Starting phenix.real_space_refine
on Sat Jul  4 00:24:04 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8haj_34592/07_2026/8haj_34592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8haj_34592/07_2026/8haj_34592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8haj_34592/07_2026/8haj_34592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8haj_34592/07_2026/8haj_34592.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8haj_34592/07_2026/8haj_34592.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8haj_34592/07_2026/8haj_34592.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8haj_34592/07_2026/8haj_34592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8haj_34592/07_2026/8haj_34592.cif"
  }
  resolution = 4.8
  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     326      5.49       5
     S      47      5.16       5
     C    9860      2.51       5
     N    3138      2.21       5
     O    3843      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 113 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 17214
  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: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 735
          Classifications: {'peptide': 92}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'ALY:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    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: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 730
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "I"
      Number of atoms: 3362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3362
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
    Chain: "J"
      Number of atoms: 3320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 3320
          Classifications: {'DNA': 162}
          Link IDs: {'rna3p': 161}
    Chain: "K"
      Number of atoms: 4403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4403
          Classifications: {'peptide': 533}
          Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 499}
          Chain breaks: 3
  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: 3.43, per 1000 atoms: 0.20
  Number of scatterers: 17214
  At special positions: 0
  Unit cell: (107.31, 163.17, 122.01, 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      47     16.00
     P     326     15.00
     O    3843      8.00
     N    3138      7.00
     C    9860      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: 1.38
  Conformation dependent library (CDL) restraints added in 530.7 milliseconds
  

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2456

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 14 sheets defined
      60.7% alpha, 6.5% beta
      115 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.669A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.794A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.016A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.581A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    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: 4.507A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.542A  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 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.586A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.883A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 121 through 131
    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
      removed outlier: 3.810A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLU F  74 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   HIS F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    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: 4.367A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.552A  pdb=" N   GLN H  44 " --> pdb=" O   LYS H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'K' and resid 1051 through 1068
      removed outlier: 4.161A  pdb=" N   GLN K1056 " --> pdb=" O   GLU K1052 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ALA K1057 " --> pdb=" O   GLU K1053 " (cutoff:3.500A)
      Proline residue:  K1060  - end of helix
    Processing helix  chain 'K' and resid 1072 through 1077
      removed outlier: 4.399A  pdb=" N   GLN K1077 " --> pdb=" O   LEU K1073 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1088 through 1093
    Processing helix  chain 'K' and resid 1098 through 1109
    Processing helix  chain 'K' and resid 1113 through 1132
      removed outlier: 3.775A  pdb=" N   TYR K1117 " --> pdb=" O   GLU K1113 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1136 through 1159
      removed outlier: 3.596A  pdb=" N   GLU K1152 " --> pdb=" O   VAL K1148 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ASP K1154 " --> pdb=" O   GLU K1150 " (cutoff:3.500A)
      Proline residue:  K1155  - end of helix
    Processing helix  chain 'K' and resid 1201 through 1208
