Starting phenix.real_space_refine
on Sat Jun 14 14:28:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hag_34588/06_2025/8hag_34588.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hag_34588/06_2025/8hag_34588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hag_34588/06_2025/8hag_34588.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hag_34588/06_2025/8hag_34588.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hag_34588/06_2025/8hag_34588.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hag_34588/06_2025/8hag_34588.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      47      5.16       5
     C    9427      2.51       5
     N    2985      2.21       5
     O    3614      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 129 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16367
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 714
          Classifications: {'peptide': 91}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'HIS:plan': 1, 'ALY:plan-2': 2, 'ALY:plan-1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 801
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    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: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    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: 751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 751
          Classifications: {'peptide': 97}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "K"
      Number of atoms: 4260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 4260
          Classifications: {'peptide': 516}
          Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 486}
          Chain breaks: 3
    Chain: "J"
      Number of atoms: 3012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3012
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "I"
      Number of atoms: 3015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3015
          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: 9.87, per 1000 atoms: 0.60
  Number of scatterers: 16367
  At special positions: 0
  Unit cell: (106.112, 163.313, 137.614, 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     294     15.00
     O    3614      8.00
     N    2985      7.00
     C    9427      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: 3.81
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2418

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 14 sheets defined
      62.4% alpha, 7.2% beta
      114 base pairs and 231 stacking pairs defined.
    Time for finding SS restraints: 6.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.510A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.749A  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 132
      removed outlier: 3.516A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.757A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.552A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.409A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.651A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.584A  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 120 through 131
      removed outlier: 3.636A  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 47 through 76
      removed outlier: 4.379A  pdb=" N   TYR F  51 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   GLU F  52 " --> pdb=" O   GLY F  48 " (cutoff:3.500A)
      removed outlier: 3.987A  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 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.184A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.816A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.659A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'K' and resid 1052 through 1067
      Proline residue:  K1060  - end of helix
    Processing helix  chain 'K' and resid 1072 through 1076
    Processing helix  chain 'K' and resid 1080 through 1085
    Processing helix  chain 'K' and resid 1088 through 1093
    Processing helix  chain 'K' and resid 1098 through 1108
    Processing helix  chain 'K' and resid 1113 through 1132
      removed outlier: 4.256A  pdb=" N   TYR K1117 " --> pdb=" O   GLU K1113 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1136 through 1160
      removed outlier: 4.031A  pdb=" N   ASP K1154 " --> pdb=" O   GLU K1150 " (cutoff:3.500A)
      Proline residue:  K1155  - end of helix
      removed outlier: 3.676A  pdb=" N   LEU K1160 " --> pdb=" O   VAL K1156 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1256 through 1260
    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 1344 through 1347
    Processing helix  chain 'K' and resid 1407 through 1429
      removed outlier: 4.535A  pdb=" N   THR K1411 " --> pdb=" O   LYS K1407 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ALA K1412 " --> pdb=" O   CYS K1408 " (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 1523
      removed outlier: 3.937A  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 1621 through 1625
    Processing helix  chain 'K' and resid 1626 through 1637
      removed outlier: 4.335A  pdb=" N   PHE K1630 " --> pdb=" O   GLY K1626 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1643 through 1663
      removed outlier: 3.524A  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: 6.886A  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: 6.535A  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: 7.470A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.633A  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: 7.471A  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 1169 through 1170
      removed outlier: 3.697A  pdb=" N   ASP K1240 " --> pdb=" O   PHE K1170 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1198 through 1200
    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: 6.676A  pdb=" N   ALA K1359 " --> pdb=" O   VAL K1326 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ALA K1328 " --> pdb=" O   THR K1357 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   THR K1357 " --> pdb=" O   ALA K1328 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   ASP K1330 " --> pdb=" O   TYR K1355 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   TYR K1355 " --> pdb=" O   ASP K1330 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   THR K1332 " --> pdb=" O   PHE K1353 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   PHE K1353 " --> pdb=" O   THR K1332 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE K1374 " --> pdb=" O   ALA K1362 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   GLU K1364 " --> pdb=" O   CYS K1372 " (cutoff:3.500A)
      removed outlier: 5.439A  pdb=" N   CYS K1372 " --> pdb=" O   GLU K1364 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE K1366 " --> pdb=" O   ASP K1370 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   ASP K1370 " --> pdb=" O   ILE K1366 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   PHE K1373 " --> pdb=" O   SER K1400 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   SER K1400 " --> pdb=" O   PHE K1373 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   GLY K1375 " --> pdb=" O   LEU K1398 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   LEU K1398 " --> pdb=" O   GLY K1375 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   HIS K1377 " --> pdb=" O   SER K1396 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG K1392 " --> pdb=" O   TYR K1381 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   TRP K1436 " --> pdb=" O   ILE K1395 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   TYR K1397 " --> pdb=" O   TRP K1436 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG K1599 " --> pdb=" O   ASP K1482 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASP K1482 " --> pdb=" O   ARG K1599 " (cutoff:3.500A)

