -     3.31: 5631
        3.31 -     3.84: 11082
        3.84 -     4.37: 12156
        4.37 -     4.90: 21565
  Nonbonded interactions: 51990
  Sorted by model distance:
  nonbonded pdb=" O   GLY F 447 "
            pdb=" OH  TYR H  33 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" CG2 VAL F 503 "
            pdb=" OE1 GLN F 506 "
     model   vdw
     2.269 3.460
  nonbonded pdb=" OG  SER D  17 "
            pdb=" O   LEU D  83 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG  SER C  43 "
            pdb=" O   GLY D 111 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   THR H 112 "
            pdb=" OG1 THR H 112 "
     model   vdw
     2.296 3.040
  ... (remaining 51985 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:             6.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.290
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
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      :  0.008   0.188   6987  Z= 0.544
  Angle     :  1.072  31.715   9498  Z= 0.616
  Chirality :  0.106   2.655   1007
  Planarity :  0.012   0.259   1212
  Dihedral  : 14.513  89.355   2524
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.97 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -4.12 (0.25), residues: 847
  helix: -4.94 (0.50), residues: 8
  sheet: -2.25 (0.29), residues: 284
  loop : -3.16 (0.22), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  99 
 TYR   0.029   0.002   TYR D 104 
 PHE   0.017   0.002   PHE G 104 
 TRP   0.016   0.002   TRP E  33 
 HIS   0.008   0.002   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00832 ( 6977)
  covalent geometry    : angle       1.00631 ( 9475)
  SS BOND              : bond        0.04502 (    7)
  SS BOND              : angle       9.41555 (   14)
  hydrogen bonds       : bond        0.30581 (  132)
  hydrogen bonds       : angle      12.38828 (  321)
  link_BETA1-4         : bond        0.00742 (    1)
  link_BETA1-4         : angle       2.55604 (    3)
  link_NAG-ASN         : bond        0.00950 (    2)
  link_NAG-ASN         : angle       3.38705 (    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
  221 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8524 (mmm) cc_final: 0.8310 (mmt)
REVERT: D   38 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7776 (ttpt)
REVERT: E   13 ARG cc_start: 0.7980 (mmt180) cc_final: 0.7345 (mtp85)
REVERT: E   46 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7574 (mt-10)
REVERT: E   65 LYS cc_start: 0.7906 (mttt) cc_final: 0.7594 (mtmt)
REVERT: G   13 MET cc_start: 0.7521 (tpt) cc_final: 0.7214 (tpt)
REVERT: G   35 GLN cc_start: 0.8008 (mp10) cc_final: 0.7519 (mp10)
REVERT: G   78 THR cc_start: 0.9036 (p) cc_final: 0.8799 (p)
REVERT: G   85 GLN cc_start: 0.8801 (mm110) cc_final: 0.8514 (mm110)
REVERT: H   29 PHE cc_start: 0.7988 (t80) cc_final: 0.7696 (t80)
REVERT: H   60 TYR cc_start: 0.8299 (m-80) cc_final: 0.7759 (m-80)
REVERT: L    4 LEU cc_start: 0.8584 (mt) cc_final: 0.8255 (mp)
REVERT: L   37 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6514 (tm-30)
REVERT: L   88 GLN cc_start: 0.8262 (mp10) cc_final: 0.8020 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0962
  time to fit residues: 27.0324
Evaluate side-chains
  166 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
D  39 GLN
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 388 ASN
** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 448 ASN
** G  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  55 ASN
H 101 HIS
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.131033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.106166 restraints weight = 12508.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.108782 restraints weight = 7909.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.110614 restraints weight = 5897.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.111800 restraints weight = 4856.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.112450 restraints weight = 4281.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6987  Z= 0.146
  Angle     :  0.665   7.097   9498  Z= 0.348
  Chirality :  0.046   0.174   1007
  Planarity :  0.005   0.069   1212
  Dihedral  :  6.284  61.098   1012
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.75 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -3.63 (0.27), residues: 847
  helix: -4.78 (0.66), residues: 8
  sheet: -1.88 (0.28), residues: 323
  loop : -2.84 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  60 
 TYR   0.026   0.002   TYR E  32 
 PHE   0.015   0.001   PHE F 456 
 TRP   0.021   0.001   TRP D  36 
 HIS   0.003   0.001   HIS G  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6977)
  covalent geometry    : angle       0.65309 ( 9475)
  SS BOND              : bond        0.00425 (    7)
  SS BOND              : angle       1.25652 (   14)
  hydrogen bonds       : bond        0.03575 (  132)
  hydrogen bonds       : angle       7.94499 (  321)
