Starting phenix.real_space_refine
on Wed Sep 17 07:24:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vjm_43289/09_2025/8vjm_43289.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vjm_43289/09_2025/8vjm_43289.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vjm_43289/09_2025/8vjm_43289.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vjm_43289/09_2025/8vjm_43289.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vjm_43289/09_2025/8vjm_43289.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vjm_43289/09_2025/8vjm_43289.cif"
  }
  resolution = 4.0
  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=   0.021
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      28      5.16       5
     C    4423      2.51       5
     N    1083      2.21       5
     O    1132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6667
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2353
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 888
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 2353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2353
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 276}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "D"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 888
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 113}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 185
          Unusual residues: {'LMN': 2, 'PEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.71, per 1000 atoms: 0.26
  Number of scatterers: 6667
  At special positions: 0
  Unit cell: (88.2648, 78.9291, 129.002, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P       1     15.00
     O    1132      8.00
     N    1083      7.00
     C    4423      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 330.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1536

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      67.2% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 10
      removed outlier: 4.143A  pdb=" N   LEU A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 26
      removed outlier: 3.954A  pdb=" N   TRP A  18 " --> pdb=" O   HIS A  14 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE A  19 " --> pdb=" O   PRO A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 54
      removed outlier: 3.943A  pdb=" N   PHE A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 88
      removed outlier: 3.871A  pdb=" N   GLU A  83 " --> pdb=" O   PRO A  79 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 107
      removed outlier: 3.772A  pdb=" N   LEU A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 129
      removed outlier: 3.646A  pdb=" N   PHE A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 147
      removed outlier: 4.865A  pdb=" N   LEU A 144 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 178
    Processing helix  chain 'A' and resid 181 through 201
      removed outlier: 4.007A  pdb=" N   TRP A 185 " --> pdb=" O   GLN A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 215
    Processing helix  chain 'A' and resid 234 through 239
    Processing helix  chain 'A' and resid 263 through 273
      removed outlier: 3.801A  pdb=" N   VAL A 267 " --> pdb=" O   ASP A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 286
    Processing helix  chain 'B' and resid 33 through 47
    Processing helix  chain 'B' and resid 48 through 59
      removed outlier: 3.682A  pdb=" N   ARG B  52 " --> pdb=" O   ASP B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.670A  pdb=" N   ALA B  64 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 94
    Processing helix  chain 'B' and resid 102 through 126
    Processing helix  chain 'C' and resid 2 through 9
      removed outlier: 4.393A  pdb=" N   ASP C   6 " --> pdb=" O   ASN C   2 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   LEU C   7 " --> pdb=" O   LYS C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 27
    Processing helix  chain 'C' and resid 30 through 54
      removed outlier: 3.729A  pdb=" N   LEU C  34 " --> pdb=" O   MET C  30 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   CYS C  35 " --> pdb=" O   LYS C  31 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LEU C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA C  51 " --> pdb=" O   HIS C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 88
      removed outlier: 3.631A  pdb=" N   VAL C  86 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 92
      removed outlier: 3.945A  pdb=" N   LEU C  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 89 through 92'
    Processing helix  chain 'C' and resid 93 through 105
      removed outlier: 3.511A  pdb=" N   MET C 103 " --> pdb=" O   PHE C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 129
