Starting phenix.real_space_refine
on Thu Aug  6 16:06:54 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8han_34597/08_2026/8han_34597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8han_34597/08_2026/8han_34597.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2026/8han_34597.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2026/8han_34597.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2026/8han_34597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2026/8han_34597.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2026/8han_34597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2026/8han_34597.map"
  }
  resolution = 4.2
  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     294      5.49       5
     S      45      5.16       5
     C    9330      2.51       5
     N    2940      2.21       5
     O    3571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16180
  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: 687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 687
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 745
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    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: "K"
      Number of atoms: 4134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 4134
          Classifications: {'peptide': 500}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 468}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 22
    Chain: "I"
      Number of atoms: 3016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3016
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3011
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  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: 3.27, per 1000 atoms: 0.20
  Number of scatterers: 16180
  At special positions: 0
  Unit cell: (102.9, 127.89, 158.76, 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      45     16.00
     P     294     15.00
     O    3571      8.00
     N    2940      7.00
     C    9330      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: 1.19
  Conformation dependent library (CDL) restraints added in 376.3 milliseconds
  

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2374

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 14 sheets defined
      61.5% alpha, 7.5% beta
      118 base pairs and 226 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.555A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.516A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.659A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    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: 4.393A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 46 through 57
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.583A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.724A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.419A  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 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'K' and resid 1089 through 1103
      Proline residue:  K1096  - end of helix
    Processing helix  chain 'K' and resid 1108 through 1112
    Processing helix  chain 'K' and resid 1116 through 1121
    Processing helix  chain 'K' and resid 1124 through 1129
      removed outlier: 3.512A  pdb=" N   ILE K1128 " --> pdb=" O   ASP K1124 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1134 through 1145
    Processing helix  chain 'K' and resid 1149 through 1168
      removed outlier: 4.121A  pdb=" N   TYR K1153 " --> pdb=" O   GLU K1149 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1172 through 1197
      removed outlier: 4.042A  pdb=" N   ASP K1190 " --> pdb=" O   GLU K1186 " (cutoff:3.500A)
      Proline residue:  K1191  - end of helix
    Processing helix  chain 'K' and resid 1237 through 1242
      removed outlier: 3.502A  pdb=" N   PHE K1241 " --> pdb=" O   CYS K1237 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR K1242 " --> pdb=" O   GLU K1238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 1237 through 1242'
    Processing helix  chain 'K' and resid 1292 through 1296
    Processing helix  chain 'K' and resid 1308 through 1314
    Processing helix  chain 'K' and resid 1332 through 1350
    Processing helix  chain 'K' and resid 1445 through 1465
    Processing helix  chain 'K' and resid 1495 through 1513
    Processing helix  chain 'K' and resid 1522 through 1530
    Processing helix  chain 'K' and resid 1533 through 1537
    Processing helix  chain 'K' and resid 1543 through 1555
      removed outlier: 3.752A  pdb=" N   ASN K1547 " --> pdb=" O   ASP K1543 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1621 through 1628
    Processing helix  chain 'K' and resid 1663 through 1674
      removed outlier: 3.940A  pdb=" N   PHE K1667 " --> pdb=" O   GLY K1663 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1680 through 1698
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.604A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.397A  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: 6.985A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.005A  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
      removed outlier: 3.635A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.202A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 1211 through 1212
      removed outlier: 3.833A  pdb=" N   LEU K1211 " --> pdb=" O   ILE K1221 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1234 through 1236
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1280 through 1282
    Processing sheet with id=AB5, first strand: chain 'K' and resid 1357 through 1370
      removed outlier: 6.879A  pdb=" N   ALA K1395 " --> pdb=" O   VAL K1362 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   SER K1364 " --> pdb=" O   THR K1393 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   THR K1393 " --> pdb=" O   SER K1364 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   ASP K1366 " --> pdb=" O   TYR K1391 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   TYR K1391 " --> pdb=" O   ASP K1366 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   THR K1368 " --> pdb=" O   PHE K1389 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   PHE K1389 " --> pdb=" O   THR K1368 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU K1396 " --> pdb=" O   MET K1412 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET K1412 " --> pdb=" O   LEU K1396 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE K1410 " --> pdb=" O   ALA K1398 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLU K1400 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 5.523A  pdb=" N   CYS K1408 " --> pdb=" O   GLU K1400 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ILE K1402 " --> pdb=" O   ASP K1406 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   ASP K1406 " --> pdb=" O   ILE K1402 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   TYR K1433 " --> pdb=" O   HIS K1413 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   GLN K1415 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ILE K1431 " --> pdb=" O   GLN K1415 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   TYR K1417 " --> pdb=" O   VAL K1429 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   VAL K1429 " --> pdb=" O   TYR K1417 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   TRP K1472 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   TYR K1433 " --> pdb=" O   TRP K1472 " (cutoff:3.500A)

    586 hydrogen bonds defined for protein.
