Starting phenix.real_space_refine
on Thu Aug  6 17:38:39 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8hal_34595/08_2026/8hal_34595.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hal_34595/08_2026/8hal_34595.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8hal_34595/08_2026/8hal_34595.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8hal_34595/08_2026/8hal_34595.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hal_34595/08_2026/8hal_34595.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hal_34595/08_2026/8hal_34595.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hal_34595/08_2026/8hal_34595.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hal_34595/08_2026/8hal_34595.cif"
  }
  resolution = 4.4
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     302      5.49       5
     S      46      5.16       5
     C    9551      2.51       5
     N    3022      2.21       5
     O    3664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 111 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16585
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 819
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 728
          Classifications: {'peptide': 92}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ALY:plan-1': 1, 'ALY:plan-2': 2}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 673
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 764
          Classifications: {'peptide': 101}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 13
    Chain: "I"
      Number of atoms: 3094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3094
          Classifications: {'DNA': 151}
          Link IDs: {'rna3p': 150}
    Chain: "J"
      Number of atoms: 3097
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3097
          Classifications: {'DNA': 151}
          Link IDs: {'rna3p': 150}
    Chain: "K"
      Number of atoms: 4238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 4238
          Classifications: {'peptide': 513}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 481}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 14
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA C  14 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA C  14 " occ=0.00
  Time building chain proxies: 3.61, per 1000 atoms: 0.22
  Number of scatterers: 16585
  At special positions: 0
  Unit cell: (110.25, 170.52, 136.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     P     302     15.00
     O    3664      8.00
     N    3022      7.00
     C    9551      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.34
  Conformation dependent library (CDL) restraints added in 518.4 milliseconds
  

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2428

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 13 sheets defined
      61.0% alpha, 6.8% beta
      117 base pairs and 228 stacking pairs defined.
    Time for finding SS restraints: 2.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 3.730A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
      removed outlier: 3.666A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.124A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLU B  74 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.289A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.543A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.504A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.948A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.605A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 4.078A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.376A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.742A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.684A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'K' and resid 1087 through 1104
      Proline residue:  K1096  - end of helix
      removed outlier: 3.657A  pdb=" N   GLN K1104 " --> pdb=" O   ALA K1100 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1108 through 1112
    Processing helix  chain 'K' and resid 1116 through 1121
    Processing helix  chain 'K' and resid 1124 through 1129
    Processing helix  chain 'K' and resid 1134 through 1144
    Processing helix  chain 'K' and resid 1150 through 1168
    Processing helix  chain 'K' and resid 1172 through 1195
      removed outlier: 3.711A  pdb=" N   LYS K1176 " --> pdb=" O   SER K1172 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ASP K1190 " --> pdb=" O   GLU K1186 " (cutoff:3.500A)
      Proline residue:  K1191  - end of helix
      removed outlier: 3.762A  pdb=" N   SER K1195 " --> pdb=" O   PRO K1191 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1292 through 1296
    Processing helix  chain 'K' and resid 1308 through 1314
    Processing helix  chain 'K' and resid 1332 through 1350