  link_BETA1-4         : bond        0.00881 (    1)
  link_BETA1-4         : angle       1.36251 (    3)
  link_NAG-ASN         : bond        0.00165 (    2)
  link_NAG-ASN         : angle       4.76972 (    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
  198 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8459 (mmm) cc_final: 0.8254 (mmt)
REVERT: E   13 ARG cc_start: 0.7906 (mmt180) cc_final: 0.7634 (mmt180)
REVERT: G    4 MET cc_start: 0.7926 (tpp) cc_final: 0.7267 (mmm)
REVERT: G   35 GLN cc_start: 0.7983 (mp10) cc_final: 0.7742 (mp10)
REVERT: H   29 PHE cc_start: 0.7888 (t80) cc_final: 0.7632 (t80)
REVERT: H  106 ASP cc_start: 0.7164 (m-30) cc_final: 0.6801 (m-30)
REVERT: L   32 MET cc_start: 0.7653 (mtp) cc_final: 0.7439 (mtp)
REVERT: L   37 GLN cc_start: 0.6540 (tm-30) cc_final: 0.6155 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 187
  average time/residue: 0.0931
  time to fit residues: 22.1274
Evaluate side-chains
  177 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 168
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   3 GLN
D  43 GLN
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 498 GLN
** G  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  97 HIS
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.123109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.098320 restraints weight = 12977.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.100663 restraints weight = 8359.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.102223 restraints weight = 6340.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.103140 restraints weight = 5338.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.103897 restraints weight = 4800.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060   6987  Z= 0.302
  Angle     :  0.747   7.468   9498  Z= 0.397
  Chirality :  0.049   0.204   1007
  Planarity :  0.005   0.067   1212
  Dihedral  :  7.132  59.967   1012
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.81 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.67 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -3.65 (0.26), residues: 847
  helix: -5.14 (0.32), residues: 14
  sheet: -1.87 (0.29), residues: 309
  loop : -2.82 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  60 
 TYR   0.020   0.002   TYR H  27 
 PHE   0.021   0.002   PHE G 104 
 TRP   0.032   0.002   TRP D  36 
 HIS   0.006   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00702 ( 6977)
  covalent geometry    : angle       0.73873 ( 9475)
  SS BOND              : bond        0.00486 (    7)
  SS BOND              : angle       1.27121 (   14)
  hydrogen bonds       : bond        0.04120 (  132)
  hydrogen bonds       : angle       7.54957 (  321)
  link_BETA1-4         : bond        0.00338 (    1)
  link_BETA1-4         : angle       1.30851 (    3)
  link_NAG-ASN         : bond        0.00514 (    2)
  link_NAG-ASN         : angle       3.97768 (    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
  193 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8638 (mmm) cc_final: 0.8278 (mmt)
REVERT: D   29 PHE cc_start: 0.8673 (t80) cc_final: 0.8458 (t80)
REVERT: E   13 ARG cc_start: 0.7960 (mmt180) cc_final: 0.7502 (mtp85)
REVERT: G    4 MET cc_start: 0.8031 (tpp) cc_final: 0.7279 (mmm)
REVERT: G   35 GLN cc_start: 0.7945 (mp10) cc_final: 0.7678 (mp10)
REVERT: H  106 ASP cc_start: 0.7380 (m-30) cc_final: 0.7180 (m-30)
REVERT: L   37 GLN cc_start: 0.6898 (tm130) cc_final: 0.6519 (tm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 176
  average time/residue: 0.0893
  time to fit residues: 20.1707
Evaluate side-chains
  172 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   96 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0770
   chunk 18 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.129804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.104731 restraints weight = 12571.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.107318 restraints weight = 7982.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.109046 restraints weight = 5978.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.110108 restraints weight = 4980.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.110812 restraints weight = 4448.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6987  Z= 0.124
  Angle     :  0.618   6.202   9498  Z= 0.324
  Chirality :  0.045   0.173   1007
  Planarity :  0.004   0.056   1212
  Dihedral  :  6.228  47.592   1012
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.08 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -3.34 (0.27), residues: 847
  helix: -5.09 (0.36), residues: 14
  sheet: -1.67 (0.29), residues: 317
  loop : -2.59 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  60 
 TYR   0.016   0.001   TYR F 380 
 PHE   0.017   0.002   PHE H  29 
 TRP   0.017   0.001   TRP D  36 
 HIS   0.003   0.001   HIS L  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6977)
  covalent geometry    : angle       0.61055 ( 9475)