    1731 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      281 hydrogen bonds
      558 hydrogen bond angles
      0 basepair planarities
      118 basepair parallelities
      226 stacking parallelities
  Total time for adding SS restraints: 3.48

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4005
        1.34 -     1.46: 4727
        1.46 -     1.58: 7722
        1.58 -     1.70: 586
        1.70 -     1.82: 66
  Bond restraints: 17106
  Sorted by residual:
  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 1.14e+01
  bond pdb=" C3'  DT I  91 "
       pdb=" C2'  DT I  91 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  bond pdb=" C3'  DA J 116 "
       pdb=" C2'  DA J 116 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.83e+00
  bond pdb=" C3'  DA J  59 "
       pdb=" C2'  DA J  59 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.77e+00
  bond pdb=" C3'  DC J  39 "
       pdb=" C2'  DC J  39 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.74e+00
  ... (remaining 17101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 23265
        1.66 -     3.31: 1046
        3.31 -     4.97: 45
        4.97 -     6.63: 4
        6.63 -     8.28: 3
  Bond angle restraints: 24363
  Sorted by residual:
  angle pdb=" O4'  DC I 105 "
        pdb=" C4'  DC I 105 "
        pdb=" C3'  DC I 105 "
      ideal   model   delta    sigma   weight residual
     106.00  102.72    3.28 6.00e-01 2.78e+00 2.98e+01
  angle pdb=" CA  ALY B  16 "
        pdb=" C   ALY B  16 "
        pdb=" O   ALY B  16 "
      ideal   model   delta    sigma   weight residual
     120.80  129.08   -8.28 1.70e+00 3.46e-01 2.37e+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  122.58   -2.68 6.00e-01 2.78e+00 2.00e+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  122.56   -2.66 6.00e-01 2.78e+00 1.96e+01
  angle pdb=" N3   DT J 135 "
        pdb=" C4   DT J 135 "
        pdb=" O4   DT J 135 "
      ideal   model   delta    sigma   weight residual
     119.90  122.54   -2.64 6.00e-01 2.78e+00 1.94e+01
  ... (remaining 24358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.00: 8167
       34.00 -    67.99: 1416
       67.99 -   101.99: 28
      101.99 -   135.98: 1
      135.98 -   169.98: 2
  Dihedral angle restraints: 9614
    sinusoidal: 5937
      harmonic: 3677
  Sorted by residual:
  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   50.02  169.98     1      3.50e+01 8.16e-04 1.56e+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   62.06  157.94     1      3.50e+01 8.16e-04 1.51e+01
  dihedral pdb=" CG  ARG H  33 "
           pdb=" CD  ARG H  33 "
           pdb=" NE  ARG H  33 "
           pdb=" CZ  ARG H  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.34  -44.66     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 9611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1604
       0.032 -    0.064: 770
       0.064 -    0.096: 263
       0.096 -    0.128: 70
       0.128 -    0.160: 7
  Chirality restraints: 2714
  Sorted by residual:
  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   -2.57   -0.16 2.00e-01 2.50e+01 6.41e-01
  chirality pdb=" P    DA J  60 "
            pdb=" OP1  DA J  60 "
            pdb=" OP2  DA J  60 "
            pdb=" O5'  DA J  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.49   -0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  MET K1095 "
            pdb=" N   MET K1095 "
            pdb=" C   MET K1095 "
            pdb=" CB  MET K1095 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.55e-01
  ... (remaining 2711 not shown)

  Planarity restraints: 2077
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I 105 "   -0.021 2.00e-02 2.50e+03   1.09e-02 2.67e+00
        pdb=" N1   DC I 105 "    0.017 2.00e-02 2.50e+03
        pdb=" C2   DC I 105 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DC I 105 "    0.012 2.00e-02 2.50e+03
        pdb=" N3   DC I 105 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC I 105 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC I 105 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DC I 105 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DC I 105 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.023 5.00e-02 4.00e+02   3.48e-02 1.93e+00
        pdb=" N   PRO D 103 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I 151 "    0.012 2.00e-02 2.50e+03   7.46e-03 1.67e+00
        pdb=" N9   DG I 151 "   -0.014 2.00e-02 2.50e+03
        pdb=" C8   DG I 151 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I 151 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DG I 151 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I 151 "    0.015 2.00e-02 2.50e+03
        pdb=" O6   DG I 151 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1   DG I 151 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I 151 "    0.006 2.00e-02 2.50e+03