      removed outlier: 4.027A  pdb=" N   PHE C 115 " --> pdb=" O   HIS C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 150
      removed outlier: 4.213A  pdb=" N   GLN C 149 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 177
      removed outlier: 3.692A  pdb=" N   LEU C 160 " --> pdb=" O   HIS C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 181 through 201
      removed outlier: 3.511A  pdb=" N   TRP C 185 " --> pdb=" O   GLN C 181 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU C 187 " --> pdb=" O   SER C 183 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN C 201 " --> pdb=" O   GLU C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 203 through 215
      removed outlier: 3.660A  pdb=" N   VAL C 207 " --> pdb=" O   HIS C 203 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR C 215 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 241
      removed outlier: 4.062A  pdb=" N   GLU C 241 " --> pdb=" O   HIS C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 273
    Processing helix  chain 'C' and resid 280 through 286
      removed outlier: 3.595A  pdb=" N   LEU C 284 " --> pdb=" O   SER C 280 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 35 through 48
      removed outlier: 3.919A  pdb=" N   LYS D  39 " --> pdb=" O   SER D  35 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASP D  48 " --> pdb=" O   MET D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 59
      removed outlier: 3.924A  pdb=" N   ASN D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 70
      removed outlier: 3.666A  pdb=" N   ALA D  64 " --> pdb=" O   LEU D  60 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS D  69 " --> pdb=" O   HIS D  65 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 94
      removed outlier: 3.656A  pdb=" N   LEU D  80 " --> pdb=" O   ASP D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 126
      removed outlier: 3.585A  pdb=" N   TYR D 106 " --> pdb=" O   LYS D 102 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13
      removed outlier: 7.252A  pdb=" N   HIS A  12 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   TYR B  22 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230
      removed outlier: 5.707A  pdb=" N   LEU A 227 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   GLU A 253 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   VAL A 229 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE A 250 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   GLN A 261 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   ILE A 252 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 64
      removed outlier: 6.818A  pdb=" N   GLU C  71 " --> pdb=" O   LYS C  59 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   VAL C  61 " --> pdb=" O   THR C  69 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   THR C  69 " --> pdb=" O   VAL C  61 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   LEU C  63 " --> pdb=" O   GLY C  67 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   GLY C  67 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TYR D  22 " --> pdb=" O   GLY C  68 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL C  70 " --> pdb=" O   TYR D  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 227 through 230

    372 hydrogen bonds defined for protein.
    1101 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: 0.95

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1004
        1.31 -     1.44: 1844
        1.44 -     1.56: 3922
        1.56 -     1.69: 26
        1.69 -     1.82: 44
  Bond restraints: 6840
  Sorted by residual:
  bond pdb=" C1  LMN A 401 "
       pdb=" O5  LMN A 401 "
    ideal  model  delta    sigma   weight residual
    1.403  1.538 -0.135 2.00e-02 2.50e+03 4.54e+01
  bond pdb=" C1  LMN A 403 "
       pdb=" O5  LMN A 403 "
    ideal  model  delta    sigma   weight residual
    1.403  1.535 -0.132 2.00e-02 2.50e+03 4.37e+01
  bond pdb=" CBS LMN A 401 "
       pdb=" CCM LMN A 401 "
    ideal  model  delta    sigma   weight residual
    1.529  1.631 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C4  LMN A 403 "
       pdb=" O4  LMN A 403 "
    ideal  model  delta    sigma   weight residual
    1.409  1.510 -0.101 2.00e-02 2.50e+03 2.55e+01
  bond pdb=" CBS LMN A 403 "
       pdb=" CCM LMN A 403 "
    ideal  model  delta    sigma   weight residual
    1.529  1.629 -0.100 2.00e-02 2.50e+03 2.52e+01
  ... (remaining 6835 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.10: 9096
        3.10 -     6.21: 146
        6.21 -     9.31: 13
        9.31 -    12.42: 3
       12.42 -    15.52: 1
  Bond angle restraints: 9259
  Sorted by residual:
  angle pdb=" O3P PEF A 402 "
        pdb=" P   PEF A 402 "
        pdb=" O4P PEF A 402 "
      ideal   model   delta    sigma   weight residual
      93.96  109.48  -15.52 3.00e+00 1.11e-01 2.68e+01
