Starting phenix.real_space_refine
on Thu Jun  5 23:12:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wp8_32678/06_2025/7wp8_32678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wp8_32678/06_2025/7wp8_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wp8_32678/06_2025/7wp8_32678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wp8_32678/06_2025/7wp8_32678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wp8_32678/06_2025/7wp8_32678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wp8_32678/06_2025/7wp8_32678.cif"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.38, per 1000 atoms: 0.79
  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: 1.71
  Conformation dependent library (CDL) restraints added in 955.4 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: 1.02
  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: 1.83

  Time building geometry restraints manager: 2.03 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:             4.530
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.000
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.280
-------------------------------------------------------------------------------
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 : 7.91
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.016   0.002   TRP E  33 
 HIS   0.008   0.002   HIS H 101 
 PHE   0.017   0.002   PHE G 104 
 TYR   0.029   0.002   TYR D 104 
 ARG   0.005   0.001   ARG D  99 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00950 (    2)
  link_NAG-ASN         : angle       3.38705 (    6)
  link_BETA1-4         : bond        0.00742 (    1)
  link_BETA1-4         : angle       2.55604 (    3)
  hydrogen bonds       : bond        0.30581 (  132)
  hydrogen bonds       : angle      12.38828 (  321)
  SS BOND              : bond        0.04502 (    7)
  SS BOND              : angle       9.41555 (   14)
  covalent geometry    : bond        0.00832 ( 6977)
  covalent geometry    : angle       1.00631 ( 9475)

*********************** 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  : 0.725 
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: 0.7777 (ttpt)
REVERT: E   13 ARG cc_start: 0.7979 (mmt180) cc_final: 0.7344 (mtp85)
REVERT: E   65 LYS cc_start: 0.7906 (mttt) cc_final: 0.7596 (mtmt)
REVERT: G   13 MET cc_start: 0.7522 (tpt) cc_final: 0.7212 (tpt)
REVERT: G   35 GLN cc_start: 0.8008 (mp10) cc_final: 0.7517 (mp10)
REVERT: G   78 THR cc_start: 0.9036 (p) cc_final: 0.8800 (p)
REVERT: G   85 GLN cc_start: 0.8801 (mm110) cc_final: 0.8512 (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: 0.7761 (m-80)
REVERT: L    4 LEU cc_start: 0.8584 (mt) cc_final: 0.8254 (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: 0.8021 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2236
  time to fit residues: 62.4649
Evaluate side-chains
  165 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
C  90 GLN
D  39 GLN
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 388 ASN
** 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 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 = 0.3754 r_free = 0.3754 target = 0.129643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.104991 restraints weight = 12451.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.107550 restraints weight = 7902.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.109311 restraints weight = 5877.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6987  Z= 0.160
  Angle     :  0.673   7.602   9498  Z= 0.353
  Chirality :  0.046   0.182   1007
  Planarity :  0.006   0.074   1212
  Dihedral  :  6.418  62.581   1012
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.89 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.66 (0.26), residues: 847
  helix: -4.80 (0.65), residues: 8
  sheet: -1.89 (0.28), residues: 319
  loop : -2.87 (0.24), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D  36 
 HIS   0.002   0.001   HIS G  97 
 PHE   0.015   0.002   PHE F 456 
 TYR   0.026   0.002   TYR E  32 
 ARG   0.006   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00262 (    2)
  link_NAG-ASN         : angle       4.89780 (    6)
  link_BETA1-4         : bond        0.00710 (    1)
  link_BETA1-4         : angle       1.36287 (    3)
  hydrogen bonds       : bond        0.03783 (  132)
  hydrogen bonds       : angle       8.02479 (  321)
  SS BOND              : bond        0.00391 (    7)
  SS BOND              : angle       1.32104 (   14)
  covalent geometry    : bond        0.00369 ( 6977)
  covalent geometry    : angle       0.66038 ( 9475)