        pdb=" N2   DG I 151 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DG I 151 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DG I 151 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2074 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1818
        2.76 -     3.29: 15194
        3.29 -     3.83: 31831
        3.83 -     4.36: 35551
        4.36 -     4.90: 52884
  Nonbonded interactions: 137278
  Sorted by model distance:
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OD1 ASP A 123 "
            pdb=" NE2 HIS E 113 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" NH1 ARG C  17 "
            pdb=" OP2  DG J  48 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" NE2 HIS A 113 "
            pdb=" OD1 ASP E 123 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" N2   DG I  35 "
            pdb=" O2   DT J 147 "
     model   vdw
     2.277 3.120
  ... (remaining 137273 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 45 through 134)
  selection = (chain 'E' and resid 45 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and resid 21 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 32 through 124))
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and resid 19 through 162)
  selection = (chain 'J' and resid 19 through 162)
}

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:             1.070
  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:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.310
  Find NCS groups from input model:        0.210
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  17106  Z= 0.440
  Angle     :  0.689   8.284  24363  Z= 0.606
  Chirality :  0.042   0.160   2714
  Planarity :  0.003   0.035   2077
  Dihedral  : 24.993 169.976   7240
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.88 (0.24), residues: 1230
  helix:  2.68 (0.18), residues: 756
  sheet:  0.28 (0.63), residues: 66
  loop :  0.81 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  29 
 TYR   0.019   0.001   TYR K1102 
 PHE   0.007   0.001   PHE K1484 
 TRP   0.009   0.001   TRP K1502 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00475 /  0.44 (17106)
  covalent geometry    : angle       0.68931 /  0.61 (24363)
  hydrogen bonds       : bond        0.11059 /  7.41 (  867)
  hydrogen bonds       : angle       3.83435 /  2.72 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   62 MET cc_start: 0.8444 (mmp) cc_final: 0.8209 (mmp)
REVERT: H   62 MET cc_start: 0.8783 (mmp) cc_final: 0.8516 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.0877
  time to fit residues: 4.4045
Evaluate side-chains
  24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:   40.0000
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   50.0000
   chunk 91 optimal weight:    0.2980
   chunk 149 optimal weight:   40.0000
   overall best weight:    4.8590

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
H  63 ASN
H  95 GLN
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1628 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.047999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.034407 restraints weight = 235274.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.034996 restraints weight = 134724.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.035502 restraints weight = 92993.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.035776 restraints weight = 72111.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.035968 restraints weight = 61149.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  17106  Z= 0.242
  Angle     :  0.732  10.921  24363  Z= 0.400
  Chirality :  0.043   0.372   2714
  Planarity :  0.005   0.039   2077
  Dihedral  : 29.160 172.706   4705
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.60 (0.23), residues: 1230
  helix:  2.33 (0.18), residues: 767
  sheet:  0.25 (0.63), residues: 67
  loop :  0.90 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  17 
 TYR   0.019   0.002   TYR K1503 
 PHE   0.014   0.002   PHE A  67 
 TRP   0.019   0.002   TRP K1502 
 HIS   0.011   0.002   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00467 /  0.24 (17106)
  covalent geometry    : angle       0.73238 /  0.40 (24363)
  hydrogen bonds       : bond        0.08322 /  5.70 (  867)
  hydrogen bonds       : angle       3.57351 /  2.52 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: K 1160 MET cc_start: 0.7236 (tmm) cc_final: 0.6917 (ptt)
REVERT: K 1691 MET cc_start: 0.7503 (ptp) cc_final: 0.6532 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0880
  time to fit residues: 4.3336
Evaluate side-chains
  25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 137 optimal weight:   30.0000
   chunk 83 optimal weight:   30.0000
   chunk 64 optimal weight:    0.8980
   chunk 144 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 117 optimal weight:   20.0000
   chunk 84 optimal weight:    4.9990
   chunk 107 optimal weight:   40.0000
   chunk 118 optimal weight:    7.9990
   overall best weight:    3.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  85 GLN