  angle pdb=" N   VAL C 107 "
        pdb=" CA  VAL C 107 "
        pdb=" C   VAL C 107 "
      ideal   model   delta    sigma   weight residual
     112.98  108.06    4.92 1.25e+00 6.40e-01 1.55e+01
  angle pdb=" C4  LMN A 401 "
        pdb=" O4  LMN A 401 "
        pdb=" CCR LMN A 401 "
      ideal   model   delta    sigma   weight residual
     120.22  109.38   10.84 3.00e+00 1.11e-01 1.31e+01
  angle pdb=" O1P PEF A 402 "
        pdb=" P   PEF A 402 "
        pdb=" O2P PEF A 402 "
      ideal   model   delta    sigma   weight residual
     119.53  109.50   10.03 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" CCQ LMN A 401 "
        pdb=" OCB LMN A 401 "
        pdb=" CCS LMN A 401 "
      ideal   model   delta    sigma   weight residual
     119.65  109.82    9.83 3.00e+00 1.11e-01 1.07e+01
  ... (remaining 9254 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.63: 3781
       24.63 -    49.25: 307
       49.25 -    73.88: 60
       73.88 -    98.50: 22
       98.50 -   123.13: 35
  Dihedral angle restraints: 4205
    sinusoidal: 1841
      harmonic: 2364
  Sorted by residual:
  dihedral pdb=" CCD LMN A 403 "
           pdb=" CCS LMN A 403 "
           pdb=" OBZ LMN A 403 "
           pdb=" OCB LMN A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.96 -175.91 -123.13     1      3.00e+01 1.11e-03 1.65e+01
  dihedral pdb=" O2  LMN A 403 "
           pdb=" C2  LMN A 403 "
           pdb=" C3  LMN A 403 "
           pdb=" O3  LMN A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.11  172.74  122.37     1      3.00e+01 1.11e-03 1.64e+01
  dihedral pdb=" CCD LMN A 403 "
           pdb=" CCS LMN A 403 "
           pdb=" OBZ LMN A 403 "
           pdb=" CCW LMN A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.55   61.55 -121.10     1      3.00e+01 1.11e-03 1.62e+01
  ... (remaining 4202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 806
       0.041 -    0.082: 201
       0.082 -    0.123: 53
       0.123 -    0.164: 6
       0.164 -    0.205: 5
  Chirality restraints: 1071
  Sorted by residual:
  chirality pdb=" C1  LMN A 403 "
            pdb=" C2  LMN A 403 "
            pdb=" O1  LMN A 403 "
            pdb=" O5  LMN A 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.49    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" C1  LMN A 401 "
            pdb=" C2  LMN A 401 "
            pdb=" O1  LMN A 401 "
            pdb=" O5  LMN A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.48    0.20 2.00e-01 2.50e+01 9.54e-01
  chirality pdb=" CCV LMN A 401 "
            pdb=" CCR LMN A 401 "
            pdb=" CCT LMN A 401 "
            pdb=" OAU LMN A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.28    2.46   -0.18 2.00e-01 2.50e+01 8.00e-01
  ... (remaining 1068 not shown)

  Planarity restraints: 1110
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 225 "   -0.076 5.00e-02 4.00e+02   1.13e-01 2.04e+01
        pdb=" N   PRO C 226 "    0.195 5.00e-02 4.00e+02
        pdb=" CA  PRO C 226 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO C 226 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  90 "   -0.041 5.00e-02 4.00e+02   6.21e-02 6.16e+00
        pdb=" N   PRO A  91 "    0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A  91 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  91 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 178 "    0.027 5.00e-02 4.00e+02   4.12e-02 2.72e+00
        pdb=" N   PRO C 179 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C 179 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 179 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1107 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1182
        2.77 -     3.30: 6438
        3.30 -     3.83: 10474
        3.83 -     4.37: 11155
        4.37 -     4.90: 19505
  Nonbonded interactions: 48754
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 280 "
            pdb=" OE1 GLU A 283 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" ND2 ASN A 129 "
            pdb=" OG  SER B  21 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" O   PRO D  29 "
            pdb=" NH1 ARG D  61 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   ARG C  78 "
            pdb=" NH2 ARG C 244 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" N   SER B  33 "
            pdb=" OE2 GLU B  36 "
     model   vdw
     2.327 3.120
  ... (remaining 48749 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 1 through 288)
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             2.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.970
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
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   0.135   6840  Z= 0.393
  Angle     :  0.819  15.522   9259  Z= 0.358
  Chirality :  0.041   0.205   1071
  Planarity :  0.005   0.113   1110
