Starting phenix.real_space_refine
on Sun Aug 24 01:47:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8han_34597/08_2025/8han_34597.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8han_34597/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2025/8han_34597.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2025/8han_34597.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2025/8han_34597.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8han_34597/08_2025/8han_34597.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      45      5.16       5
     C    9330      2.51       5
     N    2940      2.21       5
     O    3571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16180
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 819
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 687
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 745
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "F"
      Number of atoms: 673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 673
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 730
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "K"
      Number of atoms: 4134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 4134
          Classifications: {'peptide': 500}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 468}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 22
    Chain: "I"
      Number of atoms: 3016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3016
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3011
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA C  14 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA C  14 " occ=0.00
  Time building chain proxies: 3.22, per 1000 atoms: 0.20
  Number of scatterers: 16180
  At special positions: 0
  Unit cell: (102.9, 127.89, 158.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      45     16.00
     P     294     15.00
     O    3571      8.00
     N    2940      7.00
     C    9330      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 483.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 2.12
  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: 2.51

  Time building geometry restraints manager: 1.67 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:                  0.010
  Normalize map: mean=0, sd=1:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.510
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.050
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.88 (0.24), residues: 1230
  helix:  2.68 (0.18), residues: 756
  sheet:  0.28 (0.63), residues: 66
  loop :  0.81 (0.30), residues: 408

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

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

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.450 
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: 0.0982
  time to fit residues: 5.0140
Evaluate side-chains
  24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.2980
   chunk 149 optimal weight:   10.0000
   overall best weight:    5.4588

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  95 GLN
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1628 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.044633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.031102 restraints weight = 212740.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.031502 restraints weight = 121742.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.031857 restraints weight = 87310.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.032020 restraints weight = 70972.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.032075 restraints weight = 64122.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  17106  Z= 0.328
  Angle     :  0.770   9.778  24363  Z= 0.433
  Chirality :  0.043   0.160   2714
  Planarity :  0.007   0.056   2077
  Dihedral  : 29.567 173.042   4705
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.80 %
    Favored  : 96.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.22), residues: 1230
  helix:  1.52 (0.17), residues: 765
  sheet:  0.07 (0.65), residues: 68
  loop :  0.62 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  35 
 TYR   0.018   0.002   TYR D  37 
 PHE   0.022   0.002   PHE A  67 
 TRP   0.019   0.003   TRP K1502 
 HIS   0.013   0.002   HIS K1297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00719 (17106)
  covalent geometry    : angle       0.76973 (24363)
  hydrogen bonds       : bond        0.09637 (  867)
  hydrogen bonds       : angle       3.88663 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: E  120 MET cc_start: 0.8016 (mmm) cc_final: 0.7597 (mmm)
REVERT: K 1160 MET cc_start: 0.7158 (tmm) cc_final: 0.6899 (ptm)
REVERT: K 1193 MET cc_start: 0.7694 (tpt) cc_final: 0.7412 (tpt)
REVERT: K 1691 MET cc_start: 0.7090 (ptp) cc_final: 0.5664 (tmm)
  outliers start: 1
  outliers final: 1
  residues processed: 32
  average time/residue: 0.0934
  time to fit residues: 5.4591
Evaluate side-chains
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 137 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 144 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 117 optimal weight:   30.0000
   chunk 84 optimal weight:    0.0040
   chunk 107 optimal weight:    8.9990
   chunk 118 optimal weight:   20.0000
   overall best weight:    2.6000

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

Flipped N/Q/H residues before XYZ refinement:
F  93 GLN
K1146 GLN
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1343 ASN
** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.046212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.033115 restraints weight = 223451.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.033563 restraints weight = 119139.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.033862 restraints weight = 80480.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.034088 restraints weight = 65140.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.034166 restraints weight = 58917.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17106  Z= 0.175
  Angle     :  0.566   6.195  24363  Z= 0.332
  Chirality :  0.035   0.146   2714
  Planarity :  0.004   0.069   2077
  Dihedral  : 29.736 179.780   4705
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.23), residues: 1230
  helix:  2.27 (0.18), residues: 765
  sheet:  0.22 (0.65), residues: 68
  loop :  0.68 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 134 
 TYR   0.018   0.001   TYR K1539 
 PHE   0.023   0.001   PHE E 104 
 TRP   0.019   0.001   TRP K1502 
 HIS   0.009   0.002   HIS K1351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (17106)
  covalent geometry    : angle       0.56643 (24363)
  hydrogen bonds       : bond        0.04671 (  867)
  hydrogen bonds       : angle       3.28354 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A  120 MET cc_start: 0.7754 (mtm) cc_final: 0.7434 (mpp)
REVERT: B   84 MET cc_start: 0.8448 (tmm) cc_final: 0.8221 (tmm)
REVERT: E  120 MET cc_start: 0.8047 (mmm) cc_final: 0.7554 (mmm)
REVERT: K 1193 MET cc_start: 0.7391 (tpt) cc_final: 0.7020 (tpt)
REVERT: K 1691 MET cc_start: 0.7277 (ptp) cc_final: 0.6091 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1059
  time to fit residues: 5.4673
Evaluate side-chains
  26 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 95 optimal weight:    0.4980
   chunk 109 optimal weight:    0.0670
   chunk 26 optimal weight:    0.0050
   chunk 72 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 146 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   overall best weight:    1.5136