  SS BOND              : bond        0.00280 (    7)
  SS BOND              : angle       0.89527 (   14)
  hydrogen bonds       : bond        0.02788 (  132)
  hydrogen bonds       : angle       6.80252 (  321)
  link_BETA1-4         : bond        0.00673 (    1)
  link_BETA1-4         : angle       1.63809 (    3)
  link_NAG-ASN         : bond        0.00087 (    2)
  link_NAG-ASN         : angle       3.45960 (    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
  198 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8462 (mmm) cc_final: 0.8183 (mmt)
REVERT: E   10 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7852 (mm-30)
REVERT: E   13 ARG cc_start: 0.7908 (mmt180) cc_final: 0.7606 (mmt180)
REVERT: G    4 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7206 (mmm)
REVERT: G   13 MET cc_start: 0.6931 (tpt) cc_final: 0.6484 (tpt)
REVERT: G   35 GLN cc_start: 0.7951 (mp10) cc_final: 0.7708 (mp10)
REVERT: G   59 THR cc_start: 0.7982 (p) cc_final: 0.7342 (p)
REVERT: H   29 PHE cc_start: 0.8130 (t80) cc_final: 0.7740 (t80)
REVERT: L   37 GLN cc_start: 0.6632 (tm130) cc_final: 0.6230 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 186
  average time/residue: 0.0875
  time to fit residues: 20.9823
Evaluate side-chains
  176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.129614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.104332 restraints weight = 12778.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.106938 restraints weight = 8098.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.108702 restraints weight = 6030.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.109852 restraints weight = 5009.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.110618 restraints weight = 4435.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6987  Z= 0.141
  Angle     :  0.633   7.535   9498  Z= 0.332
  Chirality :  0.045   0.187   1007
  Planarity :  0.004   0.054   1212
  Dihedral  :  6.127  47.541   1012
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.21 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -3.20 (0.27), residues: 847
  helix: -5.02 (0.41), residues: 14
  sheet: -1.63 (0.28), residues: 332
  loop : -2.46 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  60 
 TYR   0.014   0.001   TYR F 489 
 PHE   0.017   0.002   PHE G 104 
 TRP   0.032   0.001   TRP D  36 
 HIS   0.004   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6977)
  covalent geometry    : angle       0.62749 ( 9475)
  SS BOND              : bond        0.00244 (    7)
  SS BOND              : angle       0.88141 (   14)
  hydrogen bonds       : bond        0.02794 (  132)
  hydrogen bonds       : angle       6.60531 (  321)
  link_BETA1-4         : bond        0.00527 (    1)
  link_BETA1-4         : angle       1.46079 (    3)
  link_NAG-ASN         : bond        0.00129 (    2)
  link_NAG-ASN         : angle       3.18113 (    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
  182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8468 (mmm) cc_final: 0.8188 (mmt)
REVERT: E   13 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7681 (mmt180)
REVERT: E   52 ASP cc_start: 0.8316 (t0) cc_final: 0.8085 (t0)
REVERT: G    4 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7285 (mmm)
REVERT: G   35 GLN cc_start: 0.7951 (mp10) cc_final: 0.7683 (mp10)
REVERT: H   29 PHE cc_start: 0.8163 (t80) cc_final: 0.7779 (t80)
REVERT: H  106 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6433 (m-30)
REVERT: L   37 GLN cc_start: 0.6644 (tm130) cc_final: 0.6256 (tm-30)
  outliers start: 24
  outliers final: 18
  residues processed: 166
  average time/residue: 0.0929
  time to fit residues: 19.7082
Evaluate side-chains
  169 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  106 ASP
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 57 optimal weight:    0.4980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  43 GLN
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.127831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.102650 restraints weight = 12909.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.105195 restraints weight = 8202.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.106956 restraints weight = 6153.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.107999 restraints weight = 5102.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.108792 restraints weight = 4555.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6987  Z= 0.180
  Angle     :  0.647   7.032   9498  Z= 0.339
  Chirality :  0.045   0.174   1007
  Planarity :  0.004   0.054   1212
  Dihedral  :  6.326  50.406   1012
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.26 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -3.10 (0.27), residues: 847
  helix: -5.00 (0.41), residues: 14
  sheet: -1.54 (0.29), residues: 336
  loop : -2.41 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  60 
 TYR   0.014   0.001   TYR F 489 