*********************** 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
  195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.791 
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: C    4 MET cc_start: 0.8479 (mmm) cc_final: 0.8260 (mmt)
REVERT: C    8 HIS cc_start: 0.8496 (m90) cc_final: 0.8211 (m90)
REVERT: E   13 ARG cc_start: 0.7930 (mmt180) cc_final: 0.7634 (mmt180)
REVERT: G    4 MET cc_start: 0.7962 (tpp) cc_final: 0.7188 (mmm)
REVERT: G   35 GLN cc_start: 0.7973 (mp10) cc_final: 0.7711 (mp10)
REVERT: G   55 TYR cc_start: 0.7948 (p90) cc_final: 0.7688 (p90)
REVERT: H   29 PHE cc_start: 0.7918 (t80) cc_final: 0.7637 (t80)
REVERT: H  106 ASP cc_start: 0.7234 (m-30) cc_final: 0.6856 (m-30)
REVERT: L   32 MET cc_start: 0.7719 (mtp) cc_final: 0.7509 (mtp)
REVERT: L   37 GLN cc_start: 0.6602 (tm-30) cc_final: 0.6204 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 184
  average time/residue: 0.2375
  time to fit residues: 55.2024
Evaluate side-chains
  169 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 160
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
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 16 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   chunk 17 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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**
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.126446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.101730 restraints weight = 12761.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.104149 restraints weight = 8153.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.105746 restraints weight = 6187.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6987  Z= 0.202
  Angle     :  0.671   6.644   9498  Z= 0.353
  Chirality :  0.046   0.197   1007
  Planarity :  0.005   0.057   1212
  Dihedral  :  6.471  56.204   1012
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.44 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.47 (0.27), residues: 847
  helix: -5.13 (0.34), residues: 14
  sheet: -1.70 (0.30), residues: 307
  loop : -2.72 (0.24), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP D  36 
 HIS   0.005   0.001   HIS H 101 
 PHE   0.015   0.002   PHE G 104 
 TYR   0.017   0.002   TYR G  55 
 ARG   0.007   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00320 (    2)
  link_NAG-ASN         : angle       3.84061 (    6)
  link_BETA1-4         : bond        0.00542 (    1)
  link_BETA1-4         : angle       1.41404 (    3)
  hydrogen bonds       : bond        0.03548 (  132)
  hydrogen bonds       : angle       7.35170 (  321)
  SS BOND              : bond        0.00317 (    7)
  SS BOND              : angle       1.15816 (   14)
  covalent geometry    : bond        0.00468 ( 6977)
  covalent geometry    : angle       0.66237 ( 9475)

*********************** 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
  195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 173
  time to evaluate  : 0.827 
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: 0.8592 (mmm) cc_final: 0.8306 (mmt)
REVERT: C    8 HIS cc_start: 0.8517 (m90) cc_final: 0.8191 (m90)
REVERT: C   65 SER cc_start: 0.9018 (m) cc_final: 0.8802 (t)
REVERT: D   29 PHE cc_start: 0.8647 (t80) cc_final: 0.8417 (t80)
REVERT: E   13 ARG cc_start: 0.7925 (mmt180) cc_final: 0.7511 (mtp85)
REVERT: E  103 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7542 (mm-30)
REVERT: G    4 MET cc_start: 0.7926 (tpp) cc_final: 0.7206 (mmm)
REVERT: G   35 GLN cc_start: 0.7914 (mp10) cc_final: 0.7666 (mp10)
REVERT: G   55 TYR cc_start: 0.8070 (p90) cc_final: 0.7743 (p90)
REVERT: H   29 PHE cc_start: 0.8085 (t80) cc_final: 0.7804 (t80)
REVERT: H  106 ASP cc_start: 0.7278 (m-30) cc_final: 0.6898 (m-30)
REVERT: L   37 GLN cc_start: 0.6691 (tm130) cc_final: 0.6316 (tm-30)
REVERT: L   89 GLN cc_start: 0.8678 (pt0) cc_final: 0.8346 (pt0)
  outliers start: 22
  outliers final: 17
  residues processed: 179
  average time/residue: 0.2147
  time to fit residues: 49.2660
Evaluate side-chains
  179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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   56 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 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 75 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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  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 = 0.3756 r_free = 0.3756 target = 0.129135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.104052 restraints weight = 12719.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.106615 restraints weight = 8111.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.108363 restraints weight = 6084.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2799