      removed outlier: 3.584A  pdb=" N   PHE K1205 " --> pdb=" O   CYS K1201 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ASN K1206 " --> pdb=" O   GLU K1202 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU K1207 " --> pdb=" O   LYS K1203 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE K1208 " --> pdb=" O   CYS K1204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 1201 through 1208'
    Processing helix  chain 'K' and resid 1272 through 1279
    Processing helix  chain 'K' and resid 1296 through 1314
    Processing helix  chain 'K' and resid 1336 through 1343
    Processing helix  chain 'K' and resid 1406 through 1429
      removed outlier: 4.100A  pdb=" N   THR K1411 " --> pdb=" O   LYS K1407 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ALA K1412 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS K1427 " --> pdb=" O   GLU K1423 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1459 through 1477
    Processing helix  chain 'K' and resid 1486 through 1493
    Processing helix  chain 'K' and resid 1497 through 1501
    Processing helix  chain 'K' and resid 1507 through 1519
      removed outlier: 3.881A  pdb=" N   ASN K1511 " --> pdb=" O   ASP K1507 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1579 through 1591
    Processing helix  chain 'K' and resid 1626 through 1638
      removed outlier: 3.915A  pdb=" N   PHE K1630 " --> pdb=" O   GLY K1626 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1643 through 1664
      removed outlier: 4.048A  pdb=" N   GLN K1663 " --> pdb=" O   HIS K1659 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.161A  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: 7.018A  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: 7.062A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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: 6.950A  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: 7.239A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (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 1175 through 1176
      removed outlier: 4.151A  pdb=" N   LEU K1175 " --> pdb=" O   ILE K1185 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1192 through 1194
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1244 through 1246
    Processing sheet with id=AB5, first strand: chain 'K' and resid 1321 through 1334
      removed outlier: 6.893A  pdb=" N   ALA K1359 " --> pdb=" O   VAL K1326 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ALA K1328 " --> pdb=" O   THR K1357 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR K1357 " --> pdb=" O   ALA K1328 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ASP K1330 " --> pdb=" O   TYR K1355 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   TYR K1355 " --> pdb=" O   ASP K1330 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   THR K1332 " --> pdb=" O   PHE K1353 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   PHE K1353 " --> pdb=" O   THR K1332 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE K1374 " --> pdb=" O   ALA K1362 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   GLU K1364 " --> pdb=" O   CYS K1372 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   CYS K1372 " --> pdb=" O   GLU K1364 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ILE K1366 " --> pdb=" O   ASP K1370 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   ASP K1370 " --> pdb=" O   ILE K1366 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   HIS K1377 " --> pdb=" O   SER K1396 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   TRP K1436 " --> pdb=" O   ILE K1395 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   TYR K1397 " --> pdb=" O   TRP K1436 " (cutoff:3.500A)

    587 hydrogen bonds defined for protein.
    1731 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      278 hydrogen bonds
      548 hydrogen bond angles
      0 basepair planarities
      115 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 3.35

  Time building geometry restraints manager: 1.80 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: 3161
        1.33 -     1.45: 5678
        1.45 -     1.57: 8664
        1.57 -     1.69: 650
        1.69 -     1.81: 70
  Bond restraints: 18223
  Sorted by residual:
  bond pdb=" C3'  DT I 108 "
       pdb=" C2'  DT I 108 "
    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 135 "
       pdb=" C2'  DT J 135 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.13e+01
  bond pdb=" C3'  DA I  18 "
       pdb=" C2'  DA I  18 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.11e+01
  bond pdb=" C3'  DA I  41 "
       pdb=" C2'  DA I  41 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.94e+00
  bond pdb=" C3'  DG I 111 "
       pdb=" C2'  DG I 111 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.92e+00
  ... (remaining 18218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 24770
        1.73 -     3.46: 1159
        3.46 -     5.20: 57