** K1297 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 = 0.3615 r_free = 0.3615 target = 0.047212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.033838 restraints weight = 242277.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.034539 restraints weight = 132534.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.034964 restraints weight = 88420.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.035210 restraints weight = 67323.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.035415 restraints weight = 57415.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  17106  Z= 0.176
  Angle     :  0.600   6.045  24363  Z= 0.350
  Chirality :  0.040   0.335   2714
  Planarity :  0.005   0.042   2077
  Dihedral  : 29.440 179.352   4705
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.22 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.72 (0.23), residues: 1230
  helix:  2.52 (0.18), residues: 767
  sheet:  0.09 (0.63), residues: 69
  loop :  0.79 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 134 
 TYR   0.025   0.002   TYR K1204 
 PHE   0.015   0.001   PHE K1358 
 TRP   0.007   0.001   TRP K1545 
 HIS   0.005   0.001   HIS K1297 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.18 (17106)
  covalent geometry    : angle       0.60018 /  0.35 (24363)
  hydrogen bonds       : bond        0.05376 /  3.64 (  867)
  hydrogen bonds       : angle       3.35352 /  2.38 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
REVERT: E  120 MET cc_start: 0.6691 (mmp) cc_final: 0.6470 (mmm)
REVERT: K 1133 MET cc_start: 0.7971 (ppp) cc_final: 0.7494 (ppp)
REVERT: K 1691 MET cc_start: 0.7547 (ptp) cc_final: 0.6714 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1022
  time to fit residues: 5.4168
Evaluate side-chains
  24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 146 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 68 optimal weight:    9.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN
H  67 ASN
** K1297 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 = 0.3607 r_free = 0.3607 target = 0.046988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.033804 restraints weight = 236090.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.034533 restraints weight = 130168.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.034919 restraints weight = 85777.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.035267 restraints weight = 65859.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.035386 restraints weight = 55033.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  17106  Z= 0.141
  Angle     :  0.563   6.525  24363  Z= 0.327
  Chirality :  0.039   0.358   2714
  Planarity :  0.004   0.040   2077
  Dihedral  : 29.442 176.893   4705
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.57 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.87 (0.24), residues: 1230
  helix:  2.64 (0.18), residues: 767
  sheet:  0.19 (0.64), residues: 69
  loop :  0.85 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K1202 
 TYR   0.015   0.001   TYR B  88 
 PHE   0.020   0.001   PHE K1397 
 TRP   0.005   0.001   TRP K1545 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.14 (17106)
  covalent geometry    : angle       0.56313 /  0.33 (24363)
  hydrogen bonds       : bond        0.05113 /  3.49 (  867)
  hydrogen bonds       : angle       3.13801 /  2.23 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 28
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: E  120 MET cc_start: 0.6728 (mmp) cc_final: 0.6491 (mmm)
REVERT: K 1691 MET cc_start: 0.7506 (ptp) cc_final: 0.6576 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 29
  average time/residue: 0.0997
  time to fit residues: 5.2412
Evaluate side-chains
  24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 122 optimal weight:   50.0000
   chunk 11 optimal weight:    3.9990
   chunk 147 optimal weight:   30.0000
   chunk 98 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 139 optimal weight:   30.0000
   chunk 106 optimal weight:   20.0000
   chunk 90 optimal weight:    0.5980
   chunk 117 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   overall best weight:    2.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K1146 GLN
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1343 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.046495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.032783 restraints weight = 207243.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.033341 restraints weight = 118424.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.033613 restraints weight = 82861.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.033780 restraints weight = 67659.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.033889 restraints weight = 61256.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  17106  Z= 0.144
  Angle     :  0.573   6.986  24363  Z= 0.330
