Starting phenix.real_space_refine
on Thu Mar  6 03:10:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zc1_39919/03_2025/8zc1_39919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zc1_39919/03_2025/8zc1_39919.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zc1_39919/03_2025/8zc1_39919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zc1_39919/03_2025/8zc1_39919.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zc1_39919/03_2025/8zc1_39919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zc1_39919/03_2025/8zc1_39919.cif"
  }
  resolution = 4.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2907      2.51       5
     N     767      2.21       5
     O     878      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4570
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 163, 1318
          Classifications: {'peptide': 163}
          Link IDs: {'PTRANS': 9, 'TRANS': 153}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1591
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1661
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 3.74, per 1000 atoms: 0.82
  Number of scatterers: 4570
  At special positions: 0
  Unit cell: (84.48, 76.56, 120.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     878      8.00
     N     767      7.00
     C    2907      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 145 " - pdb=" SG  CYS C 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 103 " - pdb=" SG  CYS E 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 154 " - pdb=" SG  CYS E 210 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 561.6 milliseconds
  

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1104

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 15 sheets defined
      6.9% alpha, 39.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 4.145A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.518A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'C' and resid 133 through 137
      removed outlier: 3.669A  pdb=" N   GLN C 137 " --> pdb=" O   GLU C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 199
      removed outlier: 3.635A  pdb=" N   TRP C 196 " --> pdb=" O   THR C 192 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   LYS C 197 " --> pdb=" O   PRO C 193 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER C 198 " --> pdb=" O   GLU C 194 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   HIS C 199 " --> pdb=" O   GLN C 195 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 192 through 199'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.894A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 112
      removed outlier: 4.025A  pdb=" N   TRP E 111 " --> pdb=" O   CYS E 108 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356
      removed outlier: 3.810A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP B 398 " --> pdb=" O   VAL B 512 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ARG B 509 " --> pdb=" O   TRP B 436 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   VAL B 433 " --> pdb=" O   LYS B 378 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LYS B 378 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 12
      removed outlier: 3.864A  pdb=" N   ASP C  86 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 12
    Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 23
    Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 129
      removed outlier: 3.684A  pdb=" N   THR C 127 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU C 146 " --> pdb=" O   THR C 127 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   PHE C 129 " --> pdb=" O   VAL C 144 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   VAL C 144 " --> pdb=" O   PHE C 129 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA C 185 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ASP C 149 " --> pdb=" O   TYR C 183 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   TYR C 183 " --> pdb=" O   ASP C 149 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR C 188 " --> pdb=" O   GLU C 171 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU C 171 " --> pdb=" O   TYR C 188 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 141 through 142
      removed outlier: 3.804A  pdb=" N   ALA C 184 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 164 through 166
      removed outlier: 4.451A  pdb=" N   TRP C 159 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR C 156 " --> pdb=" O   THR C 207 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 166
      removed outlier: 4.451A  pdb=" N   TRP C 159 " --> pdb=" O   VAL C 166 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR C 156 " --> pdb=" O   THR C 207 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR C 202 " --> pdb=" O   VAL C 217 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS C 215 " --> pdb=" O   CYS C 204 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6
      removed outlier: 3.615A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL E   5 " --> pdb=" O   LYS E  23 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   VAL E  20 " --> pdb=" O   MET E  81 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASP E  73 " --> pdb=" O   THR E  78 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60
      removed outlier: 4.109A  pdb=" N   ASN E  59 " --> pdb=" O   TRP E  50 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TRP E  50 " --> pdb=" O   ASN E  59 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   TRP E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ILE E  34 " --> pdb=" O   TRP E  50 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   CYS E  96 " --> pdb=" O   TRP E 117 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   TRP E 117 " --> pdb=" O   CYS E  96 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ARG E  98 " --> pdb=" O   ASP E 115 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60
      removed outlier: 4.109A  pdb=" N   ASN E  59 " --> pdb=" O   TRP E  50 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TRP E  50 " --> pdb=" O   ASN E  59 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP E  36 " --> pdb=" O   MET E  48 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   TRP E  50 " --> pdb=" O   ILE E  34 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ILE E  34 " --> pdb=" O   TRP E  50 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 137
      removed outlier: 3.631A  pdb=" N   SER E 134 " --> pdb=" O   LYS E 157 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER E 194 " --> pdb=" O   CYS E 154 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL E 195 " --> pdb=" O   HIS E 178 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 137
      removed outlier: 3.631A  pdb=" N   SER E 134 " --> pdb=" O   LYS E 157 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER E 194 " --> pdb=" O   CYS E 154 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 166 through 168
      removed outlier: 4.071A  pdb=" N   CYS E 210 " --> pdb=" O   LYS E 223 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LYS E 223 " --> pdb=" O   CYS E 210 " (cutoff:3.500A)