    Processing helix  chain 'K' and resid 1372 through 1380
    Processing helix  chain 'K' and resid 1442 through 1465
      removed outlier: 4.135A  pdb=" N   THR K1447 " --> pdb=" O   ARG K1443 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   ALA K1448 " --> pdb=" O   CYS K1444 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU K1452 " --> pdb=" O   ALA K1448 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1495 through 1513
    Processing helix  chain 'K' and resid 1522 through 1530
    Processing helix  chain 'K' and resid 1533 through 1537
    Processing helix  chain 'K' and resid 1543 through 1555
      removed outlier: 3.833A  pdb=" N   ASN K1547 " --> pdb=" O   ASP K1543 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1621 through 1628
    Processing helix  chain 'K' and resid 1663 through 1675
      removed outlier: 4.352A  pdb=" N   PHE K1667 " --> pdb=" O   GLY K1663 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1680 through 1698
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.745A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.015A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.738A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.498A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.393A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 1226 through 1229
      removed outlier: 3.740A  pdb=" N   LYS K1270 " --> pdb=" O   TYR K1227 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   SER K1229 " --> pdb=" O   GLU K1268 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLU K1268 " --> pdb=" O   SER K1229 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1280 through 1282
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1357 through 1370
      removed outlier: 6.825A  pdb=" N   ALA K1395 " --> pdb=" O   VAL K1362 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   SER K1364 " --> pdb=" O   THR K1393 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR K1393 " --> pdb=" O   SER K1364 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   ASP K1366 " --> pdb=" O   TYR K1391 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   TYR K1391 " --> pdb=" O   ASP K1366 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   THR K1368 " --> pdb=" O   PHE K1389 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   PHE K1389 " --> pdb=" O   THR K1368 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE K1410 " --> pdb=" O   ALA K1398 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   GLU K1400 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   CYS K1408 " --> pdb=" O   GLU K1400 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE K1402 " --> pdb=" O   ASP K1406 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   ASP K1406 " --> pdb=" O   ILE K1402 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   TYR K1433 " --> pdb=" O   HIS K1413 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   GLN K1415 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 5.594A  pdb=" N   ILE K1431 " --> pdb=" O   GLN K1415 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   TYR K1417 " --> pdb=" O   VAL K1429 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   VAL K1429 " --> pdb=" O   TYR K1417 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   TRP K1472 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   TYR K1433 " --> pdb=" O   TRP K1472 " (cutoff:3.500A)

    583 hydrogen bonds defined for protein.
    1725 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      280 hydrogen bonds
      560 hydrogen bond angles
      0 basepair planarities
      117 basepair parallelities
      228 stacking parallelities
  Total time for adding SS restraints: 3.73

  Time building geometry restraints manager: 1.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2780
        1.33 -     1.45: 5676
        1.45 -     1.57: 8411
        1.57 -     1.69: 602
        1.69 -     1.81: 68
  Bond restraints: 17537
  Sorted by residual:
  bond pdb=" C3'  DA I  18 "
       pdb=" C2'  DA I  18 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.19e+01
  bond pdb=" C3'  DT J 107 "
       pdb=" C2'  DT J 107 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.18e+01
  bond pdb=" C3'  DT I 108 "
       pdb=" C2'  DT I 108 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  bond pdb=" C3'  DT J 135 "
       pdb=" C2'  DT J 135 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.05e+01
  bond pdb=" C3'  DT J 145 "
       pdb=" C2'  DT J 145 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.94e+00
  ... (remaining 17532 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 23845
        1.84 -     3.67: 1062
        3.67 -     5.51: 50
        5.51 -     7.34: 15
        7.34 -     9.18: 3