        5.20 -     6.93: 15
        6.93 -     8.66: 4
  Bond angle restraints: 26005
  Sorted by residual:
  angle pdb=" O4'  DC J 106 "
        pdb=" C4'  DC J 106 "
        pdb=" C3'  DC J 106 "
      ideal   model   delta    sigma   weight residual
     106.00  103.06    2.94 6.00e-01 2.78e+00 2.40e+01
  angle pdb=" N3   DT J 153 "
        pdb=" C4   DT J 153 "
        pdb=" O4   DT J 153 "
      ideal   model   delta    sigma   weight residual
     119.90  122.54   -2.64 6.00e-01 2.78e+00 1.93e+01
  angle pdb=" N3   DT I  40 "
        pdb=" C4   DT I  40 "
        pdb=" O4   DT I  40 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.91e+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  122.49   -2.59 6.00e-01 2.78e+00 1.87e+01
  angle pdb=" N3   DT J 109 "
        pdb=" C4   DT J 109 "
        pdb=" O4   DT J 109 "
      ideal   model   delta    sigma   weight residual
     119.90  122.49   -2.59 6.00e-01 2.78e+00 1.87e+01
  ... (remaining 26000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.76: 8594
       32.76 -    65.53: 1586
       65.53 -    98.29: 38
       98.29 -   131.05: 0
      131.05 -   163.82: 2
  Dihedral angle restraints: 10220
    sinusoidal: 6415
      harmonic: 3805
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.56e+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
     220.00   56.18  163.82     1      3.50e+01 8.16e-04 1.54e+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   66.76  153.24     1      3.50e+01 8.16e-04 1.48e+01
  ... (remaining 10217 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1537
       0.030 -    0.060: 883
       0.060 -    0.091: 341
       0.091 -    0.121: 118
       0.121 -    0.151: 14
  Chirality restraints: 2893
  Sorted by residual:
  chirality pdb=" CA  PRO E 121 "
            pdb=" N   PRO E 121 "
            pdb=" C   PRO E 121 "
            pdb=" CB  PRO E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.71e-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   -2.48   -0.14 2.00e-01 2.50e+01 5.05e-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   -2.60   -0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 2890 not shown)

  Planarity restraints: 2182
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS K1336 "   -0.040 5.00e-02 4.00e+02   6.12e-02 5.99e+00
        pdb=" N   PRO K1337 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO K1337 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO K1337 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H  99 "    0.030 5.00e-02 4.00e+02   4.61e-02 3.41e+00
        pdb=" N   PRO H 100 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO H 100 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H 100 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET K1059 "    0.030 5.00e-02 4.00e+02   4.58e-02 3.35e+00
        pdb=" N   PRO K1060 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO K1060 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO K1060 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2179 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1764
        2.75 -     3.29: 16508
        3.29 -     3.83: 33626
        3.83 -     4.36: 38112
        4.36 -     4.90: 55970
  Nonbonded interactions: 145980
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN K1379 "
            pdb=" OG  SER K1396 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR G  50 "
            pdb=" OE1 GLN H  92 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   THR K1496 "
            pdb=" OG  SER K1581 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   GLU F  74 "
            pdb=" NH2 ARG H  89 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.282 3.040
  ... (remaining 145975 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 28 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 29 through 121))
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and resid 10 through 169)
  selection = (chain 'J' and resid 10 through 169)
}

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:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.520
  Find NCS groups from input model:        0.190
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
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   0.041  18223  Z= 0.455
  Angle     :  0.739   8.661  26005  Z= 0.627
  Chirality :  0.043   0.151   2893
  Planarity :  0.004   0.061   2182
  Dihedral  : 24.856 163.816   7764
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.21 (0.23), residues: 1276
  helix:  1.37 (0.19), residues: 761
  sheet:  0.14 (0.61), residues: 65
  loop :  0.06 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D  69 
 TYR   0.011   0.001   TYR K1117 
 PHE   0.020   0.001   PHE K1508 
 TRP   0.011   0.001   TRP K1466 
 HIS   0.004   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00497 /  0.45 (18223)
  covalent geometry    : angle       0.73937 /  0.63 (26005)