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

Flipped N/Q/H residues before XYZ refinement:
H  49 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.045533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.032062 restraints weight = 210812.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.032475 restraints weight = 117816.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.032925 restraints weight = 83442.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.033036 restraints weight = 67723.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.033098 restraints weight = 60302.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17106  Z= 0.148
  Angle     :  0.537   6.273  24363  Z= 0.316
  Chirality :  0.034   0.146   2714
  Planarity :  0.004   0.033   2077
  Dihedral  : 29.440 178.093   4705
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.57 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.24), residues: 1230
  helix:  2.49 (0.18), residues: 765
  sheet:  0.12 (0.65), residues: 68
  loop :  0.77 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K1530 
 TYR   0.017   0.001   TYR C  50 
 PHE   0.013   0.001   PHE E 104 
 TRP   0.021   0.001   TRP K1502 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (17106)
  covalent geometry    : angle       0.53688 (24363)
  hydrogen bonds       : bond        0.04364 (  867)
  hydrogen bonds       : angle       3.03973 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8344 (tmm) cc_final: 0.8123 (tmm)
REVERT: E  120 MET cc_start: 0.8157 (mmm) cc_final: 0.7626 (mmm)
REVERT: K 1193 MET cc_start: 0.7498 (tpt) cc_final: 0.7144 (tpt)
REVERT: K 1691 MET cc_start: 0.7202 (ptp) cc_final: 0.6046 (tmm)
  outliers start: 1
  outliers final: 1
  residues processed: 31
  average time/residue: 0.1023
  time to fit residues: 5.3071
Evaluate side-chains
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 122 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 147 optimal weight:    7.9990
   chunk 98 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 139 optimal weight:    8.9990
   chunk 106 optimal weight:   30.0000
   chunk 90 optimal weight:    0.7980
   chunk 117 optimal weight:    0.0050
   chunk 4 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    3.7398

-------------------------------------------------------------------------------
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**
K1438 HIS
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 = 0.3524 r_free = 0.3524 target = 0.044314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.031497 restraints weight = 225064.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.031984 restraints weight = 121927.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.032211 restraints weight = 82605.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.032420 restraints weight = 67390.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.032582 restraints weight = 60055.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  17106  Z= 0.239
  Angle     :  0.633   6.320  24363  Z= 0.364
  Chirality :  0.037   0.150   2714
  Planarity :  0.005   0.040   2077
  Dihedral  : 29.945 179.200   4705
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.23), residues: 1230
  helix:  2.07 (0.18), residues: 766
  sheet:  0.01 (0.64), residues: 66
  loop :  0.63 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K1530 
 TYR   0.019   0.002   TYR B  88 
 PHE   0.010   0.002   PHE K1397 
 TRP   0.030   0.002   TRP K1502 
 HIS   0.008   0.002   HIS K1291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 (17106)
  covalent geometry    : angle       0.63321 (24363)
  hydrogen bonds       : bond        0.07183 (  867)
  hydrogen bonds       : angle       3.52224 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.504 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8222 (mmm) cc_final: 0.7667 (mmm)
REVERT: K 1193 MET cc_start: 0.7434 (tpt) cc_final: 0.7065 (tpt)
REVERT: K 1691 MET cc_start: 0.7413 (ptp) cc_final: 0.6295 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.1095
  time to fit residues: 6.0696
Evaluate side-chains
  25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 145 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 93 optimal weight:   30.0000
   chunk 46 optimal weight:    0.7980
   chunk 90 optimal weight:    8.9990
   chunk 72 optimal weight:    9.9990
   chunk 100 optimal weight:   20.0000
   chunk 101 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    3.3586