  Chirality :  0.039   0.348   2714
  Planarity :  0.004   0.031   2077
  Dihedral  : 29.501 175.273   4705
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.89 (0.24), residues: 1230
  helix:  2.68 (0.18), residues: 767
  sheet:  0.07 (0.64), residues: 69
  loop :  0.80 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K1498 
 TYR   0.014   0.001   TYR K1198 
 PHE   0.018   0.001   PHE K1389 
 TRP   0.006   0.001   TRP K1158 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.14 (17106)
  covalent geometry    : angle       0.57263 /  0.33 (24363)
  hydrogen bonds       : bond        0.05057 /  3.45 (  867)
  hydrogen bonds       : angle       3.10057 /  2.21 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.469 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8355 (mmp) cc_final: 0.7633 (mmm)
REVERT: H   62 MET cc_start: 0.8803 (mmp) cc_final: 0.8569 (mmt)
REVERT: K 1193 MET cc_start: 0.7761 (tpt) cc_final: 0.7483 (tpt)
REVERT: K 1385 MET cc_start: 0.6312 (tpt) cc_final: 0.5501 (ppp)
REVERT: K 1691 MET cc_start: 0.7013 (ptp) cc_final: 0.5828 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0914
  time to fit residues: 4.5989
Evaluate side-chains
  24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 145 optimal weight:   20.0000
   chunk 12 optimal weight:    8.9990
   chunk 42 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0570
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 101 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    2.9104

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN
** K1297 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 = 0.3590 r_free = 0.3590 target = 0.045965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.032393 restraints weight = 212174.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.032788 restraints weight = 119136.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.033268 restraints weight = 82695.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.033411 restraints weight = 66386.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.033482 restraints weight = 59485.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17106  Z= 0.160
  Angle     :  0.589   6.401  24363  Z= 0.338
  Chirality :  0.040   0.348   2714
  Planarity :  0.004   0.032   2077
  Dihedral  : 29.654 174.551   4705
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.74 (0.24), residues: 1230
  helix:  2.55 (0.18), residues: 765
  sheet:  0.20 (0.63), residues: 67
  loop :  0.76 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K1202 
 TYR   0.015   0.001   TYR C  50 
 PHE   0.027   0.001   PHE K1397 
 TRP   0.033   0.003   TRP K1502 
 HIS   0.006   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.16 (17106)
  covalent geometry    : angle       0.58856 /  0.34 (24363)
  hydrogen bonds       : bond        0.05523 /  3.79 (  867)
  hydrogen bonds       : angle       3.22111 /  2.30 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B   84 MET cc_start: 0.8426 (tmm) cc_final: 0.8207 (tmm)
REVERT: E  120 MET cc_start: 0.8375 (mmp) cc_final: 0.7669 (mmm)
REVERT: K 1193 MET cc_start: 0.7473 (tpt) cc_final: 0.7174 (tpt)
REVERT: K 1385 MET cc_start: 0.6580 (tpt) cc_final: 0.6082 (ppp)
REVERT: K 1691 MET cc_start: 0.7158 (ptp) cc_final: 0.6018 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1033
  time to fit residues: 5.3041
Evaluate side-chains
  25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0170
   chunk 11 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 125 optimal weight:   20.0000
   chunk 61 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   overall best weight:    3.4026

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN
** K1297 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 = 0.3565 r_free = 0.3565 target = 0.045047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.031488 restraints weight = 210715.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.032027 restraints weight = 118873.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.032340 restraints weight = 82131.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.032453 restraints weight = 66234.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.032596 restraints weight = 60226.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17106  Z= 0.173
  Angle     :  0.611   6.442  24363  Z= 0.348
  Chirality :  0.040   0.337   2714
  Planarity :  0.004   0.038   2077
  Dihedral  : 29.863 173.193   4705
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.66 (0.23), residues: 1230
  helix:  2.46 (0.18), residues: 765
  sheet:  0.28 (0.64), residues: 66
  loop :  0.75 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG K1530 
 TYR   0.012   0.001   TYR D  40 
 PHE   0.017   0.001   PHE K1397 
 TRP   0.035   0.002   TRP K1502 
 HIS   0.020   0.002   HIS K1351 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.17 (17106)
  covalent geometry    : angle       0.61083 /  0.35 (24363)