  hydrogen bonds       : bond        0.14477 /  9.90 (  865)
  hydrogen bonds       : angle       5.51504 /  3.95 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9156 (tp30) cc_final: 0.8689 (tt0)
REVERT: D   34 TYR cc_start: 0.9157 (m-10) cc_final: 0.8885 (m-80)
REVERT: G   78 ILE cc_start: 0.9124 (mt) cc_final: 0.8806 (mm)
REVERT: K 1129 TRP cc_start: 0.7371 (m-10) cc_final: 0.7169 (m-10)
REVERT: K 1478 ARG cc_start: 0.4409 (mmp-170) cc_final: 0.3607 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1105
  time to fit residues: 16.9046
Evaluate side-chains
  63 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:    0.0670
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.0970
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:   30.0000
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:   20.0000
   chunk 149 optimal weight:    5.9990
   overall best weight:    3.0322

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 108 ASN
F  25 ASN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1132 ASN
K1236 ASN
** K1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1661 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.059268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.040813 restraints weight = 219434.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.041841 restraints weight = 125943.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.042247 restraints weight = 81668.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.042809 restraints weight = 64240.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.042991 restraints weight = 57639.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  18223  Z= 0.175
  Angle     :  0.633   6.937  26005  Z= 0.369
  Chirality :  0.042   0.297   2893
  Planarity :  0.005   0.060   2182
  Dihedral  : 28.665 168.575   5103
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.13 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.68 (0.23), residues: 1276
  helix:  1.79 (0.18), residues: 774
  sheet:  0.10 (0.61), residues: 66
  loop :  0.16 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG K1055 
 TYR   0.015   0.002   TYR F  72 
 PHE   0.018   0.002   PHE K1508 
 TRP   0.013   0.002   TRP K1122 
 HIS   0.012   0.002   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.18 (18223)
  covalent geometry    : angle       0.63346 /  0.37 (26005)
  hydrogen bonds       : bond        0.07360 /  5.05 (  865)
  hydrogen bonds       : angle       3.78968 /  2.74 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9492 (tp30) cc_final: 0.9207 (tt0)
REVERT: A  106 ASP cc_start: 0.9005 (t0) cc_final: 0.8680 (m-30)
REVERT: E   67 PHE cc_start: 0.8938 (t80) cc_final: 0.8392 (t80)
REVERT: E   92 LEU cc_start: 0.9449 (mp) cc_final: 0.9209 (tt)
REVERT: G   78 ILE cc_start: 0.9068 (mt) cc_final: 0.8855 (mm)
REVERT: H   99 LEU cc_start: 0.8058 (tp) cc_final: 0.7766 (tp)
REVERT: K 1478 ARG cc_start: 0.5619 (mmp-170) cc_final: 0.5011 (tpm170)
  outliers start: 4
  outliers final: 3
  residues processed: 82
  average time/residue: 0.1040
  time to fit residues: 14.2422
Evaluate side-chains
  63 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 90 optimal weight:   20.0000
   chunk 49 optimal weight:    5.9990
   chunk 9 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 43 optimal weight:    7.9990
   chunk 72 optimal weight:    6.9990
   chunk 116 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 106 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    4.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 HIS
E 108 ASN
F  93 GLN
H  92 GLN
K1236 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.054974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.036881 restraints weight = 233965.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.037655 restraints weight = 134071.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 77)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.038366 restraints weight = 95489.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.038579 restraints weight = 71423.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.038804 restraints weight = 62306.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  18223  Z= 0.232
  Angle     :  0.716  10.849  26005  Z= 0.411
  Chirality :  0.042   0.268   2893
  Planarity :  0.006   0.056   2182
  Dihedral  : 29.307 179.481   5103
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  3.90 %
    Favored  : 95.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.48 (0.23), residues: 1276
  helix:  1.57 (0.18), residues: 772
  sheet:  0.35 (0.71), residues: 55
  loop :  0.17 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  40 
 TYR   0.029   0.003   TYR K1355 
 PHE   0.022   0.002   PHE D  67 
 TRP   0.013   0.002   TRP K1466 
 HIS   0.008   0.002   HIS G  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.23 (18223)
  covalent geometry    : angle       0.71634 /  0.41 (26005)
