Starting phenix.real_space_refine
on Fri Aug 22 18:29:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wp8_32678/08_2025/7wp8_32678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wp8_32678/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wp8_32678/08_2025/7wp8_32678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wp8_32678/08_2025/7wp8_32678.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wp8_32678/08_2025/7wp8_32678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wp8_32678/08_2025/7wp8_32678.map"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4313      2.51       5
     N    1123      2.21       5
     O    1330      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6797
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "C"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 805
          Classifications: {'peptide': 104}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 919
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "E"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 966
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
    Chain: "F"
      Number of atoms: 1470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1470
          Classifications: {'peptide': 183}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "G"
      Number of atoms: 874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 874
          Classifications: {'peptide': 113}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 107}
    Chain: "H"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 930
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 791
          Classifications: {'peptide': 106}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 97}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.46, per 1000 atoms: 0.21
  Number of scatterers: 6797
  At special positions: 0
  Unit cell: (89.47, 112.032, 112.032, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      31     16.00
     O    1330      8.00
     N    1123      7.00
     C    4313      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.15
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 480 " - pdb=" SG  CYS F 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN F 343 "
      " NAG L 201 " - " ASN L  26 "
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 249.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 21 sheets defined
      3.6% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.850A  pdb=" N   ARG D  31 " --> pdb=" O   THR D  28 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   TYR D  32 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 28 through 32'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.866A  pdb=" N   SER D  91 " --> pdb=" O   SER D  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.703A  pdb=" N   ASP E  90 " --> pdb=" O   THR E  87 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing helix  chain 'F' and resid 403 through 410
      removed outlier: 3.524A  pdb=" N   GLU F 406 " --> pdb=" O   ARG F 403 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   ARG F 408 " --> pdb=" O   ASP F 405 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.893A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 6
      removed outlier: 4.160A  pdb=" N   ASP C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.158A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C  47 " --> pdb=" O   TRP C  35 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.697A  pdb=" N   LEU D   4 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   SER D  25 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   THR D  78 " --> pdb=" O   ASP D  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 18 through 19
    Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 60
      removed outlier: 6.289A  pdb=" N   TRP D  47 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LYS D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ARG D  98 " --> pdb=" O   ALA D 108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 59 through 60
      removed outlier: 6.289A  pdb=" N   TRP D  47 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LYS D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY D  49 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 5
      removed outlier: 3.511A  pdb=" N   THR E  71 " --> pdb=" O   TYR E  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 9 through 12
    Processing sheet with id=AA9, first strand: chain 'E' and resid 59 through 60
      removed outlier: 3.565A  pdb=" N   HIS E  59 " --> pdb=" O   ARG E  50 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   TRP E  36 " --> pdb=" O   ILE E  48 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ARG E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   MET E  34 " --> pdb=" O   ARG E  50 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL E  37 " --> pdb=" O   TYR E  95 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   TYR E 108 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 357 through 358
      removed outlier: 3.737A  pdb=" N   ASP F 398 " --> pdb=" O   VAL F 512 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL F 433 " --> pdb=" O   LYS F 378 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LYS F 378 " --> pdb=" O   VAL F 433 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 452 through 454
    Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 13
      removed outlier: 3.502A  pdb=" N   MET G  13 " --> pdb=" O   GLU G 111 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 19 through 20
    Processing sheet with id=AB5, first strand: chain 'G' and resid 50 through 52
    Processing sheet with id=AB6, first strand: chain 'G' and resid 54 through 55
      removed outlier: 3.783A  pdb=" N   THR G  59 " --> pdb=" O   TYR G  55 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.590A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR H 112 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   TYR H  94 " --> pdb=" O   THR H 112 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU H 114 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.518A  pdb=" N   ILE H  59 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   TRP H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ILE H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY H  98 " --> pdb=" O   PHE H 107 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 12
    Processing sheet with id=AC2, first strand: chain 'L' and resid 19 through 24
      removed outlier: 3.727A  pdb=" N   TYR L  70 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER L  69 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 43 through 47
      removed outlier: 6.722A  pdb=" N   TRP L  34 " --> pdb=" O   TRP L  46 " (cutoff:3.500A)

    143 hydrogen bonds defined for protein.
    321 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.94

