Starting phenix.real_space_refine
on Sat Jun 14 11:55:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8han_34597/06_2025/8han_34597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8han_34597/06_2025/8han_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8han_34597/06_2025/8han_34597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8han_34597/06_2025/8han_34597.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8han_34597/06_2025/8han_34597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8han_34597/06_2025/8han_34597.cif"
  }
  resolution = 4.2
  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=   0.003
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 3, 'ARG:plan': 2}
          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: 9.34, per 1000 atoms: 0.58
  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: 3.93
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 6.91
  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: 8.04

  Time building geometry restraints manager: 4.67 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=" 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 4.31e+00
  bond pdb=" C3'  DT I 136 "
       pdb=" O3'  DT I 136 "
    ideal  model  delta    sigma   weight residual
    1.422  1.467 -0.045 3.00e-02 1.11e+03 2.25e+00
  bond pdb=" C3'  DA J  59 "
       pdb=" O3'  DA J  59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.45e+00
  bond pdb=" N   ARG K1514 "
       pdb=" CA  ARG K1514 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.015 1.29e-02 6.01e+03 1.39e+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 1.21e+00
  ... (remaining 17101 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 23876
        1.66 -     3.31: 443
        3.31 -     4.97: 37
        4.97 -     6.63: 4
        6.63 -     8.28: 3
  Bond angle restraints: 24363
  Sorted by residual:
  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=" C   ARG E  49 "
        pdb=" N   GLU E  50 "
        pdb=" CA  GLU E  50 "
      ideal   model   delta    sigma   weight residual
     120.72  116.05    4.67 1.67e+00 3.59e-01 7.81e+00
  angle pdb=" N   GLU E  50 "
        pdb=" CA  GLU E  50 "
        pdb=" CB  GLU E  50 "
      ideal   model   delta    sigma   weight residual
     110.39  114.44   -4.05 1.66e+00 3.63e-01 5.95e+00
  angle pdb=" N   ALY B  12 "
        pdb=" CA  ALY B  12 "
        pdb=" CB  ALY B  12 "
      ideal   model   delta    sigma   weight residual
     110.50  114.61   -4.11 1.70e+00 3.46e-01 5.84e+00
  angle pdb=" CB  MET E  90 "
        pdb=" CG  MET E  90 "
        pdb=" SD  MET E  90 "
      ideal   model   delta    sigma   weight residual
     112.70  119.88   -7.18 3.00e+00 1.11e-01 5.73e+00
  ... (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 -    0.030: 1995
       0.030 -    0.060: 537
       0.060 -    0.089: 108
       0.089 -    0.119: 61
       0.119 -    0.149: 13
  Chirality restraints: 2714
  Sorted by residual:
  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
  chirality pdb=" CG  LEU A  92 "
            pdb=" CB  LEU A  92 "
            pdb=" CD1 LEU A  92 "
            pdb=" CD2 LEU A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.94e-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       2.35   -2.49   -0.14 2.00e-01 2.50e+01 4.94e-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:             0.720
  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:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     44.120
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
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   0.045  17106  Z= 0.136
  Angle     :  0.536   8.284  24363  Z= 0.330
  Chirality :  0.032   0.149   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 (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:  2.88 (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
 TRP   0.009   0.001   TRP K1502 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.007   0.001   PHE K1484 
 TYR   0.019   0.001   TYR K1102 
 ARG   0.007   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11059 (  867)
  hydrogen bonds       : angle       3.83435 ( 2289)
  covalent geometry    : bond        0.00266 (17106)
  covalent geometry    : angle       0.53630 (24363)

*********************** 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  : 2.596 
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: 0.3523
  time to fit residues: 18.3928
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  : 1.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 113 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 117 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    0.5980
   chunk 136 optimal weight:   10.0000
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1628 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.050500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.036745 restraints weight = 233919.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.037475 restraints weight = 129561.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.038071 restraints weight = 86779.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  17106  Z= 0.140
  Angle     :  0.509   5.879  24363  Z= 0.299
  Chirality :  0.033   0.150   2714
  Planarity :  0.003   0.033   2077
  Dihedral  : 28.472 170.382   4705
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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:  3.04 (0.24), residues: 1230
  helix:  2.73 (0.18), residues: 766
  sheet:  0.36 (0.63), residues: 66
  loop :  0.98 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP K1502 
 HIS   0.005   0.001   HIS A 113 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.014   0.001   TYR K1102 
 ARG   0.005   0.000   ARG G  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04495 (  867)
  hydrogen bonds       : angle       3.00747 ( 2289)
  covalent geometry    : bond        0.00297 (17106)
  covalent geometry    : angle       0.50900 (24363)