  Bond angle restraints: 24975
  Sorted by residual:
  angle pdb=" O4'  DT I 107 "
        pdb=" C4'  DT I 107 "
        pdb=" C3'  DT I 107 "
      ideal   model   delta    sigma   weight residual
     106.00  102.71    3.29 6.00e-01 2.78e+00 3.00e+01
  angle pdb=" O4'  DC I 105 "
        pdb=" C4'  DC I 105 "
        pdb=" C3'  DC I 105 "
      ideal   model   delta    sigma   weight residual
     106.00  103.15    2.85 6.00e-01 2.78e+00 2.26e+01
  angle pdb=" C   LEU H 101 "
        pdb=" N   LEU H 102 "
        pdb=" CA  LEU H 102 "
      ideal   model   delta    sigma   weight residual
     122.70  113.52    9.18 1.98e+00 2.55e-01 2.15e+01
  angle pdb=" N3   DT I  65 "
        pdb=" C4   DT I  65 "
        pdb=" O4   DT I  65 "
      ideal   model   delta    sigma   weight residual
     119.90  122.57   -2.67 6.00e-01 2.78e+00 1.98e+01
  angle pdb=" N   GLU F  63 "
        pdb=" CA  GLU F  63 "
        pdb=" CB  GLU F  63 "
      ideal   model   delta    sigma   weight residual
     110.28  117.11   -6.83 1.55e+00 4.16e-01 1.94e+01
  ... (remaining 24970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.55: 8491
       35.55 -    71.11: 1338
       71.11 -   106.66: 23
      106.66 -   142.21: 1
      142.21 -   177.77: 2
  Dihedral angle restraints: 9855
    sinusoidal: 6092
      harmonic: 3763
  Sorted by residual:
  dihedral pdb=" CA  ARG E  63 "
           pdb=" C   ARG E  63 "
           pdb=" N   LYS E  64 "
           pdb=" CA  LYS E  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.34  -26.66     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" C4'  DT I 136 "
           pdb=" C3'  DT I 136 "
           pdb=" O3'  DT I 136 "
           pdb=" P    DT I 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.77 -177.77     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA J  59 "
           pdb=" C3'  DA J  59 "
           pdb=" O3'  DA J  59 "
           pdb=" P    DA J  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   61.88  158.12     1      3.50e+01 8.16e-04 1.51e+01
  ... (remaining 9852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1818
       0.039 -    0.079: 694
       0.079 -    0.118: 238
       0.118 -    0.157: 22
       0.157 -    0.196: 2
  Chirality restraints: 2774
  Sorted by residual:
  chirality pdb=" CA  GLU G  61 "
            pdb=" N   GLU G  61 "
            pdb=" C   GLU G  61 "
            pdb=" CB  GLU G  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.64e-01
  chirality pdb=" C3'  DT I 136 "
            pdb=" C4'  DT I 136 "
            pdb=" O3'  DT I 136 "
            pdb=" C2'  DT I 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.55   -0.18 2.00e-01 2.50e+01 8.26e-01
  chirality pdb=" P    DA J  60 "
            pdb=" OP1  DA J  60 "
            pdb=" OP2  DA J  60 "
            pdb=" O5'  DA J  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.49   -0.15 2.00e-01 2.50e+01 5.77e-01
  ... (remaining 2771 not shown)

  Planarity restraints: 2132
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "    0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO H 103 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  69 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   ARG A  69 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   ARG A  69 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A  70 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.032 5.00e-02 4.00e+02   4.77e-02 3.65e+00
        pdb=" N   PRO D 103 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2129 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1032
        2.73 -     3.27: 15993
        3.27 -     3.81: 32542
        3.81 -     4.36: 37765
        4.36 -     4.90: 55123
  Nonbonded interactions: 142455
  Sorted by model distance:
  nonbonded pdb=" O2   DT J 140 "
            pdb=" N6   DA J 141 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" OD2 ASP F  68 "
            pdb=" NE2 GLN F  93 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   ILE E  62 "
            pdb=" NE2 GLN E  93 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" O2   DT I 107 "
            pdb=" N2   DG J  75 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" N   THR D  90 "
            pdb=" OE2 GLU D  93 "
     model   vdw
     2.258 3.120
  ... (remaining 142450 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 19 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 32 through 124))
  selection = (chain 'H' and resid 31 through 124)
}
ncs_group {
  reference = (chain 'I' and resid 16 through 165)
  selection = (chain 'J' and resid 16 through 165)
}

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:             1.130
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.760
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