    596 hydrogen bonds defined for protein.
    1758 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      270 hydrogen bonds
      536 hydrogen bond angles
      0 basepair planarities
      114 basepair parallelities
      231 stacking parallelities
  Total time for adding SS restraints: 7.55

  Time building geometry restraints manager: 4.57 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: 4033
        1.34 -     1.46: 4652
        1.46 -     1.58: 7950
        1.58 -     1.70: 586
        1.70 -     1.81: 70
  Bond restraints: 17291
  Sorted by residual:
  bond pdb=" NZ  ALY B  12 "
       pdb=" CH  ALY B  12 "
    ideal  model  delta    sigma   weight residual
    1.343  1.385 -0.042 2.00e-02 2.50e+03 4.39e+00
  bond pdb=" C3'  DT I 136 "
       pdb=" O3'  DT I 136 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.65e+00
  bond pdb=" CB  PRO E  38 "
       pdb=" CG  PRO E  38 "
    ideal  model  delta    sigma   weight residual
    1.492  1.554 -0.062 5.00e-02 4.00e+02 1.53e+00
  bond pdb=" CH  ALY B  12 "
       pdb=" OH  ALY B  12 "
    ideal  model  delta    sigma   weight residual
    1.225  1.247 -0.022 2.00e-02 2.50e+03 1.16e+00
  bond pdb=" CA  ASP B  24 "
       pdb=" CB  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.524  1.538 -0.014 1.31e-02 5.83e+03 1.16e+00
  ... (remaining 17286 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 24139
        1.90 -     3.80: 432
        3.80 -     5.70: 32
        5.70 -     7.60: 2
        7.60 -     9.50: 2
  Bond angle restraints: 24607
  Sorted by residual:
  angle pdb=" N   VAL B  21 "
        pdb=" CA  VAL B  21 "
        pdb=" C   VAL B  21 "
      ideal   model   delta    sigma   weight residual
     113.20  109.24    3.96 9.60e-01 1.09e+00 1.70e+01
  angle pdb=" N   ASP K1098 "
        pdb=" CA  ASP K1098 "
        pdb=" C   ASP K1098 "
      ideal   model   delta    sigma   weight residual
     108.34  113.26   -4.92 1.31e+00 5.83e-01 1.41e+01
  angle pdb=" CB  MET K1059 "
        pdb=" CG  MET K1059 "
        pdb=" SD  MET K1059 "
      ideal   model   delta    sigma   weight residual
     112.70  122.20   -9.50 3.00e+00 1.11e-01 1.00e+01
  angle pdb=" CB  MET A  90 "
        pdb=" CG  MET A  90 "
        pdb=" SD  MET A  90 "
      ideal   model   delta    sigma   weight residual
     112.70  120.71   -8.01 3.00e+00 1.11e-01 7.13e+00
  angle pdb=" CA  ARG K1494 "
        pdb=" CB  ARG K1494 "
        pdb=" CG  ARG K1494 "
      ideal   model   delta    sigma   weight residual
     114.10  118.92   -4.82 2.00e+00 2.50e-01 5.82e+00
  ... (remaining 24602 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.97: 8378
       34.97 -    69.93: 1349
       69.93 -   104.90: 27
      104.90 -   139.86: 1
      139.86 -   174.83: 2
  Dihedral angle restraints: 9757
    sinusoidal: 6011
      harmonic: 3746
  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   45.17  174.83     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   73.41  146.59     1      3.50e+01 8.16e-04 1.44e+01
  dihedral pdb=" CG  ARG C  77 "
           pdb=" CD  ARG C  77 "
           pdb=" NE  ARG C  77 "
           pdb=" CZ  ARG C  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.38  -44.38     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 9754 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 2048
       0.032 -    0.064: 533
       0.064 -    0.096: 108
       0.096 -    0.129: 51
       0.129 -    0.161: 2
  Chirality restraints: 2742
  Sorted by residual:
  chirality pdb=" CA  LEU A  65 "
            pdb=" N   LEU A  65 "
            pdb=" C   LEU A  65 "
            pdb=" CB  LEU A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  MET K1059 "
            pdb=" N   MET K1059 "
            pdb=" C   MET K1059 "
            pdb=" CB  MET K1059 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.46e-01
  chirality pdb=" CA  ILE B  46 "
            pdb=" N   ILE B  46 "
            pdb=" C   ILE B  46 "
            pdb=" CB  ILE B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 2739 not shown)