  Dihedral  : 22.667 123.128   2669
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.00 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.29 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.48 (0.31), residues: 800
  helix:  1.45 (0.24), residues: 536
  sheet:  0.08 (1.12), residues: 28
  loop : -2.39 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  61 
 TYR   0.015   0.001   TYR C 271 
 PHE   0.009   0.001   PHE C 272 
 TRP   0.013   0.001   TRP A   4 
 HIS   0.007   0.001   HIS C 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00792 ( 6840)
  covalent geometry    : angle       0.81931 ( 9259)
  hydrogen bonds       : bond        0.12450 (  372)
  hydrogen bonds       : angle       4.19369 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8565 (t80) cc_final: 0.8120 (t80)
REVERT: B   62 LEU cc_start: 0.9024 (mt) cc_final: 0.8777 (tt)
REVERT: B   79 ASP cc_start: 0.7558 (m-30) cc_final: 0.7189 (m-30)
REVERT: B   96 SER cc_start: 0.9055 (t) cc_final: 0.8796 (p)
REVERT: D   43 LEU cc_start: 0.8833 (tp) cc_final: 0.8456 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0879
  time to fit residues: 21.1310
Evaluate side-chains
  140 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.0670
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9524

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
** C  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 129 ASN
D  53 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.149858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117942 restraints weight = 11634.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.121103 restraints weight = 6614.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.123153 restraints weight = 4649.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.124012 restraints weight = 3750.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.125118 restraints weight = 3355.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6840  Z= 0.149
  Angle     :  0.704  11.976   9259  Z= 0.322
  Chirality :  0.045   0.304   1071
  Planarity :  0.005   0.076   1110
  Dihedral  : 17.343  89.343   1153
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.38 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.31 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.51 (0.31), residues: 800
  helix:  1.40 (0.23), residues: 532
  sheet:  0.09 (1.10), residues: 28
  loop : -2.12 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  52 
 TYR   0.020   0.001   TYR A 271 
 PHE   0.014   0.001   PHE A 146 
 TRP   0.011   0.001   TRP A  96 
 HIS   0.004   0.001   HIS C 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6840)
  covalent geometry    : angle       0.70422 ( 9259)
  hydrogen bonds       : bond        0.04164 (  372)
  hydrogen bonds       : angle       3.62611 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 149
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8638 (t80) cc_final: 0.8184 (t80)
REVERT: B   62 LEU cc_start: 0.9031 (mt) cc_final: 0.8749 (tt)
REVERT: B   79 ASP cc_start: 0.7483 (m-30) cc_final: 0.7252 (m-30)
REVERT: B   96 SER cc_start: 0.9000 (t) cc_final: 0.8721 (p)
  outliers start: 13
  outliers final: 7
  residues processed: 155
  average time/residue: 0.0843
  time to fit residues: 17.5833
Evaluate side-chains
  148 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 141
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain D residue   20 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 70 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 129 ASN
** C  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 129 ASN
C 237 HIS
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.144545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.112286 restraints weight = 11546.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.115332 restraints weight = 6706.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.117292 restraints weight = 4738.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.118566 restraints weight = 3839.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119025 restraints weight = 3363.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6840  Z= 0.200
  Angle     :  0.729  10.626   9259  Z= 0.341
  Chirality :  0.046   0.392   1071
  Planarity :  0.005   0.066   1110
  Dihedral  : 13.249  84.651   1153
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.75 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.11 %
    Favored  : 79.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.26 (0.31), residues: 800
  helix:  1.17 (0.23), residues: 534
  sheet: -0.08 (0.88), residues: 38
  loop : -2.21 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 208 
 TYR   0.011   0.001   TYR C 236 
 PHE   0.022   0.001   PHE C 118 
 TRP   0.014   0.002   TRP C  96 