 PHE   0.018   0.002   PHE G 104 
 TRP   0.024   0.002   TRP D  36 
 HIS   0.006   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 6977)
  covalent geometry    : angle       0.64092 ( 9475)
  SS BOND              : bond        0.00295 (    7)
  SS BOND              : angle       0.98364 (   14)
  hydrogen bonds       : bond        0.02960 (  132)
  hydrogen bonds       : angle       6.62352 (  321)
  link_BETA1-4         : bond        0.00725 (    1)
  link_BETA1-4         : angle       1.29420 (    3)
  link_NAG-ASN         : bond        0.00233 (    2)
  link_NAG-ASN         : angle       3.24770 (    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
  185 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8446 (mmm) cc_final: 0.8118 (mmt)
REVERT: D   31 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7529 (ttp-170)
REVERT: E   13 ARG cc_start: 0.7903 (mmt180) cc_final: 0.7684 (mmt180)
REVERT: E   52 ASP cc_start: 0.8403 (t0) cc_final: 0.8187 (t0)
REVERT: G    4 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7204 (mmm)
REVERT: G   35 GLN cc_start: 0.7937 (mp10) cc_final: 0.7684 (mp10)
REVERT: H   29 PHE cc_start: 0.8172 (t80) cc_final: 0.7807 (t80)
REVERT: L   37 GLN cc_start: 0.6675 (tm130) cc_final: 0.6208 (tm-30)
  outliers start: 24
  outliers final: 20
  residues processed: 169
  average time/residue: 0.0936
  time to fit residues: 20.1404
Evaluate side-chains
  175 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   10 SER
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.129390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.104425 restraints weight = 12581.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.106939 restraints weight = 8007.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.108691 restraints weight = 6018.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.109874 restraints weight = 4987.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.110540 restraints weight = 4419.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6987  Z= 0.141
  Angle     :  0.636   6.764   9498  Z= 0.330
  Chirality :  0.045   0.191   1007
  Planarity :  0.004   0.050   1212
  Dihedral  :  6.081  48.833   1012
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 19.54 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -3.02 (0.27), residues: 847
  helix: -4.94 (0.46), residues: 14
  sheet: -1.46 (0.28), residues: 338
  loop : -2.37 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  60 
 TYR   0.054   0.001   TYR G  55 
 PHE   0.020   0.002   PHE G 104 
 TRP   0.021   0.001   TRP D  36 
 HIS   0.003   0.001   HIS L  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6977)
  covalent geometry    : angle       0.63052 ( 9475)
  SS BOND              : bond        0.00240 (    7)
  SS BOND              : angle       0.87464 (   14)
  hydrogen bonds       : bond        0.02665 (  132)
  hydrogen bonds       : angle       6.39026 (  321)
  link_BETA1-4         : bond        0.00602 (    1)
  link_BETA1-4         : angle       1.28940 (    3)
  link_NAG-ASN         : bond        0.00151 (    2)
  link_NAG-ASN         : angle       3.09100 (    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
  183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 157
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8399 (mmm) cc_final: 0.8104 (mmt)
REVERT: D   31 ARG cc_start: 0.8158 (mmm-85) cc_final: 0.7741 (mtp180)
REVERT: E   13 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7421 (mmm160)
REVERT: E   52 ASP cc_start: 0.8450 (t0) cc_final: 0.8128 (t0)
REVERT: G    4 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7328 (mmm)
REVERT: G   35 GLN cc_start: 0.7969 (mp10) cc_final: 0.7745 (mp10)
REVERT: G   39 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6524 (tp)
REVERT: H   29 PHE cc_start: 0.8185 (t80) cc_final: 0.7815 (t80)
REVERT: H   63 LYS cc_start: 0.8245 (mttp) cc_final: 0.7908 (ttmm)
REVERT: L   37 GLN cc_start: 0.6629 (tm130) cc_final: 0.6246 (tm-30)
REVERT: L   60 ARG cc_start: 0.4669 (mpp80) cc_final: 0.4435 (mpp80)
REVERT: L   78 GLU cc_start: 0.5227 (mp0) cc_final: 0.4949 (mp0)
  outliers start: 26
  outliers final: 20
  residues processed: 167
  average time/residue: 0.0879
  time to fit residues: 19.0434
Evaluate side-chains
  174 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   10 SER
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0570
   chunk 7 optimal weight:    0.2980
   chunk 45 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
C  89 GLN
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.129182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.104495 restraints weight = 12733.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.107066 restraints weight = 8063.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.108832 restraints weight = 6022.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.109989 restraints weight = 4979.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.110509 restraints weight = 4405.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6987  Z= 0.148