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      :  0.005   0.042  17537  Z= 0.454
  Angle     :  0.763   9.177  24975  Z= 0.637
  Chirality :  0.044   0.196   2774
  Planarity :  0.004   0.056   2132
  Dihedral  : 24.758 177.765   7427
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.26 (0.23), residues: 1261
  helix:  1.26 (0.19), residues: 749
  sheet:  0.06 (0.66), residues: 58
  loop :  0.41 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG E  63 
 TYR   0.019   0.001   TYR G  57 
 PHE   0.015   0.001   PHE A 104 
 TRP   0.024   0.001   TRP K1502 
 HIS   0.003   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00498 /  0.45 (17537)
  covalent geometry    : angle       0.76271 /  0.64 (24975)
  hydrogen bonds       : bond        0.13883 /  8.98 (  863)
  hydrogen bonds       : angle       5.77810 /  4.15 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   41 GLU cc_start: 0.7537 (mp0) cc_final: 0.7323 (mm-30)
REVERT: E  110 CYS cc_start: 0.8206 (t) cc_final: 0.7998 (t)
REVERT: E  120 MET cc_start: 0.7713 (ptp) cc_final: 0.7493 (mpp)
REVERT: F   97 LEU cc_start: 0.8693 (tp) cc_final: 0.8338 (tp)
REVERT: K 1148 GLN cc_start: 0.6269 (pp30) cc_final: 0.5746 (tp40)
REVERT: K 1193 MET cc_start: -0.3248 (ttt) cc_final: -0.3778 (tpp)
REVERT: K 1385 MET cc_start: -0.2374 (mtt) cc_final: -0.3087 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1145
  time to fit residues: 17.3073
Evaluate side-chains
  54 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:   40.0000
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   30.0000
   chunk 149 optimal weight:    9.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
E  93 GLN
F  93 GLN
G  38 ASN
G 104 GLN
H 109 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.052911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.037468 restraints weight = 209036.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.038427 restraints weight = 110672.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.038873 restraints weight = 75443.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.039296 restraints weight = 60824.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.039439 restraints weight = 53434.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084  17537  Z= 0.299
  Angle     :  0.845  12.992  24975  Z= 0.466
  Chirality :  0.048   0.358   2774
  Planarity :  0.007   0.074   2132
  Dihedral  : 29.139 162.553   4825
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 18.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  4.90 %
    Favored  : 94.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.61 (0.22), residues: 1261
  helix:  0.65 (0.18), residues: 773
  sheet:  0.38 (0.64), residues: 62
  loop :  0.21 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  86 
 TYR   0.020   0.003   TYR H  83 
 PHE   0.023   0.003   PHE H  70 
 TRP   0.039   0.004   TRP K1502 
 HIS   0.013   0.003   HIS K1451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00564 /  0.30 (17537)
  covalent geometry    : angle       0.84509 /  0.47 (24975)
  hydrogen bonds       : bond        0.10537 /  7.10 (  863)
  hydrogen bonds       : angle       4.63909 /  3.32 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9548 (mt) cc_final: 0.9318 (mt)
REVERT: B   59 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8879 (ttpp)
REVERT: D   62 MET cc_start: 0.8708 (tpp) cc_final: 0.8444 (tpp)
REVERT: F   58 LEU cc_start: 0.9503 (tp) cc_final: 0.9117 (pp)
REVERT: F   63 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8149 (pm20)
REVERT: F   97 LEU cc_start: 0.8799 (tp) cc_final: 0.8505 (tp)
REVERT: K 1095 MET cc_start: 0.1248 (mmm) cc_final: 0.0939 (mmm)
REVERT: K 1193 MET cc_start: 0.0516 (ttt) cc_final: -0.0816 (tpp)
  outliers start: 6
  outliers final: 4
  residues processed: 74
  average time/residue: 0.1102
  time to fit residues: 13.9198
Evaluate side-chains
  50 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 86 optimal weight:   20.0000
   chunk 73 optimal weight:    2.9990
   chunk 141 optimal weight:   10.0000
   chunk 99 optimal weight:   30.0000
   chunk 129 optimal weight:    5.9990
   chunk 122 optimal weight:   20.0000
   chunk 81 optimal weight:   20.0000
   chunk 114 optimal weight:   10.0000
   chunk 138 optimal weight:    9.9990
   chunk 147 optimal weight:    5.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  67 ASN
D 109 HIS
F  93 GLN
G 104 GLN
K1297 HIS
** K1638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.049622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.034519 restraints weight = 215244.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.035426 restraints weight = 113865.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.035938 restraints weight = 76694.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.036159 restraints weight = 61683.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.036337 restraints weight = 55298.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.093  17537  Z= 0.304
  Angle     :  0.840  11.152  24975  Z= 0.472
