Starting phenix.real_space_refine
on Wed Sep 17 04:57:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zc1_39919/09_2025/8zc1_39919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zc1_39919/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zc1_39919/09_2025/8zc1_39919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zc1_39919/09_2025/8zc1_39919.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zc1_39919/09_2025/8zc1_39919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zc1_39919/09_2025/8zc1_39919.map"
  }
  resolution = 4.17
  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=   0.025
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): 0.00s

  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: 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: 1.08, per 1000 atoms: 0.24
  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: 0.31
  Conformation dependent library (CDL) restraints added in 187.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.21
  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: 0.69

  Time building geometry restraints manager: 0.42 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:             1.750
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.990
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.190
-------------------------------------------------------------------------------
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   4701  Z= 0.176
  Angle     :  0.756   8.612   6412  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 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: -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
 ARG   0.003   0.000   ARG C  80 
 TYR   0.036   0.001   TYR B 495 
 PHE   0.010   0.001   PHE B 400 
 TRP   0.028   0.003   TRP B 353 
 HIS   0.005   0.002   HIS C 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4694)
  covalent geometry    : angle       0.75495 ( 6398)
  SS BOND              : bond        0.00503 (    7)
  SS BOND              : angle       1.18527 (   14)
  hydrogen bonds       : bond        0.29842 (  107)
  hydrogen bonds       : angle      10.80937 (  330)

*********************** 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  : 0.207 
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: 0.0629
  time to fit residues: 6.0788
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  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0030
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    6.9990
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.119648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.099824 restraints weight = 16395.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.101705 restraints weight = 10631.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.103097 restraints weight = 7624.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.103951 restraints weight = 5903.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.104765 restraints weight = 4875.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7233
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4701  Z= 0.127
  Angle     :  0.565   6.208   6412  Z= 0.295
  Chirality :  0.044   0.140    701
  Planarity :  0.005   0.054    821
  Dihedral  :  4.175  14.909    643
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.39 (0.33), residues: 583
  helix: -4.29 (0.53), residues: 18
  sheet:  0.02 (0.35), residues: 181
  loop : -1.28 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 509 
 TYR   0.016   0.001   TYR B 495 
 PHE   0.008   0.001   PHE B 374 
 TRP   0.018   0.002   TRP E  36 
 HIS   0.003   0.001   HIS E 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4694)
  covalent geometry    : angle       0.56409 ( 6398)
  SS BOND              : bond        0.00453 (    7)
  SS BOND              : angle       0.91190 (   14)
  hydrogen bonds       : bond        0.04043 (  107)
  hydrogen bonds       : angle       6.90193 (  330)

*********************** 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
  61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: B  494 SER cc_start: 0.8666 (p) cc_final: 0.8421 (p)
REVERT: E  112 MET cc_start: 0.8497 (mmt) cc_final: 0.8294 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0624
  time to fit residues: 5.2074
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  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 54 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0170
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.4420

-------------------------------------------------------------------------------
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  39 GLN
E  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.119268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.099149 restraints weight = 16143.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.101058 restraints weight = 10497.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.102388 restraints weight = 7559.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.103435 restraints weight = 5857.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.104106 restraints weight = 4784.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4701  Z= 0.109
  Angle     :  0.540   7.364   6412  Z= 0.276
  Chirality :  0.045   0.153    701
  Planarity :  0.004   0.051    821
  Dihedral  :  3.984  14.351    643
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.43 (0.33), residues: 583
  helix: -4.20 (0.58), residues: 18
  sheet: -0.12 (0.34), residues: 189
  loop : -1.26 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 110 
 TYR   0.024   0.001   TYR B 495 
 PHE   0.009   0.001   PHE B 456 
 TRP   0.013   0.001   TRP E  36 
 HIS   0.003   0.001   HIS C 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4694)
  covalent geometry    : angle       0.53972 ( 6398)
  SS BOND              : bond        0.00425 (    7)
  SS BOND              : angle       0.82121 (   14)
  hydrogen bonds       : bond        0.03445 (  107)
  hydrogen bonds       : angle       6.04934 (  330)