 HIS   0.006   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 6840)
  covalent geometry    : angle       0.72926 ( 9259)
  hydrogen bonds       : bond        0.04749 (  372)
  hydrogen bonds       : angle       3.83977 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8633 (t80) cc_final: 0.8163 (t80)
REVERT: A  201 GLN cc_start: 0.7993 (mt0) cc_final: 0.7777 (mt0)
REVERT: A  281 MET cc_start: 0.7134 (ptt) cc_final: 0.6795 (ptt)
REVERT: B   79 ASP cc_start: 0.7455 (m-30) cc_final: 0.7240 (m-30)
REVERT: B   96 SER cc_start: 0.8989 (t) cc_final: 0.8738 (p)
REVERT: C  282 GLU cc_start: 0.8125 (mp0) cc_final: 0.7792 (mp0)
REVERT: D   43 LEU cc_start: 0.8890 (tp) cc_final: 0.8624 (tp)
  outliers start: 21
  outliers final: 17
  residues processed: 157
  average time/residue: 0.0837
  time to fit residues: 17.7648
Evaluate side-chains
  161 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  108 SER
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  248 HIS
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   56 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 47 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 HIS
** C  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 237 HIS
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.143908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.111680 restraints weight = 11710.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.114644 restraints weight = 6803.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.116529 restraints weight = 4847.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.117763 restraints weight = 3948.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.118409 restraints weight = 3471.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6840  Z= 0.136
  Angle     :  0.640   9.389   9259  Z= 0.303
  Chirality :  0.042   0.323   1071
  Planarity :  0.005   0.060   1110
  Dihedral  : 10.810  86.948   1153
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.50 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.91 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.41 (0.31), residues: 800
  helix:  1.28 (0.23), residues: 532
  sheet: -0.07 (0.88), residues: 38
  loop : -2.10 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  61 
 TYR   0.026   0.001   TYR A 199 
 PHE   0.013   0.001   PHE A  62 
 TRP   0.013   0.001   TRP A  96 
 HIS   0.008   0.001   HIS C 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6840)
  covalent geometry    : angle       0.63975 ( 9259)
  hydrogen bonds       : bond        0.04054 (  372)
  hydrogen bonds       : angle       3.57921 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8643 (t80) cc_final: 0.8186 (t80)
REVERT: A  281 MET cc_start: 0.7132 (ptt) cc_final: 0.6523 (ptt)
REVERT: B   62 LEU cc_start: 0.9126 (mp) cc_final: 0.8699 (tt)
REVERT: B   79 ASP cc_start: 0.7533 (m-30) cc_final: 0.7324 (m-30)
REVERT: B   96 SER cc_start: 0.8998 (t) cc_final: 0.8732 (p)
REVERT: C  282 GLU cc_start: 0.8175 (mp0) cc_final: 0.7802 (mp0)
REVERT: D   43 LEU cc_start: 0.8887 (tp) cc_final: 0.8500 (tp)
  outliers start: 22
  outliers final: 15
  residues processed: 166
  average time/residue: 0.0865
  time to fit residues: 19.1054
Evaluate side-chains
  160 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  248 HIS
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain D residue   20 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 129 ASN
C 237 HIS
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  58 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.143721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111683 restraints weight = 11874.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.114651 restraints weight = 6813.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.116553 restraints weight = 4833.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117813 restraints weight = 3902.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.118460 restraints weight = 3434.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6840  Z= 0.137
  Angle     :  0.638  12.511   9259  Z= 0.305
  Chirality :  0.041   0.268   1071
  Planarity :  0.005   0.057   1110
  Dihedral  : 10.246  87.089   1153
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.75 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 21.24 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.45 (0.31), residues: 800
  helix:  1.31 (0.23), residues: 532
  sheet:  0.01 (0.88), residues: 38
  loop : -2.09 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  61 
 TYR   0.007   0.001   TYR D  22 
 PHE   0.013   0.001   PHE A  62 
 TRP   0.012   0.001   TRP C  96 
 HIS   0.005   0.001   HIS B 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6840)
  covalent geometry    : angle       0.63809 ( 9259)
  hydrogen bonds       : bond        0.03982 (  372)