*********************** 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
  29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
REVERT: K 1160 MET cc_start: 0.7184 (tmm) cc_final: 0.6866 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.3302
  time to fit residues: 18.3055
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  : 1.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 102 optimal weight:   30.0000
   chunk 86 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 129 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 148 optimal weight:    8.9990
   chunk 136 optimal weight:   10.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** E  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  49 HIS
H  95 GLN
K1146 GLN
K1291 HIS
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.044207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.031356 restraints weight = 226462.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.031865 restraints weight = 124933.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.032109 restraints weight = 85010.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.083  17106  Z= 0.394
  Angle     :  0.821  10.028  24363  Z= 0.463
  Chirality :  0.046   0.162   2714
  Planarity :  0.007   0.071   2077
  Dihedral  : 30.027 176.167   4705
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.52 %
    Favored  : 96.20 %
  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:  1.51 (0.22), residues: 1230
  helix:  1.47 (0.17), residues: 764
  sheet: -0.09 (0.63), residues: 68
  loop :  0.49 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K1676 
 HIS   0.013   0.003   HIS K1297 
 PHE   0.020   0.003   PHE G  25 
 TYR   0.035   0.003   TYR B  88 
 ARG   0.010   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10095 (  867)
  hydrogen bonds       : angle       4.20515 ( 2289)
  covalent geometry    : bond        0.00847 (17106)
  covalent geometry    : angle       0.82096 (24363)

*********************** 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
  33 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 2.188 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8560 (mmp) cc_final: 0.7808 (mmm)
REVERT: K 1133 MET cc_start: 0.6647 (ppp) cc_final: 0.6166 (ppp)
REVERT: K 1193 MET cc_start: 0.7723 (tpt) cc_final: 0.7425 (tpt)
REVERT: K 1691 MET cc_start: 0.7387 (ptp) cc_final: 0.6156 (tmm)
  outliers start: 3
  outliers final: 2
  residues processed: 33
  average time/residue: 0.3232
  time to fit residues: 19.3837
Evaluate side-chains
  28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 1.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 130 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 81 optimal weight:    7.9990
   chunk 121 optimal weight:   20.0000
   chunk 109 optimal weight:   10.0000
   chunk 94 optimal weight:   20.0000
   chunk 21 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 140 optimal weight:    5.9990
   chunk 128 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1343 ASN
K1487 HIS
K1547 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.044847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.031820 restraints weight = 221903.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.032298 restraints weight = 119688.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.032587 restraints weight = 80238.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  17106  Z= 0.209
  Angle     :  0.608   6.353  24363  Z= 0.353
  Chirality :  0.037   0.148   2714
  Planarity :  0.005   0.080   2077
  Dihedral  : 30.251 178.250   4705
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  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:  2.11 (0.23), residues: 1230
  helix:  2.01 (0.18), residues: 766
  sheet:  0.17 (0.65), residues: 66
  loop :  0.55 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K1302 
 HIS   0.008   0.002   HIS K1351 
 PHE   0.032   0.002   PHE E 104 
 TYR   0.011   0.001   TYR D  40 
 ARG   0.007   0.001   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05172 (  867)
  hydrogen bonds       : angle       3.45468 ( 2289)
  covalent geometry    : bond        0.00452 (17106)
  covalent geometry    : angle       0.60800 (24363)