*********************** 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
  61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: B  494 SER cc_start: 0.8656 (p) cc_final: 0.8405 (p)
REVERT: E   31 ASP cc_start: 0.8008 (p0) cc_final: 0.7572 (p0)
REVERT: E  112 MET cc_start: 0.8338 (mmt) cc_final: 0.7955 (mmm)
REVERT: E  154 CYS cc_start: 0.4229 (p) cc_final: 0.3744 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0601
  time to fit residues: 5.1114
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  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 17 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 41 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0980
   chunk 57 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.117406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.097579 restraints weight = 16532.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.099353 restraints weight = 10885.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.100715 restraints weight = 7926.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.101664 restraints weight = 6162.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.102413 restraints weight = 5064.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4701  Z= 0.146
  Angle     :  0.567   8.708   6412  Z= 0.290
  Chirality :  0.045   0.149    701
  Planarity :  0.004   0.052    821
  Dihedral  :  4.123  14.864    643
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.35 (0.33), residues: 583
  helix: -4.11 (0.65), residues: 18
  sheet: -0.05 (0.34), residues: 185
  loop : -1.21 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  55 
 TYR   0.020   0.001   TYR B 495 
 PHE   0.011   0.001   PHE B 374 
 TRP   0.013   0.002   TRP B 436 
 HIS   0.004   0.001   HIS E 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4694)
  covalent geometry    : angle       0.56568 ( 6398)
  SS BOND              : bond        0.00479 (    7)
  SS BOND              : angle       0.96302 (   14)
  hydrogen bonds       : bond        0.03245 (  107)
  hydrogen bonds       : angle       5.79091 (  330)

*********************** 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
  60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: B  494 SER cc_start: 0.8697 (p) cc_final: 0.8459 (p)
REVERT: E   70 MET cc_start: 0.7864 (ttm) cc_final: 0.7216 (ttm)
REVERT: E  136 PHE cc_start: 0.7370 (t80) cc_final: 0.7054 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0562
  time to fit residues: 4.6602
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  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    0.2980
   chunk 46 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   chunk 14 optimal weight:    0.3980
   chunk 32 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   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 = 0.3893 r_free = 0.3893 target = 0.117648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.097824 restraints weight = 16367.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.099644 restraints weight = 10702.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.100983 restraints weight = 7754.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.102032 restraints weight = 6006.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.102665 restraints weight = 4871.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4701  Z= 0.125
  Angle     :  0.561   9.830   6412  Z= 0.282
  Chirality :  0.045   0.167    701
  Planarity :  0.004   0.052    821
  Dihedral  :  4.048  14.488    643
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.49 (0.33), residues: 583
  helix: -3.73 (0.61), residues: 26
  sheet: -0.17 (0.34), residues: 195
  loop : -1.27 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  80 
 TYR   0.017   0.001   TYR B 495 
 PHE   0.007   0.001   PHE B 400 
 TRP   0.028   0.002   TRP B 436 
 HIS   0.003   0.001   HIS E 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4694)
  covalent geometry    : angle       0.56024 ( 6398)
  SS BOND              : bond        0.00397 (    7)
  SS BOND              : angle       0.84857 (   14)
  hydrogen bonds       : bond        0.03022 (  107)
  hydrogen bonds       : angle       5.61425 (  330)

*********************** 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
  62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.180 
Fit side-chains
REVERT: B  494 SER cc_start: 0.8685 (p) cc_final: 0.8444 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0589
  time to fit residues: 5.0314
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  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    0.3980
   chunk 37 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0980
   chunk 14 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0670
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.3318