    139 hydrogen bonds defined for protein.
    330 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1449
        1.35 -     1.47: 1259
        1.47 -     1.59: 1964
        1.59 -     1.71: 0
        1.71 -     1.84: 22
  Bond restraints: 4694
  Sorted by residual:
  bond pdb=" C   LYS E 215 "
       pdb=" N   PRO E 216 "
    ideal  model  delta    sigma   weight residual
    1.335  1.382 -0.046 1.30e-02 5.92e+03 1.28e+01
  bond pdb=" C   VAL B 382 "
       pdb=" N   SER B 383 "
    ideal  model  delta    sigma   weight residual
    1.327  1.288  0.039 1.71e-02 3.42e+03 5.13e+00
  bond pdb=" N   ASP E 158 "
       pdb=" CA  ASP E 158 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.020 1.29e-02 6.01e+03 2.46e+00
  bond pdb=" CA  THR E  77 "
       pdb=" CB  THR E  77 "
    ideal  model  delta    sigma   weight residual
    1.527  1.554 -0.027 1.70e-02 3.46e+03 2.45e+00
  bond pdb=" C   PHE E 136 "
       pdb=" N   PRO E 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.345 -0.016 1.25e-02 6.40e+03 1.60e+00
  ... (remaining 4689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 6141
        1.72 -     3.44: 218
        3.44 -     5.17: 24
        5.17 -     6.89: 11
        6.89 -     8.61: 4
  Bond angle restraints: 6398
  Sorted by residual:
  angle pdb=" C   ILE E  76 "
        pdb=" N   THR E  77 "
        pdb=" CA  THR E  77 "
      ideal   model   delta    sigma   weight residual
     122.46  128.09   -5.63 1.41e+00 5.03e-01 1.60e+01
  angle pdb=" C   LYS C  51 "
        pdb=" N   ASN C  52 "
        pdb=" CA  ASN C  52 "
      ideal   model   delta    sigma   weight residual
     121.54  128.69   -7.15 1.91e+00 2.74e-01 1.40e+01
  angle pdb=" C   VAL E 125 "
        pdb=" N   SER E 126 "
        pdb=" CA  SER E 126 "
      ideal   model   delta    sigma   weight residual
     121.54  127.59   -6.05 1.91e+00 2.74e-01 1.00e+01
  angle pdb=" CA  THR E  77 "
        pdb=" CB  THR E  77 "
        pdb=" CG2 THR E  77 "
      ideal   model   delta    sigma   weight residual
     110.50  115.72   -5.22 1.70e+00 3.46e-01 9.42e+00
  angle pdb=" CG1 ILE E  76 "
        pdb=" CB  ILE E  76 "
        pdb=" CG2 ILE E  76 "
      ideal   model   delta    sigma   weight residual
     110.70  102.26    8.44 3.00e+00 1.11e-01 7.92e+00
  ... (remaining 6393 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 2502
       16.06 -    32.12: 205
       32.12 -    48.19: 47
       48.19 -    64.25: 10
       64.25 -    80.31: 9
  Dihedral angle restraints: 2773
    sinusoidal: 1047
      harmonic: 1726
  Sorted by residual:
  dihedral pdb=" CB  CYS E 154 "
           pdb=" SG  CYS E 154 "
           pdb=" SG  CYS E 210 "
           pdb=" CB  CYS E 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.07  -73.07     1      1.00e+01 1.00e-02 6.80e+01
  dihedral pdb=" CB  CYS B 379 "
           pdb=" SG  CYS B 379 "
           pdb=" SG  CYS B 432 "
           pdb=" CB  CYS B 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.44   39.56     1      1.00e+01 1.00e-02 2.20e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  96 "
           pdb=" CB  CYS E  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.42  -37.42     1      1.00e+01 1.00e-02 1.98e+01
  ... (remaining 2770 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 514
       0.053 -    0.105: 149
       0.105 -    0.158: 35
       0.158 -    0.210: 1
       0.210 -    0.263: 2
  Chirality restraints: 701
  Sorted by residual:
  chirality pdb=" CB  VAL E 125 "
            pdb=" CA  VAL E 125 "
            pdb=" CG1 VAL E 125 "
            pdb=" CG2 VAL E 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  ILE E  76 "
            pdb=" CA  ILE E  76 "
            pdb=" CG1 ILE E  76 "
            pdb=" CG2 ILE E  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.90   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  THR E  77 "
            pdb=" N   THR E  77 "
            pdb=" C   THR E  77 "
            pdb=" CB  THR E  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.61e-01
  ... (remaining 698 not shown)