  hydrogen bonds       : bond        0.05777 /  3.98 (  867)
  hydrogen bonds       : angle       3.29085 /  2.36 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.424 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8411 (mmp) cc_final: 0.8021 (mmm)
REVERT: K 1193 MET cc_start: 0.7471 (tpt) cc_final: 0.7174 (tpt)
REVERT: K 1385 MET cc_start: 0.6769 (tpt) cc_final: 0.6184 (ppp)
REVERT: K 1691 MET cc_start: 0.7214 (ptp) cc_final: 0.6087 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1065
  time to fit residues: 5.0279
Evaluate side-chains
  24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 106 optimal weight:    9.9990
   chunk 136 optimal weight:   50.0000
   chunk 139 optimal weight:   30.0000
   chunk 130 optimal weight:   40.0000
   chunk 101 optimal weight:    0.0040
   chunk 61 optimal weight:    1.9990
   chunk 119 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    4.8000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN
F  93 GLN
H  49 HIS
H  63 ASN
H  67 ASN
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1438 HIS
K1487 HIS
K1547 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.044082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.031346 restraints weight = 226130.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.031812 restraints weight = 122207.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.032022 restraints weight = 81456.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.032205 restraints weight = 65759.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.032265 restraints weight = 59134.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  17106  Z= 0.236
  Angle     :  0.714   7.397  24363  Z= 0.396
  Chirality :  0.044   0.327   2714
  Planarity :  0.005   0.042   2077
  Dihedral  : 30.452 171.077   4705
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 17.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  1.98 (0.23), residues: 1230
  helix:  1.91 (0.18), residues: 764
  sheet: -0.10 (0.63), residues: 68
  loop :  0.54 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG K1530 
 TYR   0.029   0.002   TYR B  88 
 PHE   0.014   0.002   PHE H  65 
 TRP   0.035   0.002   TRP K1502 
 HIS   0.008   0.002   HIS K1413 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00452 /  0.24 (17106)
  covalent geometry    : angle       0.71369 /  0.40 (24363)
  hydrogen bonds       : bond        0.08178 /  5.66 (  867)
  hydrogen bonds       : angle       3.74677 /  2.70 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.7769 (m-10) cc_final: 0.7532 (m-10)
REVERT: E  120 MET cc_start: 0.8411 (mmp) cc_final: 0.7899 (mmm)
REVERT: K 1133 MET cc_start: 0.6796 (ppp) cc_final: 0.6238 (ppp)
REVERT: K 1193 MET cc_start: 0.7596 (tpt) cc_final: 0.7286 (tpt)
REVERT: K 1691 MET cc_start: 0.7343 (ptp) cc_final: 0.6230 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1256
  time to fit residues: 5.7382
Evaluate side-chains
  26 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 124 optimal weight:   30.0000
   chunk 43 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 141 optimal weight:   30.0000
   chunk 71 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 82 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 131 optimal weight:   20.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN
** K1297 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 = 0.3512 r_free = 0.3512 target = 0.043421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.029884 restraints weight = 212460.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.030390 restraints weight = 120201.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.030626 restraints weight = 83429.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.030721 restraints weight = 68330.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 60)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.030885 restraints weight = 61177.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.5070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  17106  Z= 0.182
  Angle     :  0.653   6.492  24363  Z= 0.367
  Chirality :  0.043   0.317   2714
  Planarity :  0.004   0.034   2077
  Dihedral  : 30.554 170.770   4705
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.15 (0.23), residues: 1230
  helix:  2.09 (0.18), residues: 764
  sheet:  0.08 (0.66), residues: 63
  loop :  0.48 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  19 
 TYR   0.014   0.002   TYR D  37 
 PHE   0.009   0.001   PHE H  65 
 TRP   0.033   0.002   TRP K1502 
 HIS   0.010   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.18 (17106)
  covalent geometry    : angle       0.65271 /  0.37 (24363)
  hydrogen bonds       : bond        0.06149 /  4.22 (  867)
  hydrogen bonds       : angle       3.54662 /  2.56 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.489 
Fit side-chains
REVERT: B   84 MET cc_start: 0.8392 (tmm) cc_final: 0.8164 (tmm)