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
C   6 GLN
E 178 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.118687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.098810 restraints weight = 16496.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.100638 restraints weight = 10715.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.101955 restraints weight = 7721.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.102955 restraints weight = 5969.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.103754 restraints weight = 4867.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4701  Z= 0.100
  Angle     :  0.554   9.053   6412  Z= 0.276
  Chirality :  0.045   0.171    701
  Planarity :  0.004   0.051    821
  Dihedral  :  3.836  14.490    643
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.32 (0.33), residues: 583
  helix: -4.01 (0.54), residues: 26
  sheet: -0.00 (0.35), residues: 195
  loop : -1.16 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 509 
 TYR   0.014   0.001   TYR B 495 
 PHE   0.007   0.001   PHE B 400 
 TRP   0.013   0.001   TRP B 436 
 HIS   0.002   0.001   HIS E 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 4694)
  covalent geometry    : angle       0.55294 ( 6398)
  SS BOND              : bond        0.00393 (    7)
  SS BOND              : angle       0.87149 (   14)
  hydrogen bonds       : bond        0.02763 (  107)
  hydrogen bonds       : angle       5.38015 (  330)

*********************** 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
  60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.178 
Fit side-chains
REVERT: B  494 SER cc_start: 0.8588 (p) cc_final: 0.8360 (p)
REVERT: E   81 MET cc_start: 0.5667 (tpp) cc_final: 0.5456 (tpp)
REVERT: E  112 MET cc_start: 0.8451 (mmt) cc_final: 0.8171 (mmm)
REVERT: E  154 CYS cc_start: 0.4233 (p) cc_final: 0.3820 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0575
  time to fit residues: 4.8115
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  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    0.4980
   chunk 49 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.111386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.091961 restraints weight = 15956.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.093716 restraints weight = 10395.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.095043 restraints weight = 7547.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.096023 restraints weight = 5872.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.096715 restraints weight = 4792.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   4701  Z= 0.269
  Angle     :  0.723  12.035   6412  Z= 0.370
  Chirality :  0.048   0.179    701
  Planarity :  0.005   0.059    821
  Dihedral  :  5.042  17.203    643
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.68 (0.33), residues: 583
  helix: -4.21 (0.50), residues: 26
  sheet: -0.38 (0.35), residues: 185
  loop : -1.30 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 355 
 TYR   0.024   0.002   TYR B 495 
 PHE   0.013   0.003   PHE C  64 
 TRP   0.057   0.004   TRP B 436 
 HIS   0.008   0.002   HIS E 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00596 ( 4694)
  covalent geometry    : angle       0.71859 ( 6398)
  SS BOND              : bond        0.00634 (    7)
  SS BOND              : angle       1.78944 (   14)
  hydrogen bonds       : bond        0.03727 (  107)
  hydrogen bonds       : angle       6.22046 (  330)

*********************** REFINEMENT MACRO_CYCLE 7 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
  56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0655
  time to fit residues: 4.9935
Evaluate side-chains
  41 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.115069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.095444 restraints weight = 16387.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.097284 restraints weight = 10590.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.098619 restraints weight = 7613.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.099597 restraints weight = 5884.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.100287 restraints weight = 4801.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4701  Z= 0.130
  Angle     :  0.621  12.636   6412  Z= 0.310
  Chirality :  0.046   0.150    701
  Planarity :  0.004   0.055    821
  Dihedral  :  4.388  16.190    643
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.60 (0.34), residues: 583
  helix: -4.20 (0.50), residues: 26
  sheet: -0.42 (0.35), residues: 188
  loop : -1.18 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  62 
 TYR   0.017   0.001   TYR B 495 
 PHE   0.007   0.001   PHE B 464 
 TRP   0.030   0.002   TRP B 436 
 HIS   0.003   0.001   HIS E 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4694)
  covalent geometry    : angle       0.61974 ( 6398)
  SS BOND              : bond        0.00424 (    7)
  SS BOND              : angle       1.02661 (   14)
  hydrogen bonds       : bond        0.02979 (  107)
  hydrogen bonds       : angle       5.75594 (  330)