  Planarity restraints: 821
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 372 "    0.041 5.00e-02 4.00e+02   6.26e-02 6.26e+00
        pdb=" N   PRO B 373 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO B 373 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 373 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.018 2.00e-02 2.50e+03   1.47e-02 4.33e+00
        pdb=" CG  TYR B 495 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 478 "   -0.032 5.00e-02 4.00e+02   4.88e-02 3.80e+00
        pdb=" N   PRO B 479 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 479 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 479 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 818 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1461
        2.83 -     3.35: 3742
        3.35 -     3.87: 7351
        3.87 -     4.38: 7584
        4.38 -     4.90: 13612
  Nonbonded interactions: 33750
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 438 "
            pdb=" O   PRO B 507 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OH  TYR C  35 "
            pdb=" O   ARG E 110 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OD2 ASP B 442 "
            pdb=" OH  TYR B 451 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" OD2 ASP E  57 "
            pdb=" OG  SER E 104 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG  SER C 203 "
            pdb=" OE1 GLU C 214 "
     model   vdw
     2.343 3.040
  ... (remaining 33745 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             3.150
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.110
  Find NCS groups from input model:        0.060
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
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      :  0.003   0.046   4694  Z= 0.228
  Angle     :  0.755   8.612   6398  Z= 0.400
  Chirality :  0.052   0.263    701
  Planarity :  0.005   0.063    821
  Dihedral  : 13.383  80.311   1648
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.32), residues: 583
  helix: -4.58 (0.35), residues: 18
  sheet: -0.01 (0.39), residues: 163
  loop : -1.50 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B 353 
 HIS   0.005   0.002   HIS C 199 
 PHE   0.010   0.001   PHE B 400 
 TYR   0.036   0.001   TYR B 495 
 ARG   0.003   0.000   ARG C  80 

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.476 
Fit side-chains
REVERT: B  494 SER cc_start: 0.8642 (p) cc_final: 0.8441 (p)
REVERT: E   31 ASP cc_start: 0.7724 (p0) cc_final: 0.7388 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1347
  time to fit residues: 12.9722
Evaluate side-chains
  45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 44 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0040
   chunk 23 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7994

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 414 GLN
C   6 GLN
C  39 GLN
E  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.118272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.099254 restraints weight = 16021.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.100865 restraints weight = 10874.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.102080 restraints weight = 8051.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4694  Z= 0.223
  Angle     :  0.583   6.862   6398  Z= 0.306
  Chirality :  0.045   0.141    701
  Planarity :  0.005   0.055    821
  Dihedral  :  4.321  15.104    643
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.33), residues: 583
  helix: -4.36 (0.49), residues: 18
  sheet: -0.03 (0.35), residues: 186
  loop : -1.40 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  36 
 HIS   0.003   0.001   HIS E 178 
 PHE   0.011   0.001   PHE B 374 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.002   0.000   ARG B 457 

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: B  494 SER cc_start: 0.8693 (p) cc_final: 0.8452 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1370
  time to fit residues: 11.2123
Evaluate side-chains
  43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.114002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.094329 restraints weight = 16461.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.096127 restraints weight = 10776.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.097456 restraints weight = 7825.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4694  Z= 0.329
  Angle     :  0.656  11.941   6398  Z= 0.340
  Chirality :  0.047   0.173    701
  Planarity :  0.005   0.057    821
  Dihedral  :  4.795  15.185    643
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.33), residues: 583
  helix: -3.99 (0.62), residues: 20
  sheet: -0.37 (0.34), residues: 189
  loop : -1.37 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 436 
 HIS   0.007   0.002   HIS C 199 
 PHE   0.014   0.002   PHE B 374 
 TYR   0.031   0.002   TYR B 495 
 ARG   0.004   0.001   ARG B 355 

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   53 ASP cc_start: 0.6839 (p0) cc_final: 0.6443 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1438
  time to fit residues: 10.8917
Evaluate side-chains
  42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0980
   chunk 3 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.116476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.096551 restraints weight = 16453.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.098360 restraints weight = 10749.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.099775 restraints weight = 7811.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4694  Z= 0.189
  Angle     :  0.575  12.011   6398  Z= 0.290
  Chirality :  0.045   0.152    701
  Planarity :  0.004   0.055    821
  Dihedral  :  4.340  16.300    643
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.33), residues: 583
  helix: -4.04 (0.57), residues: 20
  sheet: -0.38 (0.34), residues: 186
  loop : -1.27 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 436 
 HIS   0.002   0.001   HIS E 214 
 PHE   0.009   0.001   PHE E 136 
 TYR   0.019   0.001   TYR B 495 
 ARG   0.002   0.000   ARG B 509 