  Chirality :  0.050   0.366   2774
  Planarity :  0.007   0.071   2132
  Dihedral  : 29.919 166.138   4825
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 20.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  5.62 %
    Favored  : 93.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.03 (0.22), residues: 1261
  helix:  0.29 (0.17), residues: 772
  sheet:  0.45 (0.65), residues: 62
  loop : -0.30 (0.28), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG A  69 
 TYR   0.028   0.003   TYR B  51 
 PHE   0.030   0.003   PHE K1206 
 TRP   0.011   0.002   TRP K1502 
 HIS   0.026   0.003   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00583 /  0.30 (17537)
  covalent geometry    : angle       0.84002 /  0.47 (24975)
  hydrogen bonds       : bond        0.08672 /  5.92 (  863)
  hydrogen bonds       : angle       4.83556 /  3.43 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9565 (mt) cc_final: 0.9358 (mt)
REVERT: B   84 MET cc_start: 0.7479 (ppp) cc_final: 0.7269 (ppp)
REVERT: C   87 ILE cc_start: 0.9198 (tp) cc_final: 0.8765 (pt)
REVERT: D  105 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7961 (tm-30)
REVERT: F   63 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8274 (pm20)
REVERT: F   68 ASP cc_start: 0.8496 (m-30) cc_final: 0.8277 (m-30)
  outliers start: 5
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1107
  time to fit residues: 13.2601
Evaluate side-chains
  50 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 150 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 79 optimal weight:   20.0000
   chunk 34 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 112 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:   50.0000
   chunk 102 optimal weight:   30.0000
   overall best weight:    2.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
K1638 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.050279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.035081 restraints weight = 210656.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.035995 restraints weight = 111040.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.036421 restraints weight = 74279.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 66)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.036792 restraints weight = 59726.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.036897 restraints weight = 52852.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  17537  Z= 0.177
  Angle     :  0.686   7.221  24975  Z= 0.393
  Chirality :  0.044   0.345   2774
  Planarity :  0.005   0.089   2132
  Dihedral  : 29.838 170.582   4825
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.52 (0.22), residues: 1261
  helix:  0.77 (0.18), residues: 776
  sheet:  0.52 (0.66), residues: 64
  loop : -0.30 (0.28), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E  63 
 TYR   0.018   0.002   TYR G  57 
 PHE   0.024   0.002   PHE G  25 
 TRP   0.026   0.002   TRP K1158 
 HIS   0.006   0.001   HIS K1451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.18 (17537)
  covalent geometry    : angle       0.68587 /  0.39 (24975)
  hydrogen bonds       : bond        0.06614 /  4.43 (  863)
  hydrogen bonds       : angle       4.32932 /  3.04 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9540 (mt) cc_final: 0.9323 (mt)
REVERT: B   84 MET cc_start: 0.8008 (ppp) cc_final: 0.7759 (ppp)
REVERT: C   87 ILE cc_start: 0.9242 (tp) cc_final: 0.8864 (pt)
REVERT: K 1193 MET cc_start: 0.1107 (ttt) cc_final: -0.0448 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1074
  time to fit residues: 13.0934
Evaluate side-chains
  46 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 84 optimal weight:   20.0000
   chunk 144 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 111 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   chunk 141 optimal weight:   40.0000
   chunk 89 optimal weight:   30.0000
   chunk 34 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1638 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.050375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.035185 restraints weight = 211007.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.036098 restraints weight = 110085.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.036509 restraints weight = 73246.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.036892 restraints weight = 58952.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.037081 restraints weight = 52636.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  17537  Z= 0.156