*********************** REFINEMENT MACRO_CYCLE 8 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
  61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: C   83 ASP cc_start: 0.7048 (m-30) cc_final: 0.6771 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0665
  time to fit residues: 5.3946
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  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0670
   chunk 43 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.114781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.095362 restraints weight = 16264.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.097149 restraints weight = 10678.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.098448 restraints weight = 7761.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.099389 restraints weight = 6032.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.100097 restraints weight = 4940.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4701  Z= 0.136
  Angle     :  0.607  11.641   6412  Z= 0.303
  Chirality :  0.046   0.152    701
  Planarity :  0.005   0.055    821
  Dihedral  :  4.314  15.692    643
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.59 (0.34), residues: 583
  helix: -4.11 (0.56), residues: 26
  sheet: -0.27 (0.36), residues: 177
  loop : -1.26 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 355 
 TYR   0.032   0.001   TYR B 495 
 PHE   0.011   0.001   PHE B 497 
 TRP   0.023   0.002   TRP B 436 
 HIS   0.006   0.002   HIS C 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4694)
  covalent geometry    : angle       0.60585 ( 6398)
  SS BOND              : bond        0.00469 (    7)
  SS BOND              : angle       1.08499 (   14)
  hydrogen bonds       : bond        0.02947 (  107)
  hydrogen bonds       : angle       5.67764 (  330)

*********************** REFINEMENT MACRO_CYCLE 9 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
  61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.207 
Fit side-chains
REVERT: B  494 SER cc_start: 0.8630 (p) cc_final: 0.8429 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0648
  time to fit residues: 5.4267
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  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 32 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN
E   6 GLN
E  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.114642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.095308 restraints weight = 16080.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.097086 restraints weight = 10609.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.098334 restraints weight = 7690.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.099338 restraints weight = 5997.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.100005 restraints weight = 4906.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4701  Z= 0.137
  Angle     :  0.617  11.594   6412  Z= 0.307
  Chirality :  0.046   0.142    701
  Planarity :  0.005   0.075    821
  Dihedral  :  4.347  15.303    643
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.58 (0.34), residues: 583
  helix: -4.15 (0.54), residues: 26
  sheet: -0.29 (0.36), residues: 178
  loop : -1.23 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 357 
 TYR   0.029   0.001   TYR B 495 
 PHE   0.010   0.001   PHE B 464 
 TRP   0.020   0.002   TRP B 436 
 HIS   0.004   0.001   HIS C 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4694)
  covalent geometry    : angle       0.61638 ( 6398)
  SS BOND              : bond        0.00489 (    7)
  SS BOND              : angle       0.89361 (   14)
  hydrogen bonds       : bond        0.02974 (  107)
  hydrogen bonds       : angle       5.56866 (  330)

********************** REFINEMENT MACRO_CYCLE 10 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
  59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.184 
Fit side-chains
REVERT: C  129 PHE cc_start: 0.8062 (m-80) cc_final: 0.7841 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0747
  time to fit residues: 5.8107
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  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 9 optimal weight:    0.3980
   chunk 57 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0770
   chunk 48 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN
E  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.115480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.096215 restraints weight = 16398.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.098062 restraints weight = 10706.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.099438 restraints weight = 7708.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.100416 restraints weight = 5925.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.101146 restraints weight = 4844.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.3649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4701  Z= 0.127
  Angle     :  0.612  11.450   6412  Z= 0.304
  Chirality :  0.046   0.142    701
  Planarity :  0.005   0.068    821
  Dihedral  :  4.273  15.237    643
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.52 (0.34), residues: 583
  helix: -4.08 (0.57), residues: 26
  sheet: -0.21 (0.36), residues: 178
  loop : -1.21 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 355 
 TYR   0.028   0.001   TYR B 495 
 PHE   0.008   0.001   PHE B 497 
 TRP   0.025   0.002   TRP E  36 
 HIS   0.003   0.001   HIS C 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4694)
  covalent geometry    : angle       0.61146 ( 6398)
  SS BOND              : bond        0.00470 (    7)
  SS BOND              : angle       0.83756 (   14)
  hydrogen bonds       : bond        0.02883 (  107)
  hydrogen bonds       : angle       5.45817 (  330)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1017.14 seconds
wall clock time: 18 minutes 11.79 seconds (1091.79 seconds total)