*********************** 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
  30 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 2.489 
Fit side-chains
   revert: symmetry clash
REVERT: E  120 MET cc_start: 0.8483 (mmp) cc_final: 0.7749 (mmm)
REVERT: K 1133 MET cc_start: 0.6240 (ppp) cc_final: 0.5874 (ppp)
REVERT: K 1193 MET cc_start: 0.7895 (tpt) cc_final: 0.7690 (tpt)
REVERT: K 1232 ASN cc_start: -0.0474 (m-40) cc_final: -0.0733 (p0)
REVERT: K 1691 MET cc_start: 0.7277 (ptp) cc_final: 0.6126 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.3394
  time to fit residues: 19.2668
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  : 3.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 98 optimal weight:   20.0000
   chunk 119 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 134 optimal weight:   10.0000
   chunk 1 optimal weight:    7.9990
   chunk 27 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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**
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1438 HIS ** 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 = 0.3517 r_free = 0.3517 target = 0.044189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.031354 restraints weight = 226447.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.031809 restraints weight = 121881.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.032080 restraints weight = 81701.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  17106  Z= 0.212
  Angle     :  0.604   6.188  24363  Z= 0.351
  Chirality :  0.036   0.144   2714
  Planarity :  0.004   0.036   2077
  Dihedral  : 30.153 179.354   4705
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  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:  2.23 (0.24), residues: 1230
  helix:  2.06 (0.18), residues: 767
  sheet:  0.12 (0.65), residues: 66
  loop :  0.71 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP K1502 
 HIS   0.009   0.002   HIS E 113 
 PHE   0.011   0.001   PHE K1397 
 TYR   0.014   0.002   TYR K1204 
 ARG   0.005   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06154 (  867)
  hydrogen bonds       : angle       3.41848 ( 2289)
  covalent geometry    : bond        0.00465 (17106)
  covalent geometry    : angle       0.60432 (24363)

*********************** 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
  33 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.523 
Fit side-chains
   revert: symmetry clash
REVERT: E  120 MET cc_start: 0.8485 (mmp) cc_final: 0.7968 (mmm)
REVERT: K 1133 MET cc_start: 0.6091 (ppp) cc_final: 0.5773 (ppp)
REVERT: K 1193 MET cc_start: 0.7755 (tpt) cc_final: 0.7499 (tpp)
REVERT: K 1232 ASN cc_start: -0.0508 (m-40) cc_final: -0.0785 (p0)
REVERT: K 1691 MET cc_start: 0.7369 (ptp) cc_final: 0.6259 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.3443
  time to fit residues: 19.7190
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  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 145 optimal weight:    6.9990
   chunk 135 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 133 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 9 optimal weight:   30.0000
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3528 r_free = 0.3528 target = 0.043963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.030367 restraints weight = 214878.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.030734 restraints weight = 122777.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.031134 restraints weight = 87298.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.4958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17106  Z= 0.154
  Angle     :  0.557   6.390  24363  Z= 0.326
  Chirality :  0.034   0.146   2714
  Planarity :  0.004   0.036   2077
  Dihedral  : 30.099 177.150   4705
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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:  2.53 (0.24), residues: 1230
  helix:  2.37 (0.18), residues: 764
  sheet: -0.09 (0.64), residues: 68
  loop :  0.76 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1686 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.012   0.001   PHE K1397 
 TYR   0.011   0.001   TYR D  40 
 ARG   0.003   0.000   ARG K1498 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  867)
  hydrogen bonds       : angle       3.16104 ( 2289)
  covalent geometry    : bond        0.00332 (17106)
  covalent geometry    : angle       0.55747 (24363)

*********************** 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  : 1.651 
Fit side-chains
   revert: symmetry clash
REVERT: E  120 MET cc_start: 0.8305 (mmp) cc_final: 0.7794 (mmm)
REVERT: K 1133 MET cc_start: 0.6286 (ppp) cc_final: 0.6042 (ppp)
REVERT: K 1193 MET cc_start: 0.7693 (tpt) cc_final: 0.7436 (tpt)
REVERT: K 1232 ASN cc_start: -0.0894 (m-40) cc_final: -0.1233 (p0)
REVERT: K 1691 MET cc_start: 0.7433 (ptp) cc_final: 0.6465 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.3893
  time to fit residues: 19.0574
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  : 3.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 147 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 110 optimal weight:   20.0000
   chunk 148 optimal weight:   10.0000
   chunk 102 optimal weight:   10.0000
   chunk 105 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 37 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
F  93 GLN
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1337 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.041622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.029371 restraints weight = 239507.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.029726 restraints weight = 130808.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.029966 restraints weight = 88259.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.6514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.075  17106  Z= 0.419
  Angle     :  0.811  11.860  24363  Z= 0.456
  Chirality :  0.045   0.170   2714
  Planarity :  0.007   0.059   2077
  Dihedral  : 31.159 179.812   4705
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 24.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  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:  1.14 (0.23), residues: 1230
  helix:  1.23 (0.17), residues: 770
  sheet: -0.55 (0.62), residues: 74
  loop :  0.28 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K1158 
 HIS   0.012   0.003   HIS K1235 
 PHE   0.021   0.003   PHE E 104 
 TYR   0.025   0.003   TYR C  39 
 ARG   0.011   0.001   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10213 (  867)
  hydrogen bonds       : angle       4.38585 ( 2289)
  covalent geometry    : bond        0.00908 (17106)
  covalent geometry    : angle       0.81085 (24363)