  hydrogen bonds       : bond        0.08915 /  6.18 (  865)
  hydrogen bonds       : angle       4.05894 /  2.94 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9570 (tp30) cc_final: 0.9094 (tt0)
REVERT: B   97 LEU cc_start: 0.8460 (tp) cc_final: 0.8003 (tp)
REVERT: E   41 TYR cc_start: 0.8579 (m-80) cc_final: 0.8097 (m-80)
REVERT: K 1478 ARG cc_start: 0.5654 (mmp-170) cc_final: 0.5119 (tpm170)
  outliers start: 4
  outliers final: 1
  residues processed: 77
  average time/residue: 0.1089
  time to fit residues: 13.7313
Evaluate side-chains
  55 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 80 optimal weight:   20.0000
   chunk 40 optimal weight:    1.9990
   chunk 136 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9990
   chunk 111 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.055771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.037757 restraints weight = 226014.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 79)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.038675 restraints weight = 128858.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.039108 restraints weight = 84300.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.039453 restraints weight = 66035.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.039832 restraints weight = 56909.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  18223  Z= 0.144
  Angle     :  0.588  12.786  26005  Z= 0.346
  Chirality :  0.040   0.340   2893
  Planarity :  0.005   0.057   2182
  Dihedral  : 29.259 176.887   5103
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.76 (0.23), residues: 1276
  helix:  1.86 (0.18), residues: 772
  sheet:  0.29 (0.70), residues: 55
  loop :  0.15 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.022   0.002   TYR A  99 
 PHE   0.031   0.002   PHE E 104 
 TRP   0.009   0.001   TRP K1466 
 HIS   0.005   0.001   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.14 (18223)
  covalent geometry    : angle       0.58846 /  0.35 (26005)
  hydrogen bonds       : bond        0.05633 /  3.91 (  865)
  hydrogen bonds       : angle       3.59385 /  2.62 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9542 (tp30) cc_final: 0.9081 (tt0)
REVERT: A  106 ASP cc_start: 0.9125 (t0) cc_final: 0.8842 (m-30)
REVERT: B   62 LEU cc_start: 0.9486 (mt) cc_final: 0.9285 (mt)
REVERT: B   97 LEU cc_start: 0.8382 (tp) cc_final: 0.7968 (tp)
REVERT: D   56 MET cc_start: 0.9351 (tmm) cc_final: 0.8983 (tpp)
REVERT: K 1157 MET cc_start: 0.3694 (ttt) cc_final: 0.2208 (ttt)
REVERT: K 1254 MET cc_start: 0.0959 (tpt) cc_final: -0.1106 (ptp)
REVERT: K 1478 ARG cc_start: 0.5881 (mmp-170) cc_final: 0.5347 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1053
  time to fit residues: 13.2499
Evaluate side-chains
  54 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 116 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 82 optimal weight:   30.0000
   chunk 29 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 60 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 135 optimal weight:   20.0000
   chunk 91 optimal weight:   30.0000
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
K1230 GLN
K1591 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.053539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.035944 restraints weight = 230721.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.036578 restraints weight = 138011.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.036983 restraints weight = 94082.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.037382 restraints weight = 72597.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.037379 restraints weight = 62723.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  18223  Z= 0.221
  Angle     :  0.691  13.111  26005  Z= 0.392
  Chirality :  0.041   0.325   2893
  Planarity :  0.006   0.062   2182
  Dihedral  : 29.554 179.255   5103
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.04 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.64 (0.23), residues: 1276
  helix:  1.78 (0.18), residues: 772
  sheet:  0.32 (0.73), residues: 55
  loop :  0.08 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K1104 
 TYR   0.021   0.002   TYR A  99 
 PHE   0.032   0.003   PHE K1374 
 TRP   0.012   0.002   TRP K1466 
 HIS   0.010   0.002   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.22 (18223)
  covalent geometry    : angle       0.69075 /  0.39 (26005)
  hydrogen bonds       : bond        0.08628 /  5.92 (  865)
  hydrogen bonds       : angle       3.85908 /  2.80 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9206 (t0) cc_final: 0.8878 (m-30)
REVERT: B   63 GLU cc_start: 0.9090 (pm20) cc_final: 0.8767 (pm20)
REVERT: B   84 MET cc_start: 0.9343 (ttp) cc_final: 0.8877 (tmm)
REVERT: D   56 MET cc_start: 0.9353 (tmm) cc_final: 0.8988 (tpp)
REVERT: E   41 TYR cc_start: 0.8486 (m-80) cc_final: 0.8194 (m-80)