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     :  0.622   6.357   9498  Z= 0.327
  Chirality :  0.044   0.154   1007
  Planarity :  0.004   0.053   1212
  Dihedral  :  6.201  49.643   1012
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.53 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.27), residues: 847
  helix: -5.06 (0.39), residues: 14
  sheet: -1.66 (0.29), residues: 314
  loop : -2.56 (0.24), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  36 
 HIS   0.003   0.001   HIS H 101 
 PHE   0.014   0.002   PHE G 104 
 TYR   0.017   0.001   TYR G  55 
 ARG   0.005   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00126 (    2)
  link_NAG-ASN         : angle       3.37890 (    6)
  link_BETA1-4         : bond        0.00572 (    1)
  link_BETA1-4         : angle       1.41063 (    3)
  hydrogen bonds       : bond        0.02927 (  132)
  hydrogen bonds       : angle       6.78453 (  321)
  SS BOND              : bond        0.00268 (    7)
  SS BOND              : angle       0.92122 (   14)
  covalent geometry    : bond        0.00347 ( 6977)
  covalent geometry    : angle       0.61554 ( 9475)

*********************** 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
  192 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8472 (mmm) cc_final: 0.8194 (mmt)
REVERT: C    8 HIS cc_start: 0.8506 (m90) cc_final: 0.8189 (m90)
REVERT: D   29 PHE cc_start: 0.8596 (t80) cc_final: 0.8387 (t80)
REVERT: E   13 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7610 (mmt180)
REVERT: E   37 VAL cc_start: 0.8283 (t) cc_final: 0.8064 (m)
REVERT: G    4 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7182 (mmm)
REVERT: G   33 TYR cc_start: 0.7342 (m-10) cc_final: 0.7122 (m-10)
REVERT: G   35 GLN cc_start: 0.7914 (mp10) cc_final: 0.7703 (mp10)
REVERT: G   55 TYR cc_start: 0.7829 (p90) cc_final: 0.7590 (p90)
REVERT: G   59 THR cc_start: 0.8155 (p) cc_final: 0.7692 (p)
REVERT: H   29 PHE cc_start: 0.8089 (t80) cc_final: 0.7799 (t80)
REVERT: L   37 GLN cc_start: 0.6631 (tm130) cc_final: 0.6141 (tm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 176
  average time/residue: 0.2156
  time to fit residues: 48.4614
Evaluate side-chains
  176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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   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 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   56 VAL
Chi-restraints excluded: chain H residue   69 THR
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 67 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 81 optimal weight:    0.2980
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    2.4186

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.123296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.099161 restraints weight = 12945.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.100829 restraints weight = 9500.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.101858 restraints weight = 7025.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065   6987  Z= 0.317
  Angle     :  0.740   7.638   9498  Z= 0.391
  Chirality :  0.048   0.197   1007
  Planarity :  0.005   0.068   1212
  Dihedral  :  7.058  56.978   1012
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.54 (0.26), residues: 847
  helix: -5.12 (0.34), residues: 14
  sheet: -1.92 (0.28), residues: 329
  loop : -2.64 (0.25), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP D  36 
 HIS   0.007   0.001   HIS H 101 
 PHE   0.018   0.003   PHE D 107 
 TYR   0.019   0.002   TYR H  27 
 ARG   0.005   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00492 (    2)
  link_NAG-ASN         : angle       3.67948 (    6)
  link_BETA1-4         : bond        0.00396 (    1)
  link_BETA1-4         : angle       1.20121 (    3)
  hydrogen bonds       : bond        0.03752 (  132)
  hydrogen bonds       : angle       7.16489 (  321)
  SS BOND              : bond        0.00384 (    7)
  SS BOND              : angle       1.04215 (   14)
  covalent geometry    : bond        0.00735 ( 6977)
  covalent geometry    : angle       0.73367 ( 9475)