  Time building geometry restraints manager: 0.66 seconds

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

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

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

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 3692
       17.87 -    35.74: 352
       35.74 -    53.61: 54
       53.61 -    71.48: 9
       71.48 -    89.35: 12
  Dihedral angle restraints: 4119
    sinusoidal: 1633
      harmonic: 2486
  Sorted by residual:
  dihedral pdb=" CA  TYR G  55 "
           pdb=" C   TYR G  55 "
           pdb=" N   PHE G  56 "
           pdb=" CA  PHE G  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -132.22  -47.78     0      5.00e+00 4.00e-02 9.13e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.81  -86.81     1      1.00e+01 1.00e-02 9.07e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.16  -64.16     1      1.00e+01 1.00e-02 5.42e+01
  ... (remaining 4116 not shown)

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

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

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1556
        2.78 -     3.31: 5631
        3.31 -     3.84: 11082
        3.84 -     4.37: 12156
        4.37 -     4.90: 21565
  Nonbonded interactions: 51990
  Sorted by model distance:
  nonbonded pdb=" O   GLY F 447 "
            pdb=" OH  TYR H  33 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" CG2 VAL F 503 "
            pdb=" OE1 GLN F 506 "
     model   vdw
     2.269 3.460
  nonbonded pdb=" OG  SER D  17 "
            pdb=" O   LEU D  83 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG  SER C  43 "
            pdb=" O   GLY D 111 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   THR H 112 "
            pdb=" OG1 THR H 112 "
     model   vdw
     2.296 3.040
  ... (remaining 51985 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.400
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.230
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.188   6987  Z= 0.544
  Angle     :  1.072  31.715   9498  Z= 0.616
  Chirality :  0.106   2.655   1007
  Planarity :  0.012   0.259   1212
  Dihedral  : 14.513  89.355   2524
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.97 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.12 (0.25), residues: 847
  helix: -4.94 (0.50), residues: 8
  sheet: -2.25 (0.29), residues: 284
  loop : -3.16 (0.22), residues: 555

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

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

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8524 (mmm) cc_final: 0.8310 (mmt)
REVERT: D   38 LYS cc_start: 0.8200 (ptmt) cc_final: 0.7776 (ttpt)
REVERT: E   13 ARG cc_start: 0.7979 (mmt180) cc_final: 0.7345 (mtp85)
REVERT: E   46 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7574 (mt-10)
REVERT: E   65 LYS cc_start: 0.7906 (mttt) cc_final: 0.7595 (mtmt)
REVERT: G   13 MET cc_start: 0.7522 (tpt) cc_final: 0.7214 (tpt)
REVERT: G   35 GLN cc_start: 0.8008 (mp10) cc_final: 0.7519 (mp10)
REVERT: G   78 THR cc_start: 0.9036 (p) cc_final: 0.8799 (p)
REVERT: G   85 GLN cc_start: 0.8801 (mm110) cc_final: 0.8514 (mm110)
REVERT: H   29 PHE cc_start: 0.7988 (t80) cc_final: 0.7696 (t80)
REVERT: H   60 TYR cc_start: 0.8299 (m-80) cc_final: 0.7759 (m-80)
REVERT: L    4 LEU cc_start: 0.8584 (mt) cc_final: 0.8255 (mp)
REVERT: L   37 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6514 (tm-30)
REVERT: L   88 GLN cc_start: 0.8262 (mp10) cc_final: 0.8020 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.0905
  time to fit residues: 25.4560
Evaluate side-chains
  166 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0870
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.6758

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

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

Total number of N/Q/H flips: 6

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

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

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.75 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.63 (0.27), residues: 847
  helix: -4.78 (0.66), residues: 8
  sheet: -1.88 (0.28), residues: 323
  loop : -2.84 (0.24), residues: 516