*********************** 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
  29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 1.502 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.7725 (m-10) cc_final: 0.7500 (m-10)
REVERT: E  120 MET cc_start: 0.8597 (mmp) cc_final: 0.7997 (mmm)
REVERT: K 1133 MET cc_start: 0.7295 (ppp) cc_final: 0.6791 (ppp)
REVERT: K 1691 MET cc_start: 0.7549 (ptp) cc_final: 0.6438 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 29
  average time/residue: 0.2662
  time to fit residues: 13.5158
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  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 136 optimal weight:   10.0000
   chunk 128 optimal weight:    3.9990
   chunk 124 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 99 optimal weight:    8.9990
   chunk 100 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 116 optimal weight:   30.0000
   chunk 72 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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**
** K1297 HIS ** 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 = 0.3469 r_free = 0.3469 target = 0.042399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.029866 restraints weight = 231062.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.030335 restraints weight = 126985.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.030633 restraints weight = 86105.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.6506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.081  17106  Z= 0.255
  Angle     :  0.663   7.413  24363  Z= 0.380
  Chirality :  0.038   0.163   2714
  Planarity :  0.005   0.038   2077
  Dihedral  : 31.192 175.358   4705
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  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:  1.46 (0.23), residues: 1230
  helix:  1.58 (0.18), residues: 768
  sheet: -0.65 (0.61), residues: 74
  loop :  0.24 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP K1502 
 HIS   0.010   0.002   HIS B  75 
 PHE   0.013   0.002   PHE K1511 
 TYR   0.016   0.002   TYR K1102 
 ARG   0.004   0.001   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06975 (  867)
  hydrogen bonds       : angle       3.88687 ( 2289)
  covalent geometry    : bond        0.00557 (17106)
  covalent geometry    : angle       0.66340 (24363)

*********************** 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
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 1.359 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.7710 (m-10) cc_final: 0.7407 (m-10)
REVERT: E  120 MET cc_start: 0.8718 (mmp) cc_final: 0.8224 (mmm)
REVERT: K 1691 MET cc_start: 0.7507 (ptp) cc_final: 0.6459 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.2350
  time to fit residues: 11.9206
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  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 42 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 115 optimal weight:    9.9990
   chunk 125 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 117 optimal weight:   30.0000
   chunk 15 optimal weight:    1.9990
   chunk 93 optimal weight:    8.9990
   overall best weight:    4.3788

-------------------------------------------------------------------------------
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**
** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1297 HIS ** 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 = 0.3466 r_free = 0.3466 target = 0.042217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.029783 restraints weight = 233315.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.030221 restraints weight = 127054.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.030451 restraints weight = 86189.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.6787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  17106  Z= 0.255
  Angle     :  0.668   7.199  24363  Z= 0.384
  Chirality :  0.038   0.155   2714
  Planarity :  0.005   0.038   2077
  Dihedral  : 31.150 175.752   4705
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 17.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  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 (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:  1.40 (0.24), residues: 1230
  helix:  1.56 (0.18), residues: 770
  sheet: -0.73 (0.64), residues: 68
  loop :  0.14 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP K1502 
 HIS   0.009   0.002   HIS B  75 
 PHE   0.021   0.002   PHE K1399 
 TYR   0.016   0.002   TYR D  40 
 ARG   0.005   0.001   ARG G  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06962 (  867)
  hydrogen bonds       : angle       3.93596 ( 2289)
  covalent geometry    : bond        0.00557 (17106)
  covalent geometry    : angle       0.66848 (24363)