*********************** 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
  193 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 167
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8591 (mmm) cc_final: 0.8223 (mmt)
REVERT: C    8 HIS cc_start: 0.8525 (m90) cc_final: 0.8183 (m90)
REVERT: D   29 PHE cc_start: 0.8651 (t80) cc_final: 0.8401 (t80)
REVERT: E   13 ARG cc_start: 0.7965 (mmt180) cc_final: 0.7688 (mmt180)
REVERT: E   37 VAL cc_start: 0.8226 (t) cc_final: 0.7989 (m)
REVERT: G    4 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7304 (mmm)
REVERT: G   35 GLN cc_start: 0.7939 (mp10) cc_final: 0.7703 (mp10)
REVERT: G   55 TYR cc_start: 0.8210 (p90) cc_final: 0.7901 (p90)
REVERT: G   59 THR cc_start: 0.8519 (p) cc_final: 0.8022 (p)
REVERT: H   67 LYS cc_start: 0.8102 (mttt) cc_final: 0.7771 (tmtt)
REVERT: L   37 GLN cc_start: 0.6831 (tm130) cc_final: 0.6349 (tm-30)
  outliers start: 26
  outliers final: 24
  residues processed: 176
  average time/residue: 0.2143
  time to fit residues: 48.3117
Evaluate side-chains
  179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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   23 LYS
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  382 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   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   69 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 11 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.127289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.102388 restraints weight = 12826.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.104920 restraints weight = 8227.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.106639 restraints weight = 6187.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6987  Z= 0.155
  Angle     :  0.663   7.465   9498  Z= 0.347
  Chirality :  0.046   0.168   1007
  Planarity :  0.004   0.062   1212
  Dihedral  :  6.504  50.387   1012
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.40 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.27), residues: 847
  helix: -5.08 (0.36), residues: 14
  sheet: -1.59 (0.29), residues: 333
  loop : -2.48 (0.25), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP D  36 
 HIS   0.004   0.001   HIS L  33 
 PHE   0.022   0.002   PHE H 107 
 TYR   0.018   0.001   TYR G  55 
 ARG   0.007   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00149 (    2)
  link_NAG-ASN         : angle       3.38223 (    6)
  link_BETA1-4         : bond        0.00585 (    1)
  link_BETA1-4         : angle       1.59195 (    3)
  hydrogen bonds       : bond        0.02917 (  132)
  hydrogen bonds       : angle       6.73835 (  321)
  SS BOND              : bond        0.00242 (    7)
  SS BOND              : angle       0.82590 (   14)
  covalent geometry    : bond        0.00366 ( 6977)
  covalent geometry    : angle       0.65682 ( 9475)

*********************** 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
  193 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.779 
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: 0.8459 (mmm) cc_final: 0.8162 (mmt)
REVERT: C    8 HIS cc_start: 0.8478 (m90) cc_final: 0.8158 (m90)
REVERT: D   29 PHE cc_start: 0.8597 (t80) cc_final: 0.8382 (t80)
REVERT: E   13 ARG cc_start: 0.7951 (mmt180) cc_final: 0.7707 (mmt180)
REVERT: F  467 ASP cc_start: 0.8855 (t0) cc_final: 0.8600 (t0)
REVERT: G    4 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7459 (mmp)
REVERT: G   35 GLN cc_start: 0.7971 (mp10) cc_final: 0.7726 (mp10)
REVERT: G   55 TYR cc_start: 0.7921 (p90) cc_final: 0.7528 (p90)
REVERT: G   59 THR cc_start: 0.8193 (p) cc_final: 0.7611 (p)
REVERT: H   29 PHE cc_start: 0.8220 (t80) cc_final: 0.7917 (t80)
REVERT: L   37 GLN cc_start: 0.6652 (tm130) cc_final: 0.6323 (tm-30)
  outliers start: 24
  outliers final: 21
  residues processed: 176
  average time/residue: 0.2037
  time to fit residues: 46.5581
Evaluate side-chains
  183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
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   40 ARG
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain E residue  114 THR
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   56 VAL
Chi-restraints excluded: chain H residue   69 THR
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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**
** 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 = 0.3706 r_free = 0.3706 target = 0.125661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.101203 restraints weight = 12801.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.103674 restraints weight = 8197.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.105339 restraints weight = 6176.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6987  Z= 0.205
  Angle     :  0.689   7.609   9498  Z= 0.361
  Chirality :  0.046   0.164   1007
  Planarity :  0.004   0.063   1212
  Dihedral  :  6.622  52.466   1012
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.57 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.21 (0.27), residues: 847
  helix: -5.06 (0.36), residues: 14
  sheet: -1.63 (0.28), residues: 343
  loop : -2.47 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  36 
 HIS   0.005   0.001   HIS H 101 
 PHE   0.019   0.002   PHE H 107 
 TYR   0.018   0.002   TYR G  55 
 ARG   0.006   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00272 (    2)
  link_NAG-ASN         : angle       3.32486 (    6)
  link_BETA1-4         : bond        0.00482 (    1)
  link_BETA1-4         : angle       1.33869 (    3)
  hydrogen bonds       : bond        0.03088 (  132)
  hydrogen bonds       : angle       6.72468 (  321)
  SS BOND              : bond        0.00286 (    7)
  SS BOND              : angle       1.07556 (   14)
  covalent geometry    : bond        0.00481 ( 6977)
  covalent geometry    : angle       0.68346 ( 9475)