  Planarity restraints: 2112
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT J 108 "   -0.031 2.00e-02 2.50e+03   1.58e-02 6.20e+00
        pdb=" N1   DT J 108 "    0.034 2.00e-02 2.50e+03
        pdb=" C2   DT J 108 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2   DT J 108 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DT J 108 "    0.009 2.00e-02 2.50e+03
        pdb=" C4   DT J 108 "   -0.009 2.00e-02 2.50e+03
        pdb=" O4   DT J 108 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5   DT J 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT J 108 "    0.004 2.00e-02 2.50e+03
        pdb=" C6   DT J 108 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  83 "   -0.010 2.00e-02 2.50e+03   1.15e-02 2.62e+00
        pdb=" CG  TYR D  83 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  83 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  83 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  83 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  83 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  83 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR D  83 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO D 103 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2109 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1867
        2.76 -     3.29: 15531
        3.29 -     3.83: 31676
        3.83 -     4.36: 35346
        4.36 -     4.90: 53216
  Nonbonded interactions: 137636
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  16 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" NE2 HIS A 113 "
            pdb=" OD1 ASP E 123 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" NH2 ARG K1133 "
            pdb=" OP1  DG J 114 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   LEU C 115 "
            pdb=" NZ  LYS F  44 "
     model   vdw
     2.263 3.120
  ... (remaining 137631 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'
}
ncs_group {
  reference = (chain 'B' and resid 20 through 101)
  selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 21 through 101))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 14 through 117)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 31 through 124)
}
ncs_group {
  reference = (chain 'I' and resid 18 through 163)
  selection = (chain 'J' and resid 18 through 163)
}