  hydrogen bonds       : angle       3.55174 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8651 (t80) cc_final: 0.8134 (t80)
REVERT: A  281 MET cc_start: 0.7100 (ptt) cc_final: 0.6360 (ptt)
REVERT: B   62 LEU cc_start: 0.9122 (mp) cc_final: 0.8714 (tt)
REVERT: B   79 ASP cc_start: 0.7471 (m-30) cc_final: 0.7264 (m-30)
REVERT: B   96 SER cc_start: 0.8993 (t) cc_final: 0.8738 (p)
REVERT: C  282 GLU cc_start: 0.8164 (mp0) cc_final: 0.7717 (mp0)
REVERT: D   43 LEU cc_start: 0.8863 (tp) cc_final: 0.8498 (tp)
  outliers start: 24
  outliers final: 18
  residues processed: 165
  average time/residue: 0.0856
  time to fit residues: 18.8461
Evaluate side-chains
  161 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  110 ILE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  248 HIS
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain D residue   20 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0050
   chunk 39 optimal weight:    8.9990
   overall best weight:    0.9598

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 HIS
C 129 ASN
C 237 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.143988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.112105 restraints weight = 11814.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.115095 restraints weight = 6773.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117037 restraints weight = 4786.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.118275 restraints weight = 3869.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.118906 restraints weight = 3392.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6840  Z= 0.132
  Angle     :  0.646  15.442   9259  Z= 0.306
  Chirality :  0.040   0.231   1071
  Planarity :  0.005   0.054   1110
  Dihedral  :  9.927  87.150   1153
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.50 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.71 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.40 (0.31), residues: 800
  helix:  1.29 (0.23), residues: 544
  sheet:  0.00 (0.85), residues: 38
  loop : -2.36 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  61 
 TYR   0.007   0.001   TYR C 204 
 PHE   0.013   0.001   PHE A  62 
 TRP   0.013   0.001   TRP A   4 
 HIS   0.004   0.001   HIS C 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6840)
  covalent geometry    : angle       0.64645 ( 9259)
  hydrogen bonds       : bond        0.03879 (  372)
  hydrogen bonds       : angle       3.49714 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8635 (t80) cc_final: 0.8146 (t80)
REVERT: A  281 MET cc_start: 0.7091 (ptt) cc_final: 0.6323 (ptt)
REVERT: B   37 GLU cc_start: 0.7964 (pp20) cc_final: 0.7719 (tt0)
REVERT: B   62 LEU cc_start: 0.9110 (mp) cc_final: 0.8693 (tt)
REVERT: B   96 SER cc_start: 0.9004 (t) cc_final: 0.8749 (p)
REVERT: C  282 GLU cc_start: 0.8094 (mp0) cc_final: 0.7631 (mp0)
REVERT: D   43 LEU cc_start: 0.8788 (tp) cc_final: 0.8470 (tp)
  outliers start: 23
  outliers final: 18
  residues processed: 164
  average time/residue: 0.0875
  time to fit residues: 19.1465
Evaluate side-chains
  164 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  110 ILE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  248 HIS
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain D residue   20 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 237 HIS
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.140203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.108356 restraints weight = 11664.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.111123 restraints weight = 6929.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.112916 restraints weight = 5021.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.113980 restraints weight = 4123.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.114531 restraints weight = 3659.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6840  Z= 0.216
  Angle     :  0.738  13.676   9259  Z= 0.353
  Chirality :  0.043   0.231   1071
  Planarity :  0.005   0.058   1110
  Dihedral  : 10.157  84.329   1153
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.25 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 23.75 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.24 (0.31), residues: 800
  helix:  1.13 (0.23), residues: 532
  sheet: -0.10 (0.84), residues: 38
  loop : -2.13 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  61 
 TYR   0.025   0.002   TYR C 199 
 PHE   0.022   0.002   PHE C 118 
 TRP   0.015   0.002   TRP A   4 
 HIS   0.009   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 6840)
  covalent geometry    : angle       0.73817 ( 9259)
  hydrogen bonds       : bond        0.04756 (  372)
  hydrogen bonds       : angle       3.86083 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   84 PHE cc_start: 0.8689 (t80) cc_final: 0.8274 (t80)