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6977)
  covalent geometry    : angle       0.65309 ( 9475)
  SS BOND              : bond        0.00425 (    7)
  SS BOND              : angle       1.25652 (   14)
  hydrogen bonds       : bond        0.03575 (  132)
  hydrogen bonds       : angle       7.94499 (  321)
  link_BETA1-4         : bond        0.00881 (    1)
  link_BETA1-4         : angle       1.36251 (    3)
  link_NAG-ASN         : bond        0.00165 (    2)
  link_NAG-ASN         : angle       4.76972 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8459 (mmm) cc_final: 0.8254 (mmt)
REVERT: E   13 ARG cc_start: 0.7906 (mmt180) cc_final: 0.7633 (mmt180)
REVERT: G    4 MET cc_start: 0.7926 (tpp) cc_final: 0.7267 (mmm)
REVERT: G   35 GLN cc_start: 0.7984 (mp10) cc_final: 0.7742 (mp10)
REVERT: H   29 PHE cc_start: 0.7887 (t80) cc_final: 0.7632 (t80)
REVERT: H  106 ASP cc_start: 0.7164 (m-30) cc_final: 0.6801 (m-30)
REVERT: L   32 MET cc_start: 0.7654 (mtp) cc_final: 0.7439 (mtp)
REVERT: L   37 GLN cc_start: 0.6540 (tm-30) cc_final: 0.6155 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 187
  average time/residue: 0.0991
  time to fit residues: 23.6449
Evaluate side-chains
  177 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 168
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    2.1990

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

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

Total number of N/Q/H flips: 5

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

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

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.81 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.67 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.65 (0.26), residues: 847
  helix: -5.14 (0.32), residues: 14
  sheet: -1.87 (0.29), residues: 309
  loop : -2.82 (0.24), residues: 524

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00702 ( 6977)
  covalent geometry    : angle       0.73873 ( 9475)
  SS BOND              : bond        0.00486 (    7)
  SS BOND              : angle       1.27121 (   14)
  hydrogen bonds       : bond        0.04120 (  132)
  hydrogen bonds       : angle       7.54957 (  321)
  link_BETA1-4         : bond        0.00338 (    1)
  link_BETA1-4         : angle       1.30851 (    3)
  link_NAG-ASN         : bond        0.00514 (    2)
  link_NAG-ASN         : angle       3.97768 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8638 (mmm) cc_final: 0.8278 (mmt)
REVERT: D   29 PHE cc_start: 0.8673 (t80) cc_final: 0.8458 (t80)
REVERT: E   13 ARG cc_start: 0.7960 (mmt180) cc_final: 0.7502 (mtp85)
REVERT: G    4 MET cc_start: 0.8031 (tpp) cc_final: 0.7279 (mmm)
REVERT: G   35 GLN cc_start: 0.7945 (mp10) cc_final: 0.7678 (mp10)
REVERT: L   37 GLN cc_start: 0.6898 (tm130) cc_final: 0.6519 (tm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 176
  average time/residue: 0.0858
  time to fit residues: 19.4371
Evaluate side-chains
  172 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   96 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0770
   chunk 18 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5338

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.129938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.104888 restraints weight = 12559.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.107480 restraints weight = 7965.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.109152 restraints weight = 5964.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.110351 restraints weight = 4987.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.111034 restraints weight = 4415.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6987  Z= 0.123
  Angle     :  0.616   6.146   9498  Z= 0.323
  Chirality :  0.045   0.175   1007
  Planarity :  0.004   0.056   1212
  Dihedral  :  6.194  47.465   1012
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 16.94 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.27), residues: 847
  helix: -5.08 (0.37), residues: 14
  sheet: -1.67 (0.29), residues: 317
  loop : -2.58 (0.24), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  60 
 TYR   0.016   0.001   TYR F 380 
 PHE   0.018   0.002   PHE H  29 
 TRP   0.017   0.001   TRP D  36 
 HIS   0.003   0.001   HIS L  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6977)
  covalent geometry    : angle       0.60883 ( 9475)
  SS BOND              : bond        0.00279 (    7)
  SS BOND              : angle       0.89107 (   14)
  hydrogen bonds       : bond        0.02758 (  132)
  hydrogen bonds       : angle       6.77568 (  321)
  link_BETA1-4         : bond        0.00641 (    1)
  link_BETA1-4         : angle       1.68011 (    3)
  link_NAG-ASN         : bond        0.00109 (    2)
  link_NAG-ASN         : angle       3.38650 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 0.253 
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: 0.8177 (mmt)
REVERT: E   10 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7851 (mm-30)
REVERT: E   13 ARG cc_start: 0.7902 (mmt180) cc_final: 0.7612 (mmt180)
REVERT: G    4 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7221 (mmm)
REVERT: G   13 MET cc_start: 0.6885 (tpt) cc_final: 0.6420 (tpt)
REVERT: G   33 TYR cc_start: 0.7331 (m-10) cc_final: 0.7131 (m-10)
REVERT: G   35 GLN cc_start: 0.7951 (mp10) cc_final: 0.7706 (mp10)
REVERT: G   59 THR cc_start: 0.7977 (p) cc_final: 0.7320 (p)
REVERT: H   29 PHE cc_start: 0.8135 (t80) cc_final: 0.7743 (t80)
REVERT: L   37 GLN cc_start: 0.6621 (tm130) cc_final: 0.6222 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 186
  average time/residue: 0.1010
  time to fit residues: 24.1001
Evaluate side-chains
  175 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    3 VAL
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   chunk 58 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.129328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.104189 restraints weight = 12770.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.106808 restraints weight = 8067.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.108579 restraints weight = 6022.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.109436 restraints weight = 4984.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.110386 restraints weight = 4476.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3053