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 individual isotropic
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:             2.660
  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:          0.650
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     42.440
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  17291  Z= 0.139
  Angle     :  0.560   9.502  24607  Z= 0.342
  Chirality :  0.033   0.161   2742
  Planarity :  0.003   0.040   2112
  Dihedral  : 24.831 174.830   7339
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.23), residues: 1255
  helix:  1.98 (0.19), residues: 759
  sheet:  1.13 (0.60), residues: 83
  loop :  0.51 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP K1115 
 HIS   0.012   0.001   HIS K1415 
 PHE   0.008   0.001   PHE K1090 
 TYR   0.028   0.001   TYR D  83 
 ARG   0.006   0.000   ARG H  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12109 (  866)
  hydrogen bonds       : angle       4.38763 ( 2294)
  covalent geometry    : bond        0.00276 (17291)
  covalent geometry    : angle       0.55995 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.278 
Fit side-chains
REVERT: A   41 TYR cc_start: 0.7741 (m-80) cc_final: 0.7497 (m-80)
REVERT: H   62 MET cc_start: 0.8981 (tpp) cc_final: 0.8334 (tpt)
REVERT: K 1124 MET cc_start: 0.6849 (mmp) cc_final: 0.6475 (mmm)
REVERT: K 1349 MET cc_start: 0.5182 (ttp) cc_final: 0.4886 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.2654
  time to fit residues: 41.6655
Evaluate side-chains
  70 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 2.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    7.9990
   chunk 115 optimal weight:    7.9990
   chunk 63 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 119 optimal weight:   30.0000
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 88 optimal weight:   20.0000
   chunk 138 optimal weight:   20.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
** D  49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS
K1451 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.085988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.049983 restraints weight = 85648.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 3.99
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.4459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.074  17291  Z= 0.363
  Angle     :  0.786   9.653  24607  Z= 0.438
  Chirality :  0.046   0.216   2742
  Planarity :  0.006   0.047   2112
  Dihedral  : 29.389 174.216   4739
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  6.33 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.22), residues: 1255
  helix:  1.31 (0.18), residues: 773
  sheet:  1.05 (0.59), residues: 71
  loop :  0.14 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K1509 
 HIS   0.013   0.002   HIS H  49 
 PHE   0.037   0.003   PHE K1200 
 TYR   0.035   0.003   TYR D  83 
 ARG   0.010   0.001   ARG F  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07204 (  866)
  hydrogen bonds       : angle       3.93072 ( 2294)
  covalent geometry    : bond        0.00834 (17291)
  covalent geometry    : angle       0.78595 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
REVERT: B   63 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8282 (mm-30)
REVERT: F   84 MET cc_start: 0.8927 (tpp) cc_final: 0.8613 (mmm)
REVERT: G   64 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8550 (tm-30)
REVERT: H   54 ILE cc_start: 0.8831 (mm) cc_final: 0.8527 (mm)
REVERT: K 1097 MET cc_start: 0.7293 (ppp) cc_final: 0.6417 (ppp)
REVERT: K 1124 MET cc_start: 0.6711 (mmp) cc_final: 0.6395 (mmm)
REVERT: K 1349 MET cc_start: 0.6530 (ttp) cc_final: 0.6186 (ttm)
REVERT: K 1652 MET cc_start: -0.2342 (mmt) cc_final: -0.2616 (mtp)
  outliers start: 18
  outliers final: 6
  residues processed: 90
  average time/residue: 0.2682
  time to fit residues: 37.3437
Evaluate side-chains
  58 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue  108 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:   40.0000
   chunk 32 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 141 optimal weight:    6.9990
   chunk 126 optimal weight:   10.0000
   chunk 91 optimal weight:   40.0000
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
K1415 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.087178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.051368 restraints weight = 84426.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 3.98
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  17291  Z= 0.146
  Angle     :  0.545   7.911  24607  Z= 0.317
  Chirality :  0.035   0.138   2742
  Planarity :  0.004   0.042   2112
  Dihedral  : 28.955 174.281   4739
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.24 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.23), residues: 1255
  helix:  1.95 (0.18), residues: 776
  sheet:  1.43 (0.66), residues: 61
  loop :  0.38 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K1466 
 HIS   0.006   0.001   HIS K1415 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.019   0.001   TYR D  83 
 ARG   0.004   0.000   ARG C  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04292 (  866)
  hydrogen bonds       : angle       3.13786 ( 2294)
  covalent geometry    : bond        0.00319 (17291)
  covalent geometry    : angle       0.54519 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 1.398 
Fit side-chains