REVERT: A  281 MET cc_start: 0.7236 (ptt) cc_final: 0.6464 (ptt)
REVERT: B   96 SER cc_start: 0.9022 (t) cc_final: 0.8771 (p)
REVERT: C  282 GLU cc_start: 0.8142 (mp0) cc_final: 0.7646 (mp0)
  outliers start: 25
  outliers final: 20
  residues processed: 162
  average time/residue: 0.0858
  time to fit residues: 18.6816
Evaluate side-chains
  162 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 SER
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  110 ILE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  248 HIS
Chi-restraints excluded: chain C residue  279 SER
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   56 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0170
   chunk 32 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 237 HIS
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.146324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.114729 restraints weight = 11520.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117789 restraints weight = 6585.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.119758 restraints weight = 4634.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120801 restraints weight = 3728.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121672 restraints weight = 3293.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6840  Z= 0.117
  Angle     :  0.641   9.386   9259  Z= 0.309
  Chirality :  0.038   0.184   1071
  Planarity :  0.004   0.051   1110
  Dihedral  :  9.577  87.499   1153
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.88 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 24.48 %
    Favored  : 72.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.49 (0.31), residues: 800
  helix:  1.33 (0.23), residues: 544
  sheet:  0.03 (0.84), residues: 38
  loop : -2.26 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  61 
 TYR   0.022   0.001   TYR C 199 
 PHE   0.016   0.001   PHE A  66 
 TRP   0.014   0.001   TRP A  96 
 HIS   0.009   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6840)
  covalent geometry    : angle       0.64109 ( 9259)
  hydrogen bonds       : bond        0.03499 (  372)
  hydrogen bonds       : angle       3.42870 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8636 (t80) cc_final: 0.8243 (t80)
REVERT: A  281 MET cc_start: 0.7112 (ptt) cc_final: 0.6439 (ptt)
REVERT: B   37 GLU cc_start: 0.8006 (pp20) cc_final: 0.7585 (tt0)
REVERT: B   96 SER cc_start: 0.8980 (t) cc_final: 0.8726 (p)
REVERT: C  282 GLU cc_start: 0.8025 (mp0) cc_final: 0.7425 (mp0)
REVERT: D   43 LEU cc_start: 0.8715 (tp) cc_final: 0.8432 (tp)
  outliers start: 18
  outliers final: 14
  residues processed: 167
  average time/residue: 0.0847
  time to fit residues: 18.9011
Evaluate side-chains
  162 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 148
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  272 PHE
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  110 ILE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  248 HIS
Chi-restraints excluded: chain D residue   20 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  75 HIS
A 111 HIS
A 201 GLN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.110558 restraints weight = 11842.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.113348 restraints weight = 6946.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.115180 restraints weight = 4969.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.116338 restraints weight = 4053.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.116681 restraints weight = 3577.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6840  Z= 0.186
  Angle     :  0.724  11.956   9259  Z= 0.350
  Chirality :  0.043   0.224   1071
  Planarity :  0.005   0.053   1110
  Dihedral  :  9.708  84.783   1153
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.75 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 26.11 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.37 (0.31), residues: 800
  helix:  1.24 (0.23), residues: 532
  sheet:  0.06 (0.85), residues: 38
  loop : -2.11 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  61 
 TYR   0.023   0.002   TYR C 199 
 PHE   0.017   0.001   PHE C 118 
 TRP   0.015   0.002   TRP A   4 
 HIS   0.009   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6840)
  covalent geometry    : angle       0.72428 ( 9259)
  hydrogen bonds       : bond        0.04410 (  372)
  hydrogen bonds       : angle       3.73895 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8655 (t80) cc_final: 0.8270 (t80)
REVERT: A  108 SER cc_start: 0.7901 (p) cc_final: 0.7673 (t)
REVERT: A  281 MET cc_start: 0.7151 (ptt) cc_final: 0.6442 (ptt)
REVERT: B   37 GLU cc_start: 0.7990 (pp20) cc_final: 0.7594 (tt0)
REVERT: B   92 ILE cc_start: 0.8978 (tp) cc_final: 0.8770 (tt)