  Angle     :  0.648   7.475   9498  Z= 0.337
  Chirality :  0.046   0.263   1007
  Planarity :  0.004   0.048   1212
  Dihedral  :  6.022  47.676   1012
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.36 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -2.98 (0.27), residues: 847
  helix: -4.87 (0.49), residues: 14
  sheet: -1.45 (0.28), residues: 344
  loop : -2.33 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  60 
 TYR   0.044   0.001   TYR G  55 
 PHE   0.018   0.002   PHE G 104 
 TRP   0.050   0.002   TRP D  36 
 HIS   0.003   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6977)
  covalent geometry    : angle       0.64290 ( 9475)
  SS BOND              : bond        0.00213 (    7)
  SS BOND              : angle       0.84990 (   14)
  hydrogen bonds       : bond        0.02750 (  132)
  hydrogen bonds       : angle       6.31470 (  321)
  link_BETA1-4         : bond        0.00579 (    1)
  link_BETA1-4         : angle       1.24627 (    3)
  link_NAG-ASN         : bond        0.00165 (    2)
  link_NAG-ASN         : angle       3.07170 (    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
  182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8367 (mmm) cc_final: 0.8057 (mmt)
REVERT: C   89 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.8000 (tt0)
REVERT: D   31 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7612 (mtp180)
REVERT: E   13 ARG cc_start: 0.7886 (mmt180) cc_final: 0.7555 (mmt180)
REVERT: G    4 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7576 (mmp)
REVERT: G   21 MET cc_start: 0.7451 (mtp) cc_final: 0.7243 (mtt)
REVERT: G   39 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6481 (tp)
REVERT: H   29 PHE cc_start: 0.8176 (t80) cc_final: 0.7833 (t80)
REVERT: H   56 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7517 (t)
REVERT: H   63 LYS cc_start: 0.8252 (mttp) cc_final: 0.7911 (ttmm)
REVERT: L   37 GLN cc_start: 0.6626 (tm130) cc_final: 0.6270 (tm-30)
REVERT: L   78 GLU cc_start: 0.5409 (mp0) cc_final: 0.4923 (mp0)
  outliers start: 24
  outliers final: 19
  residues processed: 168
  average time/residue: 0.0842
  time to fit residues: 18.4326
Evaluate side-chains
  175 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 152
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   10 SER
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0470
   chunk 34 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.1884

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

Flipped N/Q/H residues before XYZ refinement:
C  89 GLN
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   1 GLN
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.127966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.103384 restraints weight = 12765.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.105938 restraints weight = 8098.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.107660 restraints weight = 6041.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.108573 restraints weight = 5012.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.109419 restraints weight = 4483.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6987  Z= 0.185
  Angle     :  0.674   7.716   9498  Z= 0.352
  Chirality :  0.046   0.189   1007
  Planarity :  0.004   0.048   1212
  Dihedral  :  6.235  50.029   1012
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 20.22 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -4.91 (0.45), residues: 14
  sheet: -1.42 (0.29), residues: 331
  loop : -2.34 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  60 
 TYR   0.051   0.002   TYR G  55 
 PHE   0.020   0.002   PHE G 104 
 TRP   0.038   0.002   TRP D  36 
 HIS   0.006   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 6977)
  covalent geometry    : angle       0.66871 ( 9475)
  SS BOND              : bond        0.00330 (    7)
  SS BOND              : angle       0.97986 (   14)
  hydrogen bonds       : bond        0.02892 (  132)
  hydrogen bonds       : angle       6.37912 (  321)
  link_BETA1-4         : bond        0.00502 (    1)
  link_BETA1-4         : angle       1.14812 (    3)
  link_NAG-ASN         : bond        0.00269 (    2)
  link_NAG-ASN         : angle       3.15859 (    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
  181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 156
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8438 (mmm) cc_final: 0.8123 (mmt)
REVERT: D   29 PHE cc_start: 0.8616 (t80) cc_final: 0.8285 (t80)
REVERT: D   31 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7795 (mtp180)
REVERT: E   13 ARG cc_start: 0.7889 (mmt180) cc_final: 0.7562 (mmt180)
REVERT: G    4 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7597 (mmp)
REVERT: G   21 MET cc_start: 0.7566 (mtp) cc_final: 0.7345 (mtt)
REVERT: G   39 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6531 (tp)