*********************** 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
  186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8505 (mmm) cc_final: 0.8163 (mmt)
REVERT: C    8 HIS cc_start: 0.8481 (m90) cc_final: 0.8158 (m90)
REVERT: E   13 ARG cc_start: 0.7969 (mmt180) cc_final: 0.7711 (mmt180)
REVERT: F  467 ASP cc_start: 0.8891 (t0) cc_final: 0.8631 (t0)
REVERT: G    4 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7281 (mmm)
REVERT: G   35 GLN cc_start: 0.7959 (mp10) cc_final: 0.7668 (mp10)
REVERT: G   55 TYR cc_start: 0.7998 (p90) cc_final: 0.7600 (p90)
REVERT: G   59 THR cc_start: 0.8323 (p) cc_final: 0.7724 (p)
REVERT: H   29 PHE cc_start: 0.8249 (t80) cc_final: 0.7960 (t80)
REVERT: L   37 GLN cc_start: 0.6699 (tm130) cc_final: 0.6290 (tm-30)
  outliers start: 28
  outliers final: 23
  residues processed: 167
  average time/residue: 0.2044
  time to fit residues: 44.2345
Evaluate side-chains
  178 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
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   40 ARG
Chi-restraints excluded: chain D residue  115 LEU
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   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   69 THR
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   22 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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**
** 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 = 0.3721 r_free = 0.3721 target = 0.126576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.101977 restraints weight = 12886.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.104439 restraints weight = 8225.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.106101 restraints weight = 6201.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6987  Z= 0.180
  Angle     :  0.689   7.758   9498  Z= 0.358
  Chirality :  0.046   0.159   1007
  Planarity :  0.004   0.060   1212
  Dihedral  :  6.501  51.333   1012
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.92 %
    Favored  : 90.08 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.54 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.28), residues: 847
  helix: -5.04 (0.37), residues: 14
  sheet: -1.56 (0.28), residues: 342
  loop : -2.35 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  36 
 HIS   0.004   0.001   HIS H 101 
 PHE   0.040   0.002   PHE D  29 
 TYR   0.018   0.001   TYR G  55 
 ARG   0.007   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00195 (    2)
  link_NAG-ASN         : angle       3.28735 (    6)
  link_BETA1-4         : bond        0.00661 (    1)
  link_BETA1-4         : angle       1.43083 (    3)
  hydrogen bonds       : bond        0.02921 (  132)
  hydrogen bonds       : angle       6.60007 (  321)
  SS BOND              : bond        0.00250 (    7)
  SS BOND              : angle       0.87728 (   14)
  covalent geometry    : bond        0.00425 ( 6977)
  covalent geometry    : angle       0.68385 ( 9475)