REVERT: A   92 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9231 (mm)
REVERT: B   53 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7731 (mm-30)
REVERT: B   63 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8229 (mm-30)
REVERT: D   71 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8353 (mm-30)
REVERT: F   88 TYR cc_start: 0.8623 (m-10) cc_final: 0.8338 (m-80)
REVERT: G   64 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: H   54 ILE cc_start: 0.8913 (mm) cc_final: 0.8698 (mm)
REVERT: H   93 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8314 (mp0)
REVERT: K 1097 MET cc_start: 0.7298 (ppp) cc_final: 0.6452 (ppp)
REVERT: K 1124 MET cc_start: 0.6703 (mmp) cc_final: 0.6325 (mmm)
REVERT: K 1349 MET cc_start: 0.6922 (ttp) cc_final: 0.6589 (ttm)
  outliers start: 9
  outliers final: 4
  residues processed: 75
  average time/residue: 0.2573
  time to fit residues: 31.2554
Evaluate side-chains
  64 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 88 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 115 optimal weight:   20.0000
   chunk 38 optimal weight:    4.9990
   chunk 125 optimal weight:   10.0000
   chunk 84 optimal weight:   40.0000
   chunk 31 optimal weight:    0.6980
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS
K1236 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.084939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.048661 restraints weight = 84726.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 4.02
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.5083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  17291  Z= 0.225
  Angle     :  0.592   7.505  24607  Z= 0.341
  Chirality :  0.037   0.155   2742
  Planarity :  0.005   0.084   2112
  Dihedral  : 29.026 175.537   4739
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  8.69 %
    Favored  : 89.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.23), residues: 1255
  helix:  2.00 (0.18), residues: 783
  sheet:  1.31 (0.67), residues: 62
  loop :  0.28 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1509 
 HIS   0.010   0.001   HIS K1415 
 PHE   0.010   0.001   PHE E 104 
 TYR   0.022   0.001   TYR D  83 
 ARG   0.021   0.001   ARG K1055 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05183 (  866)
  hydrogen bonds       : angle       3.27900 ( 2294)
  covalent geometry    : bond        0.00514 (17291)
  covalent geometry    : angle       0.59205 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 1.471 
Fit side-chains
REVERT: B   53 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7697 (mm-30)
REVERT: G   64 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8327 (tm-30)
REVERT: H   93 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8239 (mp0)
REVERT: K 1097 MET cc_start: 0.7354 (ppp) cc_final: 0.6730 (ppp)
REVERT: K 1124 MET cc_start: 0.6702 (mmp) cc_final: 0.6267 (mmm)
REVERT: K 1349 MET cc_start: 0.7066 (ttp) cc_final: 0.6739 (ttm)
  outliers start: 16
  outliers final: 9
  residues processed: 68
  average time/residue: 0.2702
  time to fit residues: 30.5412
Evaluate side-chains
  59 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 123 optimal weight:   30.0000
   chunk 144 optimal weight:    6.9990
   chunk 78 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.085566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.049801 restraints weight = 86579.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 4.03
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17291  Z= 0.144
  Angle     :  0.528   5.772  24607  Z= 0.309
  Chirality :  0.034   0.140   2742
  Planarity :  0.004   0.041   2112
  Dihedral  : 28.920 175.259   4739
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.23 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.23), residues: 1255
  helix:  2.24 (0.18), residues: 783
  sheet:  1.45 (0.70), residues: 58
  loop :  0.34 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1466 
 HIS   0.006   0.001   HIS K1415 
 PHE   0.007   0.001   PHE H  70 
 TYR   0.015   0.001   TYR D  83 
 ARG   0.004   0.000   ARG K1055 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  866)
  hydrogen bonds       : angle       3.01858 ( 2294)
  covalent geometry    : bond        0.00316 (17291)
  covalent geometry    : angle       0.52836 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7513 (mm-30)
REVERT: G   91 GLU cc_start: 0.8267 (pp20) cc_final: 0.7852 (tm-30)
REVERT: H   54 ILE cc_start: 0.8996 (mm) cc_final: 0.8765 (mm)
REVERT: H   93 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8236 (mp0)
REVERT: K 1097 MET cc_start: 0.7315 (ppp) cc_final: 0.6728 (ppp)
REVERT: K 1124 MET cc_start: 0.6631 (mmp) cc_final: 0.6196 (mmm)
REVERT: K 1349 MET cc_start: 0.7251 (ttp) cc_final: 0.6940 (ttm)
  outliers start: 15
  outliers final: 9
  residues processed: 71
  average time/residue: 0.2478
  time to fit residues: 28.7167
Evaluate side-chains
  66 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain K residue 1470 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 147 optimal weight:    7.9990
   chunk 54 optimal weight:    9.9990
   chunk 9 optimal weight:   40.0000
   chunk 122 optimal weight:   40.0000
   chunk 7 optimal weight:    0.8980
   chunk 114 optimal weight:   30.0000
   chunk 62 optimal weight:    1.9990
   chunk 48 optimal weight:    0.4980
   chunk 107 optimal weight:   20.0000
   chunk 67 optimal weight:    0.8980
   chunk 95 optimal weight:   20.0000
   overall best weight:    2.4584