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.043441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.029897 restraints weight = 213383.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.030378 restraints weight = 120969.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.030627 restraints weight = 84991.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.030796 restraints weight = 70374.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.030872 restraints weight = 63486.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.5157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17106  Z= 0.197
  Angle     :  0.588   6.587  24363  Z= 0.341
  Chirality :  0.035   0.146   2714
  Planarity :  0.004   0.034   2077
  Dihedral  : 30.187 178.042   4705
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.24), residues: 1230
  helix:  2.26 (0.18), residues: 766
  sheet:  0.09 (0.66), residues: 63
  loop :  0.60 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  88 
 TYR   0.034   0.002   TYR B  88 
 PHE   0.010   0.001   PHE K1397 
 TRP   0.024   0.002   TRP K1502 
 HIS   0.008   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (17106)
  covalent geometry    : angle       0.58804 (24363)
  hydrogen bonds       : bond        0.05027 (  867)
  hydrogen bonds       : angle       3.36228 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.319 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.7659 (m-10) cc_final: 0.7440 (m-10)
REVERT: E  120 MET cc_start: 0.8313 (mmm) cc_final: 0.7750 (mmm)
REVERT: K 1133 MET cc_start: 0.6426 (ppp) cc_final: 0.6183 (ppp)
REVERT: K 1193 MET cc_start: 0.7200 (tpt) cc_final: 0.6928 (tpp)
REVERT: K 1232 ASN cc_start: -0.1061 (m-40) cc_final: -0.1411 (p0)
REVERT: K 1691 MET cc_start: 0.7408 (ptp) cc_final: 0.6348 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1035
  time to fit residues: 5.2677
Evaluate side-chains
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 110 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 125 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 46 optimal weight:    0.4980
   overall best weight:    2.0184

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3528 r_free = 0.3528 target = 0.043618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.030557 restraints weight = 215149.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.030979 restraints weight = 120464.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.031239 restraints weight = 84100.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.031412 restraints weight = 67617.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.031459 restraints weight = 61431.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  17106  Z= 0.159
  Angle     :  0.557   5.951  24363  Z= 0.325
  Chirality :  0.034   0.152   2714
  Planarity :  0.004   0.034   2077
  Dihedral  : 30.065 176.529   4705
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.63 (0.24), residues: 1230
  helix:  2.46 (0.18), residues: 765
  sheet: -0.15 (0.65), residues: 68
  loop :  0.77 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  45 
 TYR   0.011   0.001   TYR K1460 
 PHE   0.009   0.001   PHE K1397 
 TRP   0.020   0.001   TRP K1502 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (17106)
  covalent geometry    : angle       0.55707 (24363)
  hydrogen bonds       : bond        0.04626 (  867)
  hydrogen bonds       : angle       3.14423 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.395 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8275 (mmm) cc_final: 0.7681 (mmm)
REVERT: K 1133 MET cc_start: 0.5616 (ppp) cc_final: 0.5385 (ppp)
REVERT: K 1193 MET cc_start: 0.7595 (tpt) cc_final: 0.7190 (tpt)
REVERT: K 1232 ASN cc_start: -0.0967 (m-40) cc_final: -0.1305 (p0)
REVERT: K 1691 MET cc_start: 0.7384 (ptp) cc_final: 0.6297 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1042
  time to fit residues: 5.5419
Evaluate side-chains
  26 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 106 optimal weight:   30.0000
   chunk 136 optimal weight:   20.0000
   chunk 139 optimal weight:    8.9990
   chunk 130 optimal weight:   10.0000
   chunk 101 optimal weight:   40.0000
   chunk 61 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    0.6980
   chunk 39 optimal weight:    9.9990
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  76 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 = 0.3488 r_free = 0.3488 target = 0.042885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.030276 restraints weight = 232311.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.030690 restraints weight = 126656.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.031150 restraints weight = 87340.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.031251 restraints weight = 68723.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.031324 restraints weight = 62004.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.6048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  17106  Z= 0.291
  Angle     :  0.672   7.790  24363  Z= 0.383
  Chirality :  0.038   0.148   2714
  Planarity :  0.005   0.042   2077
  Dihedral  : 30.554 178.005   4705
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.24), residues: 1230
  helix:  2.06 (0.18), residues: 764
  sheet: -0.43 (0.64), residues: 68
  loop :  0.55 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG K1530 
 TYR   0.017   0.002   TYR D  40 
 PHE   0.014   0.002   PHE K1399 
 TRP   0.020   0.002   TRP K1502 
 HIS   0.008   0.002   HIS K1413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 (17106)
  covalent geometry    : angle       0.67243 (24363)
  hydrogen bonds       : bond        0.07710 (  867)
  hydrogen bonds       : angle       3.72110 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.502 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8204 (mmm) cc_final: 0.7635 (mmm)
REVERT: K 1193 MET cc_start: 0.7114 (tpt) cc_final: 0.6796 (tpt)
REVERT: K 1691 MET cc_start: 0.7432 (ptp) cc_final: 0.6467 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0967
  time to fit residues: 4.8595
Evaluate side-chains
  24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 124 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 141 optimal weight:    6.9990
   chunk 71 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 82 optimal weight:    0.3980
   chunk 54 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 131 optimal weight:    5.9990
   overall best weight:    4.0788