REVERT: K 1157 MET cc_start: 0.4168 (ttt) cc_final: 0.2745 (ttt)
REVERT: K 1254 MET cc_start: 0.0949 (tpt) cc_final: -0.1011 (ptp)
REVERT: K 1478 ARG cc_start: 0.5612 (mmp-170) cc_final: 0.5058 (tpm170)
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1203
  time to fit residues: 13.9343
Evaluate side-chains
  53 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 130 optimal weight:   20.0000
   chunk 101 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0670
   chunk 83 optimal weight:   30.0000
   chunk 99 optimal weight:   30.0000
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    2.4924

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
K1261 HIS
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.054292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.036346 restraints weight = 227105.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 75)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.037329 restraints weight = 126375.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.037713 restraints weight = 83271.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.038067 restraints weight = 65876.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.038460 restraints weight = 57044.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18223  Z= 0.148
  Angle     :  0.599   8.229  26005  Z= 0.350
  Chirality :  0.040   0.334   2893
  Planarity :  0.005   0.070   2182
  Dihedral  : 29.582 178.551   5103
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.33 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.71 (0.23), residues: 1276
  helix:  1.91 (0.18), residues: 772
  sheet:  0.27 (0.71), residues: 55
  loop : -0.04 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K1494 
 TYR   0.025   0.002   TYR A  99 
 PHE   0.019   0.001   PHE K1508 
 TRP   0.023   0.001   TRP K1466 
 HIS   0.011   0.001   HIS K1415 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.15 (18223)
  covalent geometry    : angle       0.59875 /  0.35 (26005)
  hydrogen bonds       : bond        0.05471 /  3.79 (  865)
  hydrogen bonds       : angle       3.65601 /  2.69 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9133 (t0) cc_final: 0.8859 (m-30)
REVERT: B   62 LEU cc_start: 0.9546 (mt) cc_final: 0.9310 (mt)
REVERT: B   84 MET cc_start: 0.9304 (ttp) cc_final: 0.8861 (tmm)
REVERT: D   56 MET cc_start: 0.9359 (tmm) cc_final: 0.8995 (tpp)
REVERT: D   68 GLU cc_start: 0.9108 (pp20) cc_final: 0.8808 (pp20)
REVERT: K 1157 MET cc_start: 0.4133 (ttt) cc_final: 0.2959 (ttt)
REVERT: K 1254 MET cc_start: 0.2564 (tpt) cc_final: 0.0570 (ptp)
REVERT: K 1478 ARG cc_start: 0.5719 (mmp-170) cc_final: 0.5199 (tpm170)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1100
  time to fit residues: 12.0662
Evaluate side-chains
  53 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 141 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 54 optimal weight:    4.9990
   chunk 107 optimal weight:    5.9990
   chunk 111 optimal weight:    9.9990
   chunk 84 optimal weight:   20.0000
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    7.9990
   chunk 106 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** K1415 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 = 0.3286 r_free = 0.3286 target = 0.051533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.034235 restraints weight = 231984.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.034913 restraints weight = 134520.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.035666 restraints weight = 88827.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.035893 restraints weight = 68970.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.036084 restraints weight = 59319.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  18223  Z= 0.258
  Angle     :  0.747   8.587  26005  Z= 0.422
  Chirality :  0.044   0.332   2893
  Planarity :  0.006   0.062   2182
  Dihedral  : 30.039 179.953   5103
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.20 (0.23), residues: 1276
  helix:  1.51 (0.18), residues: 765
  sheet: -0.34 (0.67), residues: 60
  loop : -0.16 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG E  40 
 TYR   0.023   0.002   TYR C  57 
 PHE   0.018   0.002   PHE K1630 
 TRP   0.022   0.002   TRP K1466 
 HIS   0.010   0.002   HIS G  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00482 /  0.26 (18223)
  covalent geometry    : angle       0.74661 /  0.42 (26005)
  hydrogen bonds       : bond        0.10647 /  7.29 (  865)
  hydrogen bonds       : angle       4.13804 /  3.02 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  106 ASP cc_start: 0.9245 (t0) cc_final: 0.8888 (m-30)
REVERT: B   84 MET cc_start: 0.9354 (ttp) cc_final: 0.8899 (tmm)
REVERT: D   68 GLU cc_start: 0.9167 (pp20) cc_final: 0.8934 (pp20)
REVERT: K 1157 MET cc_start: 0.4537 (ttt) cc_final: 0.3435 (ttt)
REVERT: K 1254 MET cc_start: 0.2146 (tpt) cc_final: 0.0053 (ptp)