REVERT: H   29 PHE cc_start: 0.8213 (t80) cc_final: 0.7873 (t80)
REVERT: H   63 LYS cc_start: 0.8263 (mttp) cc_final: 0.7896 (ttmm)
REVERT: L   37 GLN cc_start: 0.6626 (tm130) cc_final: 0.6173 (tm-30)
  outliers start: 25
  outliers final: 21
  residues processed: 168
  average time/residue: 0.0860
  time to fit residues: 18.8254
Evaluate side-chains
  176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   10 SER
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   88 SER
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.129691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.104895 restraints weight = 12679.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.107510 restraints weight = 8003.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.109315 restraints weight = 5957.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.110468 restraints weight = 4922.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.111034 restraints weight = 4349.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6987  Z= 0.148
  Angle     :  0.682   8.108   9498  Z= 0.355
  Chirality :  0.046   0.190   1007
  Planarity :  0.004   0.045   1212
  Dihedral  :  6.114  48.773   1012
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.90 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -4.85 (0.49), residues: 14
  sheet: -1.37 (0.29), residues: 333
  loop : -2.38 (0.26), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  60 
 TYR   0.051   0.001   TYR G  55 
 PHE   0.019   0.002   PHE H 107 
 TRP   0.034   0.001   TRP D  36 
 HIS   0.004   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6977)
  covalent geometry    : angle       0.67739 ( 9475)
  SS BOND              : bond        0.00264 (    7)
  SS BOND              : angle       0.93235 (   14)
  hydrogen bonds       : bond        0.02655 (  132)
  hydrogen bonds       : angle       6.28609 (  321)
  link_BETA1-4         : bond        0.00676 (    1)
  link_BETA1-4         : angle       1.29208 (    3)
  link_NAG-ASN         : bond        0.00145 (    2)
  link_NAG-ASN         : angle       3.08762 (    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
  181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 158
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8384 (mmm) cc_final: 0.8084 (mmt)
REVERT: D   29 PHE cc_start: 0.8610 (t80) cc_final: 0.8396 (t80)
REVERT: D   31 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7827 (mtp180)
REVERT: E   13 ARG cc_start: 0.7892 (mmt180) cc_final: 0.7570 (mmt180)
REVERT: E   65 LYS cc_start: 0.7265 (mppt) cc_final: 0.7018 (mtmm)
REVERT: G    4 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7607 (mmp)
REVERT: G   21 MET cc_start: 0.7524 (mtp) cc_final: 0.7315 (mtt)
REVERT: G   39 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6538 (tp)
REVERT: H   29 PHE cc_start: 0.8223 (t80) cc_final: 0.7883 (t80)
REVERT: H   63 LYS cc_start: 0.8281 (mttp) cc_final: 0.7906 (ttmm)
REVERT: L   37 GLN cc_start: 0.6586 (tm130) cc_final: 0.6237 (tm-30)
  outliers start: 23
  outliers final: 20
  residues processed: 167
  average time/residue: 0.0889
  time to fit residues: 19.2589
Evaluate side-chains
  174 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   10 SER
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.129120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.104426 restraints weight = 12643.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.106966 restraints weight = 8021.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.108693 restraints weight = 6001.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.109714 restraints weight = 4979.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.110257 restraints weight = 4433.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6987  Z= 0.160
  Angle     :  0.684   8.066   9498  Z= 0.353
  Chirality :  0.047   0.280   1007
  Planarity :  0.004   0.045   1212
  Dihedral  :  6.142  48.699   1012
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 20.36 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -2.96 (0.27), residues: 847
  helix: -4.86 (0.48), residues: 14
  sheet: -1.42 (0.28), residues: 344
  loop : -2.33 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  60 
 TYR   0.049   0.001   TYR G  55 
 PHE   0.019   0.002   PHE H 107 
 TRP   0.033   0.001   TRP D  36 
 HIS   0.005   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6977)
  covalent geometry    : angle       0.67898 ( 9475)
  SS BOND              : bond        0.00233 (    7)
  SS BOND              : angle       0.89698 (   14)
  hydrogen bonds       : bond        0.02684 (  132)
  hydrogen bonds       : angle       6.27691 (  321)
  link_BETA1-4         : bond        0.00570 (    1)
  link_BETA1-4         : angle       1.18744 (    3)
  link_NAG-ASN         : bond        0.00198 (    2)
  link_NAG-ASN         : angle       3.09724 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1351.99 seconds
wall clock time: 24 minutes 4.72 seconds (1444.72 seconds total)