  Angle     :  0.660   6.982  24975  Z= 0.379
  Chirality :  0.042   0.347   2774
  Planarity :  0.004   0.057   2132
  Dihedral  : 29.786 170.899   4825
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.80 (0.23), residues: 1261
  helix:  1.04 (0.18), residues: 774
  sheet:  0.43 (0.67), residues: 64
  loop : -0.23 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG K1173 
 TYR   0.014   0.001   TYR K1482 
 PHE   0.019   0.001   PHE A  67 
 TRP   0.010   0.001   TRP K1502 
 HIS   0.006   0.001   HIS D 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.16 (17537)
  covalent geometry    : angle       0.66013 /  0.38 (24975)
  hydrogen bonds       : bond        0.05894 /  3.94 (  863)
  hydrogen bonds       : angle       4.14530 /  2.90 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9506 (mt) cc_final: 0.9280 (mt)
REVERT: B   63 GLU cc_start: 0.8973 (mp0) cc_final: 0.8762 (mp0)
REVERT: B   88 TYR cc_start: 0.8694 (m-10) cc_final: 0.8317 (m-10)
REVERT: C   87 ILE cc_start: 0.9302 (tp) cc_final: 0.8962 (pt)
REVERT: K 1193 MET cc_start: 0.0810 (ttt) cc_final: -0.0924 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1074
  time to fit residues: 13.2050
Evaluate side-chains
  45 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 138 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 78 optimal weight:   30.0000
   chunk 95 optimal weight:   20.0000
   chunk 114 optimal weight:    0.5980
   chunk 85 optimal weight:   20.0000
   chunk 0 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 121 optimal weight:    0.3980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  24 GLN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.050688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.035535 restraints weight = 208699.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.036516 restraints weight = 107671.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.036931 restraints weight = 71040.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 65)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.037302 restraints weight = 57338.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.037366 restraints weight = 50541.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  17537  Z= 0.138
  Angle     :  0.647   8.288  24975  Z= 0.370
  Chirality :  0.042   0.340   2774
  Planarity :  0.004   0.058   2132
  Dihedral  : 29.658 170.753   4825
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.18 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.02 (0.23), residues: 1261
  helix:  1.20 (0.18), residues: 777
  sheet:  0.35 (0.64), residues: 64
  loop : -0.10 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  72 
 TYR   0.010   0.001   TYR B  72 
 PHE   0.019   0.001   PHE A  67 
 TRP   0.019   0.002   TRP K1472 
 HIS   0.005   0.001   HIS K1413 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.14 (17537)
  covalent geometry    : angle       0.64663 /  0.37 (24975)
  hydrogen bonds       : bond        0.05229 /  3.46 (  863)
  hydrogen bonds       : angle       4.00002 /  2.80 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9494 (mt) cc_final: 0.9264 (mt)
REVERT: B   63 GLU cc_start: 0.8825 (mp0) cc_final: 0.8549 (mp0)
REVERT: B   88 TYR cc_start: 0.8655 (m-10) cc_final: 0.8347 (m-10)
REVERT: C   87 ILE cc_start: 0.9267 (tp) cc_final: 0.8996 (pt)
REVERT: K 1193 MET cc_start: 0.0962 (ttt) cc_final: 0.0459 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1076
  time to fit residues: 12.9276
Evaluate side-chains
  46 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 93 optimal weight:   20.0000
   chunk 83 optimal weight:   20.0000
   chunk 13 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 92 optimal weight:   20.0000
   chunk 125 optimal weight:   20.0000
   chunk 71 optimal weight:    1.9990
   overall best weight:    2.1188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.050225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.035015 restraints weight = 210981.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.035978 restraints weight = 108195.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.036405 restraints weight = 71399.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.036773 restraints weight = 57249.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.036997 restraints weight = 50549.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.4152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17537  Z= 0.156
  Angle     :  0.654   7.031  24975  Z= 0.374
  Chirality :  0.042   0.334   2774
  Planarity :  0.005   0.130   2132
  Dihedral  : 29.660 171.137   4825
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.96 (0.23), residues: 1261
  helix:  1.14 (0.18), residues: 777