REVERT: K 1470 MET cc_start: 0.4333 (mtp) cc_final: 0.4039 (mtm)
REVERT: K 1478 ARG cc_start: 0.5783 (mmp-170) cc_final: 0.5243 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1184
  time to fit residues: 11.7196
Evaluate side-chains
  46 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 59 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 111 optimal weight:    6.9990
   chunk 73 optimal weight:   50.0000
   overall best weight:    2.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  84 GLN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
K1261 HIS
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.052687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.035205 restraints weight = 229621.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.035819 restraints weight = 133491.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.036558 restraints weight = 91484.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.036794 restraints weight = 70725.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.037024 restraints weight = 61475.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.4732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  18223  Z= 0.155
  Angle     :  0.620   6.600  26005  Z= 0.359
  Chirality :  0.041   0.331   2893
  Planarity :  0.005   0.057   2182
  Dihedral  : 30.088 177.771   5103
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.47 (0.23), residues: 1276
  helix:  1.80 (0.18), residues: 766
  sheet: -0.41 (0.65), residues: 60
  loop : -0.19 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K1137 
 TYR   0.024   0.002   TYR A  99 
 PHE   0.019   0.002   PHE K1508 
 TRP   0.017   0.002   TRP K1466 
 HIS   0.005   0.001   HIS D 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.15 (18223)
  covalent geometry    : angle       0.62012 /  0.36 (26005)
  hydrogen bonds       : bond        0.05690 /  3.92 (  865)
  hydrogen bonds       : angle       3.82986 /  2.81 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9172 (t0) cc_final: 0.8879 (m-30)
REVERT: B   84 MET cc_start: 0.9384 (ttp) cc_final: 0.8908 (tmm)
REVERT: D   56 MET cc_start: 0.9326 (tmm) cc_final: 0.8994 (tpp)
REVERT: D   68 GLU cc_start: 0.9118 (pp20) cc_final: 0.8811 (pp20)
REVERT: K 1157 MET cc_start: 0.4532 (ttt) cc_final: 0.3688 (ttt)
REVERT: K 1254 MET cc_start: 0.2715 (tpt) cc_final: 0.0672 (ptp)
REVERT: K 1470 MET cc_start: 0.3551 (mtp) cc_final: 0.3123 (mtm)
REVERT: K 1478 ARG cc_start: 0.5830 (mmp-170) cc_final: 0.5352 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1111
  time to fit residues: 11.7369
Evaluate side-chains
  52 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 101 optimal weight:   20.0000
   chunk 152 optimal weight:    6.9990
   chunk 129 optimal weight:   10.0000
   chunk 92 optimal weight:   30.0000
   chunk 42 optimal weight:    6.9990
   chunk 9 optimal weight:   30.0000
   chunk 83 optimal weight:   20.0000
   chunk 114 optimal weight:    6.9990
   chunk 119 optimal weight:    8.9990
   chunk 86 optimal weight:   20.0000
   chunk 75 optimal weight:   30.0000
   overall best weight:    7.9992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
E 125 GLN
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1464 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.049983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.033116 restraints weight = 237592.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.033751 restraints weight = 139541.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.034335 restraints weight = 95802.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.034568 restraints weight = 73952.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.034689 restraints weight = 63166.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.5710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  18223  Z= 0.325
  Angle     :  0.812   9.695  26005  Z= 0.457
  Chirality :  0.047   0.363   2893
  Planarity :  0.007   0.062   2182
  Dihedral  : 30.584 177.573   5103
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 25.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  0.70 (0.23), residues: 1276
  helix:  1.12 (0.18), residues: 773
  sheet: -0.79 (0.65), residues: 60
  loop : -0.40 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG G  88 
 TYR   0.026   0.003   TYR A  99 
 PHE   0.022   0.003   PHE K1508 
 TRP   0.021   0.002   TRP K1466 
 HIS   0.010   0.003   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00604 /  0.33 (18223)
  covalent geometry    : angle       0.81186 /  0.46 (26005)
  hydrogen bonds       : bond        0.11976 /  8.21 (  865)
  hydrogen bonds       : angle       4.55673 /  3.36 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8060 (ptm) cc_final: 0.7855 (ptm)
REVERT: B   84 MET cc_start: 0.9403 (ttp) cc_final: 0.8947 (tmm)
REVERT: D   68 GLU cc_start: 0.9116 (pp20) cc_final: 0.8880 (pp20)
REVERT: K 1470 MET cc_start: 0.3941 (mtp) cc_final: 0.3561 (mtm)