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

Flipped N/Q/H residues before XYZ refinement:
B  64 ASN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.084004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.048091 restraints weight = 86398.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 3.84
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.5683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  17291  Z= 0.197
  Angle     :  0.561   5.972  24607  Z= 0.326
  Chirality :  0.035   0.132   2742
  Planarity :  0.004   0.044   2112
  Dihedral  : 29.045 176.265   4739
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.86 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.24), residues: 1255
  helix:  2.18 (0.18), residues: 783
  sheet:  1.41 (0.72), residues: 58
  loop :  0.34 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K1509 
 HIS   0.007   0.001   HIS K1415 
 PHE   0.009   0.001   PHE K1090 
 TYR   0.016   0.001   TYR D  83 
 ARG   0.006   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04566 (  866)
  hydrogen bonds       : angle       3.12314 ( 2294)
  covalent geometry    : bond        0.00444 (17291)
  covalent geometry    : angle       0.56100 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 1.422 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7610 (mm-30)
REVERT: G   91 GLU cc_start: 0.8254 (pp20) cc_final: 0.7887 (tm-30)
REVERT: H   93 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8266 (mp0)
REVERT: K 1097 MET cc_start: 0.7247 (ppp) cc_final: 0.6697 (ppp)
REVERT: K 1124 MET cc_start: 0.6879 (mmp) cc_final: 0.6344 (mmm)
REVERT: K 1349 MET cc_start: 0.6074 (ttp) cc_final: 0.5646 (ttm)
  outliers start: 16
  outliers final: 12
  residues processed: 69
  average time/residue: 0.2407
  time to fit residues: 27.6221
Evaluate side-chains
  62 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 1.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain K residue 1470 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 126 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 97 optimal weight:   20.0000
   chunk 120 optimal weight:    0.7980
   chunk 90 optimal weight:    0.0470
   chunk 51 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 129 optimal weight:    8.9990
   chunk 6 optimal weight:    3.9990
   chunk 151 optimal weight:   10.0000
   chunk 112 optimal weight:    8.9990
   overall best weight:    2.1482