  sheet:  0.30 (0.64), residues: 64
  loop : -0.10 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG E  63 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.016   0.001   PHE A  67 
 TRP   0.011   0.002   TRP K1472 
 HIS   0.012   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.16 (17537)
  covalent geometry    : angle       0.65397 /  0.37 (24975)
  hydrogen bonds       : bond        0.05720 /  3.81 (  863)
  hydrogen bonds       : angle       4.07807 /  2.84 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9506 (mt) cc_final: 0.9281 (mt)
REVERT: B   63 GLU cc_start: 0.8885 (mp0) cc_final: 0.8620 (mp0)
REVERT: B   88 TYR cc_start: 0.8657 (m-10) cc_final: 0.8319 (m-10)
REVERT: C   87 ILE cc_start: 0.9276 (tp) cc_final: 0.9009 (pt)
REVERT: E  105 GLU cc_start: 0.8632 (pm20) cc_final: 0.8403 (pm20)
REVERT: F   68 ASP cc_start: 0.8481 (m-30) cc_final: 0.8278 (m-30)
REVERT: K 1193 MET cc_start: 0.0960 (ttt) cc_final: -0.1017 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1039
  time to fit residues: 11.8181
Evaluate side-chains
  47 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 75 optimal weight:   30.0000
   chunk 7 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 96 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 103 optimal weight:   50.0000
   chunk 33 optimal weight:    7.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    2.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.050036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.034905 restraints weight = 212133.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.035829 restraints weight = 110164.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.036367 restraints weight = 73069.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.036584 restraints weight = 58033.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.036774 restraints weight = 52014.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  17537  Z= 0.154
  Angle     :  0.650   7.074  24975  Z= 0.372
  Chirality :  0.041   0.337   2774
  Planarity :  0.005   0.090   2132
  Dihedral  : 29.674 171.444   4825
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.07 (0.23), residues: 1261
  helix:  1.26 (0.18), residues: 777
  sheet:  0.32 (0.65), residues: 64
  loop : -0.12 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E  63 
 TYR   0.018   0.001   TYR K1204 
 PHE   0.016   0.001   PHE A  67 
 TRP   0.011   0.002   TRP K1472 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.15 (17537)
  covalent geometry    : angle       0.64967 /  0.37 (24975)
  hydrogen bonds       : bond        0.05518 /  3.69 (  863)
  hydrogen bonds       : angle       4.03060 /  2.81 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9501 (mt) cc_final: 0.9275 (mt)
REVERT: B   63 GLU cc_start: 0.8768 (mp0) cc_final: 0.8550 (mp0)
REVERT: B   88 TYR cc_start: 0.8619 (m-10) cc_final: 0.8364 (m-10)
REVERT: C   87 ILE cc_start: 0.9286 (tp) cc_final: 0.9023 (pt)
REVERT: K 1193 MET cc_start: 0.1127 (ttt) cc_final: -0.0885 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1007
  time to fit residues: 12.1423
Evaluate side-chains
  44 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 59 optimal weight:    4.9990
   chunk 75 optimal weight:   30.0000
   chunk 144 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 147 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 138 optimal weight:    7.9990
   chunk 126 optimal weight:    7.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    1.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.049962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.034828 restraints weight = 212322.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.035752 restraints weight = 110265.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.036288 restraints weight = 73288.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.036601 restraints weight = 58180.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.036662 restraints weight = 51400.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17537  Z= 0.150
  Angle     :  0.651   7.618  24975  Z= 0.373
  Chirality :  0.041   0.336   2774
  Planarity :  0.005   0.078   2132
  Dihedral  : 29.682 172.010   4825
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  1.10 (0.23), residues: 1261
  helix:  1.29 (0.18), residues: 775
  sheet:  0.34 (0.64), residues: 64
  loop : -0.13 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  63 
 TYR   0.013   0.001   TYR D  40 
 PHE   0.017   0.001   PHE A  67 
 TRP   0.015   0.002   TRP K1151 
 HIS   0.007   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.15 (17537)
  covalent geometry    : angle       0.65135 /  0.37 (24975)
  hydrogen bonds       : bond        0.05446 /  3.64 (  863)