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= 0.149
  Angle     :  0.635   7.566   9498  Z= 0.333
  Chirality :  0.045   0.185   1007
  Planarity :  0.004   0.054   1212
  Dihedral  :  6.158  48.061   1012
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.62 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.21 (0.27), residues: 847
  helix: -5.03 (0.40), residues: 14
  sheet: -1.64 (0.28), residues: 332
  loop : -2.46 (0.25), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  60 
 TYR   0.019   0.001   TYR E  32 
 PHE   0.017   0.002   PHE G 104 
 TRP   0.034   0.002   TRP D  36 
 HIS   0.003   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6977)
  covalent geometry    : angle       0.62913 ( 9475)
  SS BOND              : bond        0.00236 (    7)
  SS BOND              : angle       0.85775 (   14)
  hydrogen bonds       : bond        0.02843 (  132)
  hydrogen bonds       : angle       6.59725 (  321)
  link_BETA1-4         : bond        0.00643 (    1)
  link_BETA1-4         : angle       1.37086 (    3)
  link_NAG-ASN         : bond        0.00173 (    2)
  link_NAG-ASN         : angle       3.17522 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.234 
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: 0.8489 (mmm) cc_final: 0.8197 (mmt)
REVERT: E   13 ARG cc_start: 0.7907 (mmt180) cc_final: 0.7684 (mmt180)
REVERT: E   52 ASP cc_start: 0.8346 (t0) cc_final: 0.8129 (t0)
REVERT: G    4 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7254 (mmm)
REVERT: G   35 GLN cc_start: 0.7950 (mp10) cc_final: 0.7687 (mp10)
REVERT: H   29 PHE cc_start: 0.8168 (t80) cc_final: 0.7785 (t80)
REVERT: L   37 GLN cc_start: 0.6639 (tm130) cc_final: 0.6272 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 168
  average time/residue: 0.0980
  time to fit residues: 20.9783
Evaluate side-chains
  174 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   10 SER
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain L residue   10 ILE
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0670
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.5918