REVERT: B   96 SER cc_start: 0.8964 (t) cc_final: 0.8724 (p)
REVERT: C  282 GLU cc_start: 0.8041 (mp0) cc_final: 0.7468 (mp0)
  outliers start: 19
  outliers final: 15
  residues processed: 163
  average time/residue: 0.0879
  time to fit residues: 19.1149
Evaluate side-chains
  165 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  110 ILE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  248 HIS
Chi-restraints excluded: chain D residue   20 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0970
   chunk 64 optimal weight:    0.0370
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 HIS
C 129 ASN
C 237 HIS
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.145957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.114351 restraints weight = 11617.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.117392 restraints weight = 6622.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.119325 restraints weight = 4661.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120580 restraints weight = 3760.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.121226 restraints weight = 3285.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6840  Z= 0.124
  Angle     :  0.669  12.763   9259  Z= 0.322
  Chirality :  0.039   0.226   1071
  Planarity :  0.005   0.050   1110
  Dihedral  :  9.284  87.431   1153
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.25 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 25.81 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.45 (0.31), residues: 800
  helix:  1.32 (0.23), residues: 544
  sheet:  0.41 (0.83), residues: 36
  loop : -2.40 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  61 
 TYR   0.021   0.001   TYR C 199 
 PHE   0.012   0.001   PHE A  62 
 TRP   0.015   0.001   TRP A   4 
 HIS   0.007   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6840)
  covalent geometry    : angle       0.66913 ( 9259)
  hydrogen bonds       : bond        0.03659 (  372)
  hydrogen bonds       : angle       3.48097 ( 1101)

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 PHE cc_start: 0.8614 (t80) cc_final: 0.8184 (t80)
REVERT: A  108 SER cc_start: 0.7801 (p) cc_final: 0.7538 (t)
REVERT: A  281 MET cc_start: 0.7098 (ptt) cc_final: 0.6452 (ptt)
REVERT: B   37 GLU cc_start: 0.7927 (pp20) cc_final: 0.7647 (tt0)
REVERT: B   92 ILE cc_start: 0.8978 (tp) cc_final: 0.8773 (tt)
REVERT: B   96 SER cc_start: 0.8986 (t) cc_final: 0.8752 (p)
REVERT: C  282 GLU cc_start: 0.8028 (mp0) cc_final: 0.7342 (mp0)
REVERT: D   50 HIS cc_start: 0.7711 (t-90) cc_final: 0.7296 (t70)
  outliers start: 18
  outliers final: 14
  residues processed: 162
  average time/residue: 0.0826
  time to fit residues: 17.8549
Evaluate side-chains
  161 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue   63 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue  110 ILE
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  172 CYS
Chi-restraints excluded: chain C residue  178 ILE
Chi-restraints excluded: chain C residue  248 HIS
Chi-restraints excluded: chain D residue   20 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 60 optimal weight:    0.3980
   chunk 59 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0870
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 111 HIS
B  65 HIS
C 129 ASN
** D  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.147339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.115911 restraints weight = 11506.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118933 restraints weight = 6566.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.120913 restraints weight = 4616.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.122141 restraints weight = 3717.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.122765 restraints weight = 3251.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6840  Z= 0.120
  Angle     :  0.660  12.649   9259  Z= 0.318
  Chirality :  0.039   0.227   1071
  Planarity :  0.005   0.050   1110
  Dihedral  :  9.144  88.239   1153
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.38 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 27.43 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.62 (0.31), residues: 800
  helix:  1.44 (0.23), residues: 532
  sheet:  0.50 (0.83), residues: 36
  loop : -2.10 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  61 
 TYR   0.020   0.001   TYR C 199 
 PHE   0.012   0.001   PHE A  66 
 TRP   0.014   0.001   TRP A   4 
 HIS   0.005   0.001   HIS C 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6840)
  covalent geometry    : angle       0.66046 ( 9259)
  hydrogen bonds       : bond        0.03504 (  372)
  hydrogen bonds       : angle       3.42109 ( 1101)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1233.07 seconds
wall clock time: 22 minutes 5.47 seconds (1325.47 seconds total)