  hydrogen bonds       : angle       4.00747 /  2.79 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9508 (mt) cc_final: 0.9281 (mt)
REVERT: B   88 TYR cc_start: 0.8607 (m-10) cc_final: 0.8375 (m-10)
REVERT: C   87 ILE cc_start: 0.9284 (tp) cc_final: 0.9026 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1031
  time to fit residues: 12.2657
Evaluate side-chains
  46 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 90 optimal weight:   40.0000
   chunk 38 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   chunk 60 optimal weight:    2.9990
   chunk 152 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 153 optimal weight:    7.9990
   chunk 88 optimal weight:   50.0000
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.049081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.034007 restraints weight = 214261.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.034919 restraints weight = 111638.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.035450 restraints weight = 74420.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.035730 restraints weight = 59522.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.035787 restraints weight = 52920.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.4868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  17537  Z= 0.184
  Angle     :  0.700   9.266  24975  Z= 0.395
  Chirality :  0.042   0.341   2774
  Planarity :  0.005   0.071   2132
  Dihedral  : 29.891 173.065   4825
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.91 (0.23), residues: 1261
  helix:  1.13 (0.18), residues: 772
  sheet:  0.29 (0.64), residues: 64
  loop : -0.17 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  69 
 TYR   0.017   0.002   TYR D  40 
 PHE   0.018   0.002   PHE A  67 
 TRP   0.025   0.002   TRP K1158 
 HIS   0.006   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.18 (17537)
  covalent geometry    : angle       0.69965 /  0.39 (24975)
  hydrogen bonds       : bond        0.06727 /  4.56 (  863)
  hydrogen bonds       : angle       4.28051 /  2.98 ( 2285)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9540 (mt) cc_final: 0.9325 (mt)
REVERT: B   88 TYR cc_start: 0.8529 (m-10) cc_final: 0.8125 (m-10)
REVERT: C   87 ILE cc_start: 0.9335 (tp) cc_final: 0.9119 (pt)
REVERT: F   58 LEU cc_start: 0.9389 (tp) cc_final: 0.9065 (pp)
REVERT: F   68 ASP cc_start: 0.8529 (m-30) cc_final: 0.8325 (m-30)
REVERT: K 1095 MET cc_start: 0.1637 (mmm) cc_final: 0.1124 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0998
  time to fit residues: 10.6235
Evaluate side-chains
  44 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 139 optimal weight:    9.9990
   chunk 89 optimal weight:   40.0000
   chunk 145 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 117 optimal weight:    7.9990
   chunk 26 optimal weight:    0.6980
   chunk 103 optimal weight:   50.0000
   chunk 150 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 146 optimal weight:    5.9990
   overall best weight:    4.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  39 HIS
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1272 ASN
K1292 GLN
K1336 ASN
** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.048051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.033198 restraints weight = 216823.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.033887 restraints weight = 117016.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.034406 restraints weight = 76500.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.034745 restraints weight = 60259.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.034818 restraints weight = 52543.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.5410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  17537  Z= 0.222
  Angle     :  0.742   7.383  24975  Z= 0.418
  Chirality :  0.044   0.358   2774
  Planarity :  0.005   0.066   2132
  Dihedral  : 30.214 174.850   4825
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 18.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 are not related in a simple way.
  whole:  0.59 (0.23), residues: 1261
  helix:  0.87 (0.18), residues: 773
  sheet:  0.33 (0.63), residues: 64
  loop : -0.34 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  63 
 TYR   0.018   0.002   TYR D  40 
 PHE   0.028   0.002   PHE A  67 
 TRP   0.099   0.005   TRP K1158 
 HIS   0.008   0.002   HIS K1628 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.22 (17537)
  covalent geometry    : angle       0.74168 /  0.42 (24975)
  hydrogen bonds       : bond        0.07525 /  5.12 (  863)
  hydrogen bonds       : angle       4.45442 /  3.10 ( 2285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3161.73 seconds
wall clock time: 55 minutes 18.73 seconds (3318.73 seconds total)