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.130665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.105598 restraints weight = 12800.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.108242 restraints weight = 8051.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.110059 restraints weight = 5975.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.111227 restraints weight = 4931.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.111844 restraints weight = 4361.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6987  Z= 0.130
  Angle     :  0.621   6.950   9498  Z= 0.325
  Chirality :  0.044   0.168   1007
  Planarity :  0.004   0.051   1212
  Dihedral  :  5.962  47.095   1012
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.26 %
    Favored  : 77.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.03 (0.27), residues: 847
  helix: -4.93 (0.47), residues: 14
  sheet: -1.47 (0.28), residues: 336
  loop : -2.37 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  60 
 TYR   0.013   0.001   TYR F 489 
 PHE   0.015   0.001   PHE G 104 
 TRP   0.031   0.001   TRP D  36 
 HIS   0.003   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6977)
  covalent geometry    : angle       0.61600 ( 9475)
  SS BOND              : bond        0.00358 (    7)
  SS BOND              : angle       0.82654 (   14)
  hydrogen bonds       : bond        0.02666 (  132)
  hydrogen bonds       : angle       6.45103 (  321)
  link_BETA1-4         : bond        0.00603 (    1)
  link_BETA1-4         : angle       1.33611 (    3)
  link_NAG-ASN         : bond        0.00100 (    2)
  link_NAG-ASN         : angle       3.02704 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.164 
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: 0.8401 (mmm) cc_final: 0.8132 (mmt)
REVERT: E   13 ARG cc_start: 0.7870 (mmt180) cc_final: 0.7602 (mmt180)
REVERT: G    4 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7292 (mmm)
REVERT: G   35 GLN cc_start: 0.7985 (mp10) cc_final: 0.7731 (mp10)
REVERT: G   55 TYR cc_start: 0.8002 (p90) cc_final: 0.7741 (p90)
REVERT: H   29 PHE cc_start: 0.8184 (t80) cc_final: 0.7805 (t80)
REVERT: H   56 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7473 (t)
REVERT: H   63 LYS cc_start: 0.8245 (mttp) cc_final: 0.7917 (ttmm)
REVERT: L   37 GLN cc_start: 0.6582 (tm130) cc_final: 0.6228 (tm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 164
  average time/residue: 0.0851
  time to fit residues: 17.9736
Evaluate side-chains
  167 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 33 optimal weight:    0.3980
   chunk 15 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.129968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.105122 restraints weight = 12550.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.107685 restraints weight = 8004.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.109446 restraints weight = 5990.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.110480 restraints weight = 4955.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.111337 restraints weight = 4411.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3406