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

Flipped N/Q/H residues before XYZ refinement:
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.084054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.048142 restraints weight = 86029.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 3.81
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.5959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  17291  Z= 0.169
  Angle     :  0.543   6.265  24607  Z= 0.318
  Chirality :  0.035   0.160   2742
  Planarity :  0.004   0.041   2112
  Dihedral  : 29.005 176.643   4739
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 10.41 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.24), residues: 1255
  helix:  2.30 (0.19), residues: 783
  sheet:  1.38 (0.72), residues: 58
  loop :  0.38 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1466 
 HIS   0.005   0.001   HIS K1415 
 PHE   0.008   0.001   PHE E  78 
 TYR   0.010   0.001   TYR D  83 
 ARG   0.009   0.000   ARG K1055 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  866)
  hydrogen bonds       : angle       2.98567 ( 2294)
  covalent geometry    : bond        0.00378 (17291)
  covalent geometry    : angle       0.54288 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 1.462 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7598 (mm-30)
REVERT: G   91 GLU cc_start: 0.8206 (pp20) cc_final: 0.7903 (tm-30)
REVERT: H   93 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8257 (mp0)
REVERT: K 1097 MET cc_start: 0.7252 (ppp) cc_final: 0.6731 (ppp)
REVERT: K 1124 MET cc_start: 0.6869 (mmp) cc_final: 0.6350 (mmm)
REVERT: K 1349 MET cc_start: 0.5893 (ttp) cc_final: 0.5487 (ttm)
  outliers start: 16
  outliers final: 10
  residues processed: 68
  average time/residue: 0.2435
  time to fit residues: 27.4312
Evaluate side-chains
  62 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain K residue 1470 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 134 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 37 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 98 optimal weight:   30.0000
   chunk 76 optimal weight:    9.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.084138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.048162 restraints weight = 85776.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 3.93
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.6076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  17291  Z= 0.155
  Angle     :  0.539   8.159  24607  Z= 0.314
  Chirality :  0.034   0.206   2742
  Planarity :  0.004   0.041   2112
  Dihedral  : 28.992 177.300   4739
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.86 %
    Favored  : 87.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.24), residues: 1255
  helix:  2.35 (0.18), residues: 783
  sheet:  1.31 (0.71), residues: 58
  loop :  0.39 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1466 
 HIS   0.005   0.001   HIS K1415 
 PHE   0.008   0.001   PHE K1090 
 TYR   0.012   0.001   TYR D  83 
 ARG   0.004   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  866)
  hydrogen bonds       : angle       2.96443 ( 2294)
  covalent geometry    : bond        0.00342 (17291)
  covalent geometry    : angle       0.53878 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 56
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7492 (mm-30)
REVERT: G   91 GLU cc_start: 0.8159 (pp20) cc_final: 0.7762 (tm-30)
REVERT: H   93 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8242 (mp0)
REVERT: K 1097 MET cc_start: 0.7262 (ppp) cc_final: 0.6826 (ppp)
REVERT: K 1124 MET cc_start: 0.6793 (mmp) cc_final: 0.6280 (mmm)
REVERT: K 1349 MET cc_start: 0.6716 (ttp) cc_final: 0.6355 (ttm)
  outliers start: 14
  outliers final: 12
  residues processed: 67
  average time/residue: 0.2442
  time to fit residues: 27.0985
Evaluate side-chains
  67 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Chi-restraints excluded: chain K residue 1470 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 126 optimal weight:   10.0000
   chunk 149 optimal weight:    7.9990
   chunk 129 optimal weight:    8.9990
   chunk 116 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 127 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 117 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 138 optimal weight:   20.0000
   chunk 8 optimal weight:    4.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** H  63 ASN ** 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 = 0.4056 r_free = 0.4056 target = 0.081348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.045165 restraints weight = 86515.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 3.94
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.6865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055  17291  Z= 0.318
  Angle     :  0.673   9.481  24607  Z= 0.383
  Chirality :  0.041   0.256   2742
  Planarity :  0.005   0.069   2112
  Dihedral  : 29.578 177.512   4739
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.04 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.23), residues: 1255
  helix:  1.81 (0.18), residues: 783
  sheet:  1.03 (0.70), residues: 58
  loop :  0.16 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K1129 
 HIS   0.006   0.001   HIS K1415 
 PHE   0.016   0.002   PHE E  78 
 TYR   0.018   0.002   TYR D  83 
 ARG   0.016   0.001   ARG K1055 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06306 (  866)
  hydrogen bonds       : angle       3.51139 ( 2294)
  covalent geometry    : bond        0.00729 (17291)
  covalent geometry    : angle       0.67333 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 1.445 
Fit side-chains
REVERT: F   25 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8293 (p0)
REVERT: H   93 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8305 (mp0)
REVERT: K 1097 MET cc_start: 0.6941 (ppp) cc_final: 0.6462 (ppp)
REVERT: K 1124 MET cc_start: 0.7064 (mmp) cc_final: 0.6632 (mmm)
REVERT: K 1349 MET cc_start: 0.6749 (ttp) cc_final: 0.6255 (ttm)
  outliers start: 14
  outliers final: 10
  residues processed: 63
  average time/residue: 0.2668
  time to fit residues: 27.7355
Evaluate side-chains
  59 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 1.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 141 optimal weight:    6.9990
   chunk 94 optimal weight:   40.0000
   chunk 99 optimal weight:   20.0000
   chunk 89 optimal weight:   30.0000
   chunk 88 optimal weight:    0.0770
   chunk 67 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0770
   chunk 140 optimal weight:    7.9990
   chunk 149 optimal weight:    6.9990
   chunk 133 optimal weight:    7.9990
   overall best weight:    3.0300