*********************** 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
  25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 1.759 
Fit side-chains
REVERT: E   90 MET cc_start: 0.8727 (tpp) cc_final: 0.8422 (tpp)
REVERT: E  120 MET cc_start: 0.8763 (mmp) cc_final: 0.8269 (mmm)
REVERT: K 1193 MET cc_start: 0.7272 (tpt) cc_final: 0.6988 (tpt)
REVERT: K 1691 MET cc_start: 0.7647 (ptp) cc_final: 0.6680 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.3032
  time to fit residues: 15.1094
Evaluate side-chains
  23 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 1.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 124 optimal weight:    7.9990
   chunk 125 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 72 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 87 optimal weight:    8.9990
   chunk 107 optimal weight:   30.0000
   chunk 61 optimal weight:    1.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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**
** K1297 HIS ** 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 = 0.3480 r_free = 0.3480 target = 0.042709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.030226 restraints weight = 229778.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.030571 restraints weight = 124134.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.030858 restraints weight = 84259.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.6730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094  17106  Z= 0.187
  Angle     :  0.629  10.888  24363  Z= 0.362
  Chirality :  0.036   0.157   2714
  Planarity :  0.004   0.041   2077
  Dihedral  : 30.964 174.008   4705
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  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:  1.75 (0.24), residues: 1230
  helix:  1.85 (0.18), residues: 773
  sheet: -0.61 (0.65), residues: 68
  loop :  0.22 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP K1502 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.022   0.001   PHE K1399 
 TYR   0.014   0.002   TYR D  40 
 ARG   0.003   0.000   ARG G  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05468 (  867)
  hydrogen bonds       : angle       3.67176 ( 2289)
  covalent geometry    : bond        0.00410 (17106)
  covalent geometry    : angle       0.62949 (24363)

********************** 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
  28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 1.529 
Fit side-chains
REVERT: B   84 MET cc_start: 0.8105 (tmm) cc_final: 0.7894 (tmm)
REVERT: B   88 TYR cc_start: 0.7686 (m-10) cc_final: 0.7356 (m-10)
REVERT: E  120 MET cc_start: 0.8732 (mmp) cc_final: 0.8239 (mmm)
REVERT: K 1193 MET cc_start: 0.7296 (tpt) cc_final: 0.7034 (tpt)
REVERT: K 1691 MET cc_start: 0.7592 (ptp) cc_final: 0.6602 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.2738
  time to fit residues: 14.4993
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  : 3.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 119 optimal weight:    5.9990
   chunk 138 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0570
   chunk 147 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 73 optimal weight:    7.9990
   chunk 123 optimal weight:   10.0000
   chunk 118 optimal weight:    5.9990
   chunk 121 optimal weight:    7.9990
   overall best weight:    3.4106

-------------------------------------------------------------------------------
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**
** K1297 HIS ** 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 = 0.3469 r_free = 0.3469 target = 0.042317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.029915 restraints weight = 232301.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.030327 restraints weight = 126830.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.030574 restraints weight = 85310.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.6886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  17106  Z= 0.218
  Angle     :  0.648  16.340  24363  Z= 0.371
  Chirality :  0.036   0.154   2714
  Planarity :  0.004   0.042   2077
  Dihedral  : 30.916 174.997   4705
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 15.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  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:  1.73 (0.24), residues: 1230
  helix:  1.85 (0.18), residues: 768
  sheet: -0.56 (0.66), residues: 68
  loop :  0.18 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP K1502 
 HIS   0.009   0.001   HIS B  75 
 PHE   0.018   0.001   PHE K1399 
 TYR   0.015   0.002   TYR D  40 
 ARG   0.005   0.000   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06520 (  867)
  hydrogen bonds       : angle       3.73875 ( 2289)
  covalent geometry    : bond        0.00477 (17106)
  covalent geometry    : angle       0.64815 (24363)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5992.20 seconds
wall clock time: 110 minutes 12.89 seconds (6612.89 seconds total)