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= 0.137
  Angle     :  0.633   7.221   9498  Z= 0.329
  Chirality :  0.045   0.197   1007
  Planarity :  0.004   0.049   1212
  Dihedral  :  5.873  46.628   1012
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.26 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.96 (0.27), residues: 847
  helix: -4.88 (0.51), residues: 14
  sheet: -1.41 (0.29), residues: 338
  loop : -2.34 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  60 
 TYR   0.016   0.001   TYR E  32 
 PHE   0.012   0.001   PHE D 107 
 TRP   0.025   0.001   TRP D  36 
 HIS   0.003   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6977)
  covalent geometry    : angle       0.62771 ( 9475)
  SS BOND              : bond        0.00258 (    7)
  SS BOND              : angle       0.89087 (   14)
  hydrogen bonds       : bond        0.02585 (  132)
  hydrogen bonds       : angle       6.29396 (  321)
  link_BETA1-4         : bond        0.00569 (    1)
  link_BETA1-4         : angle       1.16646 (    3)
  link_NAG-ASN         : bond        0.00157 (    2)
  link_NAG-ASN         : angle       2.96302 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.201 
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: 0.8428 (mmm) cc_final: 0.8146 (mmt)
REVERT: E   13 ARG cc_start: 0.7891 (mmt180) cc_final: 0.7345 (mmm160)
REVERT: G    4 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7226 (mmm)
REVERT: G   35 GLN cc_start: 0.8010 (mp10) cc_final: 0.7794 (mp10)
REVERT: G   39 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6506 (tp)
REVERT: G   55 TYR cc_start: 0.7956 (p90) cc_final: 0.7671 (p90)
REVERT: H   29 PHE cc_start: 0.8159 (t80) cc_final: 0.7781 (t80)
REVERT: H   56 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7450 (t)
REVERT: H   63 LYS cc_start: 0.8243 (mttp) cc_final: 0.7917 (ttmm)
REVERT: L   37 GLN cc_start: 0.6623 (tm130) cc_final: 0.6250 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 160
  average time/residue: 0.0953
  time to fit residues: 19.5880
Evaluate side-chains
  169 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.2980
   chunk 80 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   1 GLN
E   3 GLN
** F 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.129314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.104269 restraints weight = 12757.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.106792 restraints weight = 8093.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.108595 restraints weight = 6086.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.109743 restraints weight = 5031.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.110535 restraints weight = 4452.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6987  Z= 0.153
  Angle     :  0.646   7.261   9498  Z= 0.336
  Chirality :  0.045   0.266   1007
  Planarity :  0.004   0.049   1212
  Dihedral  :  5.958  47.923   1012
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.67 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.87 (0.28), residues: 847
  helix: -4.89 (0.49), residues: 14
  sheet: -1.37 (0.29), residues: 340
  loop : -2.26 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  60 
 TYR   0.019   0.001   TYR G  55 
 PHE   0.024   0.002   PHE G 104 
 TRP   0.025   0.001   TRP D  36 
 HIS   0.003   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6977)
  covalent geometry    : angle       0.64097 ( 9475)
  SS BOND              : bond        0.00235 (    7)
  SS BOND              : angle       0.80933 (   14)
  hydrogen bonds       : bond        0.02645 (  132)
  hydrogen bonds       : angle       6.27100 (  321)
  link_BETA1-4         : bond        0.00606 (    1)
  link_BETA1-4         : angle       1.14662 (    3)
  link_NAG-ASN         : bond        0.00177 (    2)
  link_NAG-ASN         : angle       3.03617 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 MET cc_start: 0.8422 (mmm) cc_final: 0.8123 (mmt)
REVERT: C   45 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8732 (mtmt)
REVERT: E   73 ASP cc_start: 0.7521 (t0) cc_final: 0.6916 (p0)
REVERT: G    4 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7237 (mmm)
REVERT: G   35 GLN cc_start: 0.7993 (mp10) cc_final: 0.7786 (mp10)
REVERT: G   39 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6525 (tp)
REVERT: G   55 TYR cc_start: 0.8029 (p90) cc_final: 0.7785 (p90)
REVERT: H   29 PHE cc_start: 0.8192 (t80) cc_final: 0.7854 (t80)
REVERT: H   56 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7512 (t)
REVERT: H   63 LYS cc_start: 0.8255 (mttp) cc_final: 0.7919 (ttmm)
REVERT: L   37 GLN cc_start: 0.6629 (tm130) cc_final: 0.6274 (tm-30)
  outliers start: 24
  outliers final: 17
  residues processed: 161
  average time/residue: 0.0997
  time to fit residues: 20.6918
Evaluate side-chains
  170 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue    4 MET
Chi-restraints excluded: chain G residue   39 LEU
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain L residue   22 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.4980
   chunk 61 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0970
   chunk 21 optimal weight:    0.0770
   chunk 34 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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**
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 439 ASN
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.131171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.106466 restraints weight = 12584.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.109067 restraints weight = 7895.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.110825 restraints weight = 5851.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.112030 restraints weight = 4835.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.112706 restraints weight = 4257.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6987  Z= 0.118
  Angle     :  0.632   7.704   9498  Z= 0.327
  Chirality :  0.044   0.173   1007
  Planarity :  0.004   0.045   1212
  Dihedral  :  5.672  46.260   1012
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 21.45 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.77 (0.28), residues: 847
  helix: -4.81 (0.52), residues: 14
  sheet: -1.24 (0.30), residues: 317
  loop : -2.23 (0.25), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  60 
 TYR   0.021   0.001   TYR G  55 
 PHE   0.023   0.001   PHE G 104 
 TRP   0.026   0.001   TRP D  36 
 HIS   0.002   0.000   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6977)
  covalent geometry    : angle       0.62733 ( 9475)
  SS BOND              : bond        0.00213 (    7)
  SS BOND              : angle       0.75456 (   14)
  hydrogen bonds       : bond        0.02404 (  132)
  hydrogen bonds       : angle       6.08849 (  321)
  link_BETA1-4         : bond        0.00468 (    1)
  link_BETA1-4         : angle       1.16512 (    3)
  link_NAG-ASN         : bond        0.00116 (    2)
  link_NAG-ASN         : angle       2.82534 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 159
  time to evaluate  : 0.196 
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: 0.8408 (mmm) cc_final: 0.8150 (mmt)
REVERT: C   45 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8668 (mtmt)
REVERT: C   89 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7886 (tt0)
REVERT: D   29 PHE cc_start: 0.8550 (t80) cc_final: 0.8323 (t80)
REVERT: E   13 ARG cc_start: 0.7935 (mmt180) cc_final: 0.7246 (mtp85)
REVERT: G   55 TYR cc_start: 0.7875 (p90) cc_final: 0.7588 (p90)
REVERT: H   29 PHE cc_start: 0.8196 (t80) cc_final: 0.7849 (t80)
REVERT: H   56 VAL cc_start: 0.7714 (OUTLIER) cc_final: 0.7392 (t)
REVERT: H   63 LYS cc_start: 0.8274 (mttp) cc_final: 0.7930 (ttmm)
REVERT: L   37 GLN cc_start: 0.6555 (tm130) cc_final: 0.6205 (tm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 166
  average time/residue: 0.0832
  time to fit residues: 17.8137
Evaluate side-chains
  169 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 56 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 23 optimal weight:    5.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.130685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.106094 restraints weight = 12539.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.108672 restraints weight = 7894.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.110406 restraints weight = 5879.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.111583 restraints weight = 4864.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.112191 restraints weight = 4285.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6987  Z= 0.138
  Angle     :  0.665   8.336   9498  Z= 0.342
  Chirality :  0.046   0.190   1007
  Planarity :  0.004   0.043   1212
  Dihedral  :  5.750  45.672   1012
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.72 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.82 (0.27), residues: 847
  helix: -4.74 (0.57), residues: 14
  sheet: -1.29 (0.29), residues: 318
  loop : -2.25 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  60 
 TYR   0.021   0.001   TYR G  55 
 PHE   0.020   0.002   PHE G 104 
 TRP   0.029   0.001   TRP D  36 
 HIS   0.003   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6977)
  covalent geometry    : angle       0.66069 ( 9475)
  SS BOND              : bond        0.00264 (    7)
  SS BOND              : angle       0.80563 (   14)
  hydrogen bonds       : bond        0.02451 (  132)
  hydrogen bonds       : angle       6.08028 (  321)
  link_BETA1-4         : bond        0.00591 (    1)
  link_BETA1-4         : angle       1.17083 (    3)
  link_NAG-ASN         : bond        0.00104 (    2)
  link_NAG-ASN         : angle       2.88205 (    6)