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

Flipped N/Q/H residues before XYZ refinement:
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.082011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.045871 restraints weight = 85737.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 3.83
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8613
moved from start:          0.6900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  17291  Z= 0.212
  Angle     :  0.595   8.793  24607  Z= 0.343
  Chirality :  0.036   0.148   2742
  Planarity :  0.004   0.063   2112
  Dihedral  : 29.511 178.253   4739
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.13 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.23), residues: 1255
  helix:  2.01 (0.18), residues: 777
  sheet:  0.97 (0.70), residues: 58
  loop :  0.17 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K1509 
 HIS   0.005   0.001   HIS K1415 
 PHE   0.017   0.001   PHE K1090 
 TYR   0.012   0.001   TYR D  83 
 ARG   0.007   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04698 (  866)
  hydrogen bonds       : angle       3.18977 ( 2294)
  covalent geometry    : bond        0.00483 (17291)
  covalent geometry    : angle       0.59470 (24607)

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

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

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2510 Ramachandran restraints generated.
    1255 Oldfield, 0 Emsley, 1255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 1.411 
Fit side-chains
   revert: symmetry clash
REVERT: G   91 GLU cc_start: 0.8263 (pp20) cc_final: 0.7865 (tm-30)
REVERT: H   93 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8298 (mp0)
REVERT: K 1097 MET cc_start: 0.6989 (ppp) cc_final: 0.6452 (ppp)
REVERT: K 1124 MET cc_start: 0.7248 (mmp) cc_final: 0.6750 (mmm)
REVERT: K 1349 MET cc_start: 0.6179 (ttp) cc_final: 0.5449 (ttm)
  outliers start: 14
  outliers final: 11
  residues processed: 65
  average time/residue: 0.2595
  time to fit residues: 28.0308
Evaluate side-chains
  63 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 1.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain H residue   93 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 126 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 148 optimal weight:    6.9990
   chunk 149 optimal weight:    7.9990
   chunk 137 optimal weight:   10.0000
   chunk 140 optimal weight:    8.9990
   chunk 45 optimal weight:    0.7980
   chunk 145 optimal weight:    6.9990
   chunk 91 optimal weight:   20.0000
   overall best weight:    2.3584

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

Flipped N/Q/H residues before XYZ refinement:
H  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.082295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.046252 restraints weight = 85597.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 3.82
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.6952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  17291  Z= 0.184
  Angle     :  0.576   8.180  24607  Z= 0.333
  Chirality :  0.035   0.252   2742
  Planarity :  0.004   0.052   2112
  Dihedral  : 29.431 177.461   4739
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 11.13 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.24), residues: 1255
  helix:  2.19 (0.19), residues: 776
  sheet:  0.85 (0.66), residues: 62
  loop :  0.19 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K1509 
 HIS   0.005   0.001   HIS K1415 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.011   0.001   TYR D  83 
 ARG   0.005   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  866)
  hydrogen bonds       : angle       3.09529 ( 2294)
  covalent geometry    : bond        0.00415 (17291)
  covalent geometry    : angle       0.57584 (24607)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9687.37 seconds
wall clock time: 166 minutes 25.53 seconds (9985.53 seconds total)