*********************** 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
  183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 155
  time to evaluate  : 0.994 
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: 0.8455 (mmm) cc_final: 0.8143 (mmt)
REVERT: C    8 HIS cc_start: 0.8471 (m90) cc_final: 0.8155 (m90)
REVERT: C   89 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7936 (tt0)
REVERT: E   13 ARG cc_start: 0.7946 (mmt180) cc_final: 0.7682 (mmt180)
REVERT: F  467 ASP cc_start: 0.8884 (t0) cc_final: 0.8631 (t0)
REVERT: G    4 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7451 (mmp)
REVERT: G   35 GLN cc_start: 0.7927 (mp10) cc_final: 0.7620 (mp10)
REVERT: G   55 TYR cc_start: 0.7926 (p90) cc_final: 0.7690 (p90)
REVERT: G   59 THR cc_start: 0.8303 (p) cc_final: 0.7946 (p)
REVERT: H   29 PHE cc_start: 0.8234 (t80) cc_final: 0.7939 (t80)
REVERT: L   37 GLN cc_start: 0.6644 (tm130) cc_final: 0.6340 (tm-30)
  outliers start: 28
  outliers final: 23
  residues processed: 165
  average time/residue: 0.2552
  time to fit residues: 54.7582
Evaluate side-chains
  178 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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   89 GLN
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue   40 ARG
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain E residue  114 THR
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   84 VAL
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
C  89 GLN
** C  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** 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 = 0.3741 r_free = 0.3741 target = 0.127962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.103420 restraints weight = 12896.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.105879 restraints weight = 8241.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.107583 restraints weight = 6223.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6987  Z= 0.156
  Angle     :  0.667   7.720   9498  Z= 0.347
  Chirality :  0.045   0.159   1007
  Planarity :  0.004   0.057   1212
  Dihedral  :  6.211  48.861   1012
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.27), residues: 847
  helix: -4.96 (0.42), residues: 14
  sheet: -1.49 (0.29), residues: 331
  loop : -2.33 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  36 
 HIS   0.003   0.001   HIS H 101 
 PHE   0.031   0.002   PHE D  29 
 TYR   0.018   0.001   TYR G  55 
 ARG   0.005   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00168 (    2)
  link_NAG-ASN         : angle       3.08970 (    6)
  link_BETA1-4         : bond        0.00531 (    1)
  link_BETA1-4         : angle       1.29660 (    3)
  hydrogen bonds       : bond        0.02703 (  132)
  hydrogen bonds       : angle       6.37583 (  321)
  SS BOND              : bond        0.00241 (    7)
  SS BOND              : angle       0.87180 (   14)
  covalent geometry    : bond        0.00369 ( 6977)
  covalent geometry    : angle       0.66232 ( 9475)

*********************** 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
  190 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8409 (mmm) cc_final: 0.8112 (mmt)
REVERT: C    8 HIS cc_start: 0.8470 (m90) cc_final: 0.8158 (m90)
REVERT: C   89 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7948 (tt0)
REVERT: E   13 ARG cc_start: 0.7905 (mmt180) cc_final: 0.7423 (mmm160)
REVERT: E   62 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8349 (tm-30)
REVERT: E   73 ASP cc_start: 0.7594 (t0) cc_final: 0.6931 (p0)
REVERT: F  467 ASP cc_start: 0.8870 (t0) cc_final: 0.8634 (t0)
REVERT: G    4 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7320 (mmm)
REVERT: G   35 GLN cc_start: 0.7907 (mp10) cc_final: 0.7686 (mp10)
REVERT: G   55 TYR cc_start: 0.7756 (p90) cc_final: 0.7508 (p90)
REVERT: G   59 THR cc_start: 0.8253 (p) cc_final: 0.7768 (p)
REVERT: H   29 PHE cc_start: 0.8249 (t80) cc_final: 0.7952 (t80)
REVERT: H   63 LYS cc_start: 0.8265 (mttp) cc_final: 0.7882 (ttmm)
REVERT: L   37 GLN cc_start: 0.6572 (tm130) cc_final: 0.6288 (tm-30)
  outliers start: 28
  outliers final: 22
  residues processed: 174
  average time/residue: 0.2031
  time to fit residues: 45.8190
Evaluate side-chains
  177 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 153
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
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  102 VAL
Chi-restraints excluded: chain E residue  114 THR
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   84 VAL
Chi-restraints excluded: chain G residue   89 LEU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   69 THR
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   22 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 57 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 79 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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**
** 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 = 0.3746 r_free = 0.3746 target = 0.128395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.103674 restraints weight = 13001.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.106172 restraints weight = 8304.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.107925 restraints weight = 6253.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6987  Z= 0.156
  Angle     :  0.682   8.023   9498  Z= 0.354
  Chirality :  0.046   0.191   1007
  Planarity :  0.004   0.054   1212
  Dihedral  :  6.172  48.996   1012
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.45 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.49 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.27), residues: 847
  helix: -4.90 (0.45), residues: 14
  sheet: -1.40 (0.29), residues: 325
  loop : -2.39 (0.25), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP D  36 
 HIS   0.003   0.001   HIS H 101 
 PHE   0.028   0.002   PHE D  29 
 TYR   0.019   0.001   TYR G  55 
 ARG   0.005   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00166 (    2)
  link_NAG-ASN         : angle       3.12785 (    6)
  link_BETA1-4         : bond        0.00685 (    1)
  link_BETA1-4         : angle       1.30522 (    3)
  hydrogen bonds       : bond        0.02754 (  132)
  hydrogen bonds       : angle       6.39410 (  321)
  SS BOND              : bond        0.00295 (    7)
  SS BOND              : angle       1.00853 (   14)
  covalent geometry    : bond        0.00371 ( 6977)
  covalent geometry    : angle       0.67654 ( 9475)