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
REVERT: B  494 SER cc_start: 0.8757 (p) cc_final: 0.8533 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1420
  time to fit residues: 12.1402
Evaluate side-chains
  44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN
C 195 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.116905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.096847 restraints weight = 16343.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.098704 restraints weight = 10587.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.100083 restraints weight = 7616.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4694  Z= 0.172
  Angle     :  0.567  10.376   6398  Z= 0.284
  Chirality :  0.046   0.175    701
  Planarity :  0.004   0.054    821
  Dihedral  :  4.158  14.585    643
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.33), residues: 583
  helix: -3.99 (0.59), residues: 20
  sheet: -0.28 (0.35), residues: 186
  loop : -1.20 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 436 
 HIS   0.002   0.001   HIS C 199 
 PHE   0.006   0.001   PHE B 374 
 TYR   0.017   0.001   TYR B 495 
 ARG   0.002   0.000   ARG B 346 

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
REVERT: B  494 SER cc_start: 0.8733 (p) cc_final: 0.8490 (p)
REVERT: E   70 MET cc_start: 0.8401 (ttm) cc_final: 0.8167 (ttm)
REVERT: E  112 MET cc_start: 0.8372 (mmt) cc_final: 0.8071 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1336
  time to fit residues: 11.9448
Evaluate side-chains
  44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 46 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.116312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.096628 restraints weight = 16135.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.098469 restraints weight = 10525.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.099758 restraints weight = 7566.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4694  Z= 0.200
  Angle     :  0.584  12.487   6398  Z= 0.292
  Chirality :  0.046   0.172    701
  Planarity :  0.004   0.054    821
  Dihedral  :  4.192  15.600    643
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.33), residues: 583
  helix: -3.99 (0.59), residues: 20
  sheet: -0.25 (0.35), residues: 185
  loop : -1.20 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 436 
 HIS   0.003   0.001   HIS E 214 
 PHE   0.008   0.001   PHE B 374 
 TYR   0.016   0.001   TYR B 495 
 ARG   0.005   0.001   ARG C  80 

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: E   70 MET cc_start: 0.8469 (ttm) cc_final: 0.8203 (ttm)
REVERT: E  112 MET cc_start: 0.8419 (mmt) cc_final: 0.8021 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1300
  time to fit residues: 11.1376
Evaluate side-chains
  44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3829 > 50:
  distance: 12 - 97:  37.616
  distance: 27 - 83:  34.984
  distance: 30 - 80:  32.073
  distance: 46 - 52:  34.350
  distance: 52 - 58:  40.730
  distance: 53 - 54:  40.145
  distance: 53 - 56:  39.043
  distance: 54 - 55:  57.621
  distance: 56 - 57:  68.667
  distance: 57 - 58:  40.651
  distance: 59 - 60:  41.220
  distance: 60 - 61:  66.528
  distance: 61 - 62:  53.189
  distance: 61 - 63:  66.252
  distance: 63 - 64:  39.389
  distance: 64 - 65:  64.204
  distance: 64 - 67:  45.233
  distance: 65 - 66:  40.989
  distance: 65 - 68:  62.978
  distance: 69 - 70:  41.114
  distance: 69 - 72:  55.457
  distance: 70 - 71:  57.080
  distance: 70 - 73:  60.040
  distance: 73 - 74:  44.475
  distance: 73 - 79:  60.150
  distance: 74 - 75:  69.552
  distance: 75 - 80:  56.949
  distance: 77 - 78:  40.326
  distance: 78 - 79:  68.743
  distance: 80 - 81:  42.368
  distance: 81 - 82:  13.590
  distance: 81 - 84:  15.215
  distance: 82 - 83:  56.608
  distance: 82 - 89:  34.301
  distance: 84 - 85:  32.954
  distance: 85 - 86:  56.272
  distance: 86 - 87:  56.080
  distance: 87 - 88:  41.106
  distance: 89 - 90:  59.212
  distance: 90 - 91:  45.561
  distance: 90 - 93:  24.842
  distance: 91 - 92:  39.688
  distance: 91 - 97:  56.180
  distance: 93 - 94:  56.242
  distance: 94 - 95:  57.061
  distance: 94 - 96:  50.495
  distance: 97 - 98:  69.598
  distance: 98 - 99:  34.614
  distance: 98 - 101:  56.268
  distance: 99 - 100:  12.621
  distance: 99 - 105:  39.573
  distance: 102 - 103:  68.621
  distance: 102 - 104:  58.330
  distance: 105 - 106:  40.654
  distance: 106 - 107:  69.169
  distance: 106 - 109:  40.638
  distance: 107 - 108:  56.268
  distance: 107 - 113:  40.449
  distance: 109 - 110:  57.739
  distance: 109 - 111:  59.445
  distance: 110 - 112:  24.596
  distance: 113 - 114:  56.606
  distance: 114 - 115:  41.157
  distance: 114 - 117:  40.132
  distance: 115 - 125:  32.449
  distance: 117 - 118:  57.936
  distance: 118 - 119:  37.520
  distance: 118 - 120:  35.420
  distance: 119 - 121:  50.286
  distance: 120 - 122:  53.367
  distance: 121 - 123:  13.127
  distance: 122 - 123:  13.957
  distance: 123 - 124:  49.267