Starting phenix.real_space_refine
on Sun Aug 24 05:03:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8haj_34592/08_2025/8haj_34592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8haj_34592/08_2025/8haj_34592.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2025/8haj_34592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2025/8haj_34592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2025/8haj_34592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2025/8haj_34592.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     326      5.49       5
     S      47      5.16       5
     C    9860      2.51       5
     N    3138      2.21       5
     O    3843      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17214
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 819
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 735
          Classifications: {'peptide': 92}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'ALY:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 673
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 730
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "I"
      Number of atoms: 3362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3362
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
    Chain: "J"
      Number of atoms: 3320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 3320
          Classifications: {'DNA': 162}
          Link IDs: {'rna3p': 161}
    Chain: "K"
      Number of atoms: 4403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4403
          Classifications: {'peptide': 533}
          Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 499}
          Chain breaks: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA C  14 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA C  14 " occ=0.00
  Time building chain proxies: 4.44, per 1000 atoms: 0.26
  Number of scatterers: 17214
  At special positions: 0
  Unit cell: (107.31, 163.17, 122.01, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P     326     15.00
     O    3843      8.00
     N    3138      7.00
     C    9860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 674.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 14 sheets defined
      60.7% alpha, 6.5% beta
      115 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 2.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.669A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.794A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.016A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.581A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.507A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.542A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.586A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.883A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 121 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.810A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLU F  74 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   HIS F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.367A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.552A  pdb=" N   GLN H  44 " --> pdb=" O   LYS H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'K' and resid 1051 through 1068
      removed outlier: 4.161A  pdb=" N   GLN K1056 " --> pdb=" O   GLU K1052 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ALA K1057 " --> pdb=" O   GLU K1053 " (cutoff:3.500A)
      Proline residue:  K1060  - end of helix
    Processing helix  chain 'K' and resid 1072 through 1077
      removed outlier: 4.399A  pdb=" N   GLN K1077 " --> pdb=" O   LEU K1073 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1088 through 1093
    Processing helix  chain 'K' and resid 1098 through 1109
    Processing helix  chain 'K' and resid 1113 through 1132
      removed outlier: 3.775A  pdb=" N   TYR K1117 " --> pdb=" O   GLU K1113 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1136 through 1159
      removed outlier: 3.596A  pdb=" N   GLU K1152 " --> pdb=" O   VAL K1148 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ASP K1154 " --> pdb=" O   GLU K1150 " (cutoff:3.500A)
      Proline residue:  K1155  - end of helix
    Processing helix  chain 'K' and resid 1201 through 1208
      removed outlier: 3.584A  pdb=" N   PHE K1205 " --> pdb=" O   CYS K1201 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ASN K1206 " --> pdb=" O   GLU K1202 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU K1207 " --> pdb=" O   LYS K1203 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE K1208 " --> pdb=" O   CYS K1204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 1201 through 1208'
    Processing helix  chain 'K' and resid 1272 through 1279
    Processing helix  chain 'K' and resid 1296 through 1314
    Processing helix  chain 'K' and resid 1336 through 1343
    Processing helix  chain 'K' and resid 1406 through 1429
      removed outlier: 4.100A  pdb=" N   THR K1411 " --> pdb=" O   LYS K1407 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ALA K1412 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS K1427 " --> pdb=" O   GLU K1423 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1459 through 1477
    Processing helix  chain 'K' and resid 1486 through 1493
    Processing helix  chain 'K' and resid 1497 through 1501
    Processing helix  chain 'K' and resid 1507 through 1519
      removed outlier: 3.881A  pdb=" N   ASN K1511 " --> pdb=" O   ASP K1507 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1579 through 1591
    Processing helix  chain 'K' and resid 1626 through 1638
      removed outlier: 3.915A  pdb=" N   PHE K1630 " --> pdb=" O   GLY K1626 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1643 through 1664
      removed outlier: 4.048A  pdb=" N   GLN K1663 " --> pdb=" O   HIS K1659 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.161A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 7.018A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.062A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.950A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.239A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 1175 through 1176
      removed outlier: 4.151A  pdb=" N   LEU K1175 " --> pdb=" O   ILE K1185 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1192 through 1194
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1244 through 1246
    Processing sheet with id=AB5, first strand: chain 'K' and resid 1321 through 1334
      removed outlier: 6.893A  pdb=" N   ALA K1359 " --> pdb=" O   VAL K1326 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ALA K1328 " --> pdb=" O   THR K1357 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR K1357 " --> pdb=" O   ALA K1328 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ASP K1330 " --> pdb=" O   TYR K1355 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   TYR K1355 " --> pdb=" O   ASP K1330 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   THR K1332 " --> pdb=" O   PHE K1353 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   PHE K1353 " --> pdb=" O   THR K1332 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE K1374 " --> pdb=" O   ALA K1362 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   GLU K1364 " --> pdb=" O   CYS K1372 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   CYS K1372 " --> pdb=" O   GLU K1364 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ILE K1366 " --> pdb=" O   ASP K1370 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   ASP K1370 " --> pdb=" O   ILE K1366 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   HIS K1377 " --> pdb=" O   SER K1396 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   TRP K1436 " --> pdb=" O   ILE K1395 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   TYR K1397 " --> pdb=" O   TRP K1436 " (cutoff:3.500A)