********************** 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
  179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8416 (mmm) cc_final: 0.8108 (mmt)
REVERT: C    8 HIS cc_start: 0.8471 (m90) cc_final: 0.8143 (m90)
REVERT: E   13 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7575 (mmt180)
REVERT: E   62 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8331 (tm-30)
REVERT: F  467 ASP cc_start: 0.8871 (t0) cc_final: 0.8635 (t0)
REVERT: G    4 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7594 (mmp)
REVERT: G   35 GLN cc_start: 0.7886 (mp10) cc_final: 0.7673 (mp10)
REVERT: G   55 TYR cc_start: 0.7772 (p90) cc_final: 0.7499 (p90)
REVERT: G   59 THR cc_start: 0.8239 (p) cc_final: 0.7747 (p)
REVERT: H   29 PHE cc_start: 0.8245 (t80) cc_final: 0.7946 (t80)
REVERT: H   63 LYS cc_start: 0.8261 (mttp) cc_final: 0.7882 (ttmm)
REVERT: L   37 GLN cc_start: 0.6573 (tm130) cc_final: 0.6285 (tm-30)
  outliers start: 22
  outliers final: 21
  residues processed: 167
  average time/residue: 0.2387
  time to fit residues: 52.3307
Evaluate side-chains
  176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 154
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
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  102 VAL
Chi-restraints excluded: chain E residue  114 THR
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   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   69 THR
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   22 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 65 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    2.2788

-------------------------------------------------------------------------------
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**
** E   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 439 ASN ** 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 = 0.3682 r_free = 0.3682 target = 0.123573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.100448 restraints weight = 13162.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.102517 restraints weight = 9262.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.103810 restraints weight = 6983.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   6987  Z= 0.312
  Angle     :  0.792   9.248   9498  Z= 0.415
  Chirality :  0.050   0.279   1007
  Planarity :  0.005   0.065   1212
  Dihedral  :  7.059  57.950   1012
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.04 %
    Favored  : 87.96 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.08 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.27), residues: 847
  helix: -4.89 (0.50), residues: 14
  sheet: -1.71 (0.28), residues: 347
  loop : -2.46 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP D  36 
 HIS   0.007   0.002   HIS H 101 
 PHE   0.027   0.003   PHE D  29 
 TYR   0.020   0.002   TYR G  55 
 ARG   0.008   0.001   ARG L  60 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00541 (    2)
  link_NAG-ASN         : angle       3.70185 (    6)
  link_BETA1-4         : bond        0.00282 (    1)
  link_BETA1-4         : angle       1.21935 (    3)
  hydrogen bonds       : bond        0.03563 (  132)
  hydrogen bonds       : angle       6.90939 (  321)
  SS BOND              : bond        0.00434 (    7)
  SS BOND              : angle       1.21289 (   14)
  covalent geometry    : bond        0.00730 ( 6977)
  covalent geometry    : angle       0.78577 ( 9475)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3052.84 seconds
wall clock time: 54 minutes 53.72 seconds (3293.72 seconds total)