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

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

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

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.197 
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: 0.8404 (mmm) cc_final: 0.8116 (mmt)
REVERT: C   89 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7772 (tt0)
REVERT: D   34 MET cc_start: 0.8059 (mmm) cc_final: 0.7845 (tpp)
REVERT: G   55 TYR cc_start: 0.7900 (p90) cc_final: 0.7630 (p90)
REVERT: H   29 PHE cc_start: 0.8196 (t80) cc_final: 0.7857 (t80)
REVERT: H   56 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7392 (t)
REVERT: H   63 LYS cc_start: 0.8277 (mttp) cc_final: 0.7934 (ttmm)
REVERT: L   37 GLN cc_start: 0.6606 (tm130) cc_final: 0.6246 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 161
  average time/residue: 0.0969
  time to fit residues: 20.0764
Evaluate side-chains
  165 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 ASP
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain E residue   42 GLU
Chi-restraints excluded: chain E residue  102 VAL
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  489 TYR
Chi-restraints excluded: chain G residue   84 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    0.2980
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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**
** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   3 GLN
** G  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  88 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.130963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.106364 restraints weight = 12484.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.108976 restraints weight = 7893.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.110735 restraints weight = 5864.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.111874 restraints weight = 4837.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.112544 restraints weight = 4270.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3794

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= 0.135
  Angle     :  0.679   8.361   9498  Z= 0.349
  Chirality :  0.046   0.285   1007
  Planarity :  0.004   0.041   1212
  Dihedral  :  5.737  45.882   1012
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.72 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.83 (0.27), residues: 847
  helix: -4.76 (0.55), residues: 14
  sheet: -1.30 (0.29), residues: 318
  loop : -2.25 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  60 
 TYR   0.022   0.001   TYR G  55 
 PHE   0.022   0.002   PHE D  64 
 TRP   0.019   0.001   TRP D  36 
 HIS   0.003   0.001   HIS H 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6977)
  covalent geometry    : angle       0.67516 ( 9475)
  SS BOND              : bond        0.00203 (    7)
  SS BOND              : angle       0.82118 (   14)
  hydrogen bonds       : bond        0.02428 (  132)
  hydrogen bonds       : angle       6.03184 (  321)
  link_BETA1-4         : bond        0.00765 (    1)
  link_BETA1-4         : angle       1.09463 (    3)
  link_NAG-ASN         : bond        0.00144 (    2)
  link_NAG-ASN         : angle       2.85862 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1366.95 seconds
wall clock time: 24 minutes 22.66 seconds (1462.66 seconds total)