REVERT: B   88 TYR cc_start: 0.7845 (m-10) cc_final: 0.7609 (m-10)
REVERT: E  120 MET cc_start: 0.8582 (mmp) cc_final: 0.7952 (mmm)
REVERT: K 1133 MET cc_start: 0.6109 (ppp) cc_final: 0.5810 (ppp)
REVERT: K 1193 MET cc_start: 0.7240 (tpt) cc_final: 0.6977 (tpt)
REVERT: K 1232 ASN cc_start: -0.0797 (m-40) cc_final: -0.1081 (p0)
REVERT: K 1691 MET cc_start: 0.7272 (ptp) cc_final: 0.6117 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1132
  time to fit residues: 5.6596
Evaluate side-chains
  26 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 122 optimal weight:   50.0000
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 140 optimal weight:   30.0000
   chunk 2 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 108 optimal weight:   30.0000
   chunk 25 optimal weight:    0.2980
   chunk 24 optimal weight:    5.9990
   overall best weight:    3.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN
** K1297 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 = 0.3503 r_free = 0.3503 target = 0.043158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.029860 restraints weight = 215546.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.030246 restraints weight = 122026.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.030389 restraints weight = 86449.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.030750 restraints weight = 73104.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.030835 restraints weight = 64841.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.5316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  17106  Z= 0.178
  Angle     :  0.646   6.741  24363  Z= 0.363
  Chirality :  0.042   0.310   2714
  Planarity :  0.004   0.033   2077
  Dihedral  : 30.572 171.239   4705
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.25 (0.23), residues: 1230
  helix:  2.16 (0.18), residues: 764
  sheet:  0.07 (0.66), residues: 63
  loop :  0.53 (0.31), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  19 
 TYR   0.013   0.002   TYR K1539 
 PHE   0.010   0.001   PHE K1161 
 TRP   0.033   0.002   TRP K1502 
 HIS   0.008   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.18 (17106)
  covalent geometry    : angle       0.64594 /  0.36 (24363)
  hydrogen bonds       : bond        0.06333 /  4.37 (  867)
  hydrogen bonds       : angle       3.50865 /  2.54 ( 2289)

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.467 
Fit side-chains
REVERT: B   84 MET cc_start: 0.8322 (tmm) cc_final: 0.8106 (tmm)
REVERT: B   88 TYR cc_start: 0.7843 (m-10) cc_final: 0.7548 (m-10)
REVERT: E  120 MET cc_start: 0.8485 (mmp) cc_final: 0.7852 (mmm)
REVERT: K 1193 MET cc_start: 0.7189 (tpt) cc_final: 0.6930 (tpt)
REVERT: K 1232 ASN cc_start: -0.0771 (m-40) cc_final: -0.1102 (p0)
REVERT: K 1691 MET cc_start: 0.7485 (ptp) cc_final: 0.6365 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.1076
  time to fit residues: 5.3195
Evaluate side-chains
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 79 optimal weight:   20.0000
   chunk 134 optimal weight:   40.0000
   chunk 55 optimal weight:    0.6980
   chunk 22 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 127 optimal weight:   30.0000
   chunk 68 optimal weight:    5.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    3.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  63 ASN
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1438 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.042988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.029734 restraints weight = 215677.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.030165 restraints weight = 121848.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.030429 restraints weight = 84560.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.030649 restraints weight = 69349.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.030697 restraints weight = 62442.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.5485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  17106  Z= 0.165
  Angle     :  0.630   6.479  24363  Z= 0.357
  Chirality :  0.042   0.313   2714
  Planarity :  0.004   0.033   2077
  Dihedral  : 30.587 172.664   4705
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    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:  2.29 (0.24), residues: 1230
  helix:  2.19 (0.18), residues: 765
  sheet:  0.09 (0.67), residues: 63
  loop :  0.57 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 116 
 TYR   0.013   0.002   TYR D  40 
 PHE   0.011   0.001   PHE K1511 
 TRP   0.028   0.002   TRP K1502 
 HIS   0.009   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.16 (17106)
  covalent geometry    : angle       0.63017 /  0.36 (24363)
  hydrogen bonds       : bond        0.05720 /  3.94 (  867)
  hydrogen bonds       : angle       3.44912 /  2.49 ( 2289)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2871.83 seconds
wall clock time: 50 minutes 9.47 seconds (3009.47 seconds total)