REVERT: K 1478 ARG cc_start: 0.5878 (mmp-170) cc_final: 0.5451 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1263
  time to fit residues: 11.2459
Evaluate side-chains
  42 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 127 optimal weight:    0.9980
   chunk 64 optimal weight:    9.9990
   chunk 12 optimal weight:    0.6980
   chunk 30 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   chunk 94 optimal weight:   20.0000
   chunk 135 optimal weight:   20.0000
   chunk 21 optimal weight:    1.9990
   chunk 112 optimal weight:    8.9990
   overall best weight:    2.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
K1261 HIS
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.051898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.034581 restraints weight = 232840.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.035219 restraints weight = 132165.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.035980 restraints weight = 89727.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.036164 restraints weight = 67692.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.036393 restraints weight = 58369.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.5488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  18223  Z= 0.156
  Angle     :  0.662   6.994  26005  Z= 0.375
  Chirality :  0.042   0.361   2893
  Planarity :  0.005   0.055   2182
  Dihedral  : 30.589 177.594   5103
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.06 (0.23), residues: 1276
  helix:  1.47 (0.18), residues: 767
  sheet: -0.54 (0.66), residues: 54
  loop : -0.38 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  83 
 TYR   0.026   0.002   TYR A  99 
 PHE   0.023   0.002   PHE K1508 
 TRP   0.015   0.002   TRP K1466 
 HIS   0.007   0.001   HIS K1255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.16 (18223)
  covalent geometry    : angle       0.66210 /  0.38 (26005)
  hydrogen bonds       : bond        0.05381 /  3.68 (  865)
  hydrogen bonds       : angle       4.05923 /  3.01 ( 2279)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A  106 ASP cc_start: 0.9033 (t0) cc_final: 0.8787 (m-30)
REVERT: B   84 MET cc_start: 0.9429 (ttp) cc_final: 0.8981 (tmm)
REVERT: D   56 MET cc_start: 0.9289 (tmm) cc_final: 0.9018 (tpp)
REVERT: D   68 GLU cc_start: 0.9136 (pp20) cc_final: 0.8828 (pp20)
REVERT: K 1157 MET cc_start: 0.4663 (ttt) cc_final: 0.3360 (ppp)
REVERT: K 1254 MET cc_start: 0.2941 (tpt) cc_final: 0.0817 (ptp)
REVERT: K 1470 MET cc_start: 0.3497 (mtp) cc_final: 0.3169 (mtm)
REVERT: K 1478 ARG cc_start: 0.5824 (mmp-170) cc_final: 0.5413 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1249
  time to fit residues: 13.3184
Evaluate side-chains
  50 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 99 optimal weight:   30.0000
   chunk 118 optimal weight:    0.1980
   chunk 145 optimal weight:    7.9990
   chunk 113 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 125 optimal weight:    0.0020
   chunk 9 optimal weight:    8.9990
   chunk 83 optimal weight:   30.0000
   chunk 84 optimal weight:   20.0000
   chunk 47 optimal weight:    3.9990
   chunk 142 optimal weight:   20.0000
   overall best weight:    3.0394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
K1261 HIS
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.051466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.034283 restraints weight = 232251.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.035041 restraints weight = 134684.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.035466 restraints weight = 85884.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.035557 restraints weight = 67702.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.036073 restraints weight = 60899.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.5645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  18223  Z= 0.170
  Angle     :  0.656   9.430  26005  Z= 0.373
  Chirality :  0.041   0.360   2893
  Planarity :  0.005   0.057   2182
  Dihedral  : 30.500 178.475   5103
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 15.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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:  1.24 (0.23), residues: 1276
  helix:  1.64 (0.18), residues: 767
  sheet: -0.64 (0.64), residues: 54
  loop : -0.34 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG F  19 
 TYR   0.023   0.002   TYR A  99 
 PHE   0.020   0.002   PHE K1508 
 TRP   0.018   0.002   TRP K1466 
 HIS   0.008   0.001   HIS K1255 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.17 (18223)
  covalent geometry    : angle       0.65633 /  0.37 (26005)
  hydrogen bonds       : bond        0.06622 /  4.53 (  865)
  hydrogen bonds       : angle       3.98527 /  2.95 ( 2279)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2804.90 seconds
wall clock time: 49 minutes 19.58 seconds (2959.58 seconds total)