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

Flipped N/Q/H residues before XYZ refinement:
H  84 ASN
** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.042919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.030536 restraints weight = 230009.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.030884 restraints weight = 124983.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.031133 restraints weight = 84219.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.031292 restraints weight = 66442.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.031326 restraints weight = 60300.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.6371

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= 0.230
  Angle     :  0.631   7.093  24363  Z= 0.363
  Chirality :  0.037   0.154   2714
  Planarity :  0.004   0.035   2077
  Dihedral  : 30.723 173.356   4705
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.24), residues: 1230
  helix:  2.12 (0.18), residues: 763
  sheet: -0.61 (0.63), residues: 68
  loop :  0.41 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  35 
 TYR   0.016   0.002   TYR K1102 
 PHE   0.020   0.001   PHE K1399 
 TRP   0.019   0.002   TRP K1502 
 HIS   0.010   0.002   HIS D 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (17106)
  covalent geometry    : angle       0.63091 (24363)
  hydrogen bonds       : bond        0.05605 (  867)
  hydrogen bonds       : angle       3.62385 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.558 
Fit side-chains
REVERT: D   59 MET cc_start: 0.8566 (tpp) cc_final: 0.8317 (tpp)
REVERT: E  120 MET cc_start: 0.8359 (mmm) cc_final: 0.7811 (mmm)
REVERT: K 1193 MET cc_start: 0.7042 (tpt) cc_final: 0.6719 (tpt)
REVERT: K 1691 MET cc_start: 0.7589 (ptp) cc_final: 0.6613 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1138
  time to fit residues: 5.2311
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  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 97 optimal weight:   40.0000
   chunk 122 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 140 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 55 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 108 optimal weight:    6.9990
   chunk 25 optimal weight:    0.2980
   chunk 24 optimal weight:    7.9990
   overall best weight:    4.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** 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 = 0.3460 r_free = 0.3460 target = 0.041977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.029650 restraints weight = 234187.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.030122 restraints weight = 128394.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.030353 restraints weight = 87273.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.030525 restraints weight = 70768.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.030592 restraints weight = 63075.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.7032

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= 0.267
  Angle     :  0.683   7.538  24363  Z= 0.388
  Chirality :  0.039   0.158   2714
  Planarity :  0.005   0.042   2077
  Dihedral  : 31.031 176.003   4705
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.23), residues: 1230
  helix:  1.82 (0.18), residues: 765
  sheet: -0.89 (0.63), residues: 69
  loop :  0.26 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  33 
 TYR   0.016   0.002   TYR K1539 
 PHE   0.018   0.002   PHE K1399 
 TRP   0.017   0.002   TRP K1502 
 HIS   0.009   0.002   HIS K1413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 (17106)
  covalent geometry    : angle       0.68253 (24363)
  hydrogen bonds       : bond        0.07467 (  867)
  hydrogen bonds       : angle       3.87832 ( 2289)

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

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

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

  2460 Ramachandran restraints generated.
    1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.508 
Fit side-chains
REVERT: D   59 MET cc_start: 0.8570 (tpp) cc_final: 0.8342 (tpp)
REVERT: E  120 MET cc_start: 0.8299 (mmm) cc_final: 0.7761 (mmm)
REVERT: K 1193 MET cc_start: 0.6987 (tpt) cc_final: 0.6716 (tpt)
REVERT: K 1691 MET cc_start: 0.7659 (ptp) cc_final: 0.6729 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.1131
  time to fit residues: 5.4010
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  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 134 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 127 optimal weight:    7.9990
   chunk 68 optimal weight:    9.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.041893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.029939 restraints weight = 234086.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 80)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.029934 restraints weight = 134662.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.030180 restraints weight = 88059.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.030415 restraints weight = 69035.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.030466 restraints weight = 61049.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.7382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  17106  Z= 0.263
  Angle     :  0.678   7.592  24363  Z= 0.386
  Chirality :  0.039   0.161   2714
  Planarity :  0.005   0.037   2077
  Dihedral  : 31.180 171.261   4705
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 18.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.24), residues: 1230
  helix:  1.64 (0.18), residues: 773
  sheet: -1.02 (0.64), residues: 69
  loop :  0.18 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  33 
 TYR   0.017   0.002   TYR K1539 
 PHE   0.023   0.002   PHE K1397 
 TRP   0.015   0.002   TRP K1502 
 HIS   0.009   0.002   HIS K1413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 (17106)
  covalent geometry    : angle       0.67757 (24363)
  hydrogen bonds       : bond        0.06730 (  867)
  hydrogen bonds       : angle       3.89633 ( 2289)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3012.21 seconds
wall clock time: 52 minutes 36.91 seconds (3156.91 seconds total)