    587 hydrogen bonds defined for protein.
    1731 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      278 hydrogen bonds
      548 hydrogen bond angles
      0 basepair planarities
      115 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 4.42

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3161
        1.33 -     1.45: 5678
        1.45 -     1.57: 8664
        1.57 -     1.69: 650
        1.69 -     1.81: 70
  Bond restraints: 18223
  Sorted by residual:
  bond pdb=" NZ  ALY B  16 "
       pdb=" CH  ALY B  16 "
    ideal  model  delta    sigma   weight residual
    1.343  1.384 -0.041 2.00e-02 2.50e+03 4.31e+00
  bond pdb=" NZ  ALY B  12 "
       pdb=" CH  ALY B  12 "
    ideal  model  delta    sigma   weight residual
    1.343  1.383 -0.040 2.00e-02 2.50e+03 4.09e+00
  bond pdb=" C   LEU K1073 "
       pdb=" N   PRO K1074 "
    ideal  model  delta    sigma   weight residual
    1.335  1.352 -0.017 1.19e-02 7.06e+03 2.15e+00
  bond pdb=" C3'  DT I 136 "
       pdb=" O3'  DT I 136 "
    ideal  model  delta    sigma   weight residual
    1.422  1.466 -0.044 3.00e-02 1.11e+03 2.13e+00
  bond pdb=" CG  GLU D  68 "
       pdb=" CD  GLU D  68 "
    ideal  model  delta    sigma   weight residual
    1.516  1.484  0.032 2.50e-02 1.60e+03 1.69e+00
  ... (remaining 18218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 25364
        1.73 -     3.46: 569
        3.46 -     5.20: 53
        5.20 -     6.93: 15
        6.93 -     8.66: 4
  Bond angle restraints: 26005
  Sorted by residual:
  angle pdb=" N   GLU D  68 "
        pdb=" CA  GLU D  68 "
        pdb=" CB  GLU D  68 "
      ideal   model   delta    sigma   weight residual
     110.28  116.27   -5.99 1.55e+00 4.16e-01 1.49e+01
  angle pdb=" N   GLY D 101 "
        pdb=" CA  GLY D 101 "
        pdb=" C   GLY D 101 "
      ideal   model   delta    sigma   weight residual
     110.77  118.16   -7.39 1.93e+00 2.68e-01 1.47e+01
  angle pdb=" C   ASN B  64 "
        pdb=" N   VAL B  65 "
        pdb=" CA  VAL B  65 "
      ideal   model   delta    sigma   weight residual
     123.08  119.54    3.54 1.01e+00 9.80e-01 1.23e+01
  angle pdb=" CA  MET K1254 "
        pdb=" CB  MET K1254 "
        pdb=" CG  MET K1254 "
      ideal   model   delta    sigma   weight residual
     114.10  120.70   -6.60 2.00e+00 2.50e-01 1.09e+01
  angle pdb=" CA  GLU D  68 "
        pdb=" CB  GLU D  68 "
        pdb=" CG  GLU D  68 "
      ideal   model   delta    sigma   weight residual
     114.10  120.17   -6.07 2.00e+00 2.50e-01 9.22e+00
  ... (remaining 26000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.76: 8594
       32.76 -    65.53: 1586
       65.53 -    98.29: 38
       98.29 -   131.05: 0
      131.05 -   163.82: 2
  Dihedral angle restraints: 10220
    sinusoidal: 6415
      harmonic: 3805
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" C4'  DT I 136 "
           pdb=" C3'  DT I 136 "
           pdb=" O3'  DT I 136 "
           pdb=" P    DT I 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   56.18  163.82     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DA J  59 "
           pdb=" C3'  DA J  59 "
           pdb=" O3'  DA J  59 "
           pdb=" P    DA J  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.76  153.24     1      3.50e+01 8.16e-04 1.48e+01
  ... (remaining 10217 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 2064
       0.030 -    0.060: 608
       0.060 -    0.091: 149
       0.091 -    0.121: 61
       0.121 -    0.151: 11
  Chirality restraints: 2893
  Sorted by residual:
  chirality pdb=" CA  PRO E 121 "
            pdb=" N   PRO E 121 "
            pdb=" C   PRO E 121 "
            pdb=" CB  PRO E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" CA  ILE B  46 "
            pdb=" N   ILE B  46 "
            pdb=" C   ILE B  46 "
            pdb=" CB  ILE B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.50e-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   -2.48   -0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 2890 not shown)

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

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1764
        2.75 -     3.29: 16508
        3.29 -     3.83: 33626
        3.83 -     4.36: 38112
        4.36 -     4.90: 55970
  Nonbonded interactions: 145980
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN K1379 "
            pdb=" OG  SER K1396 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OH  TYR G  50 "
            pdb=" OE1 GLN H  92 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   THR K1496 "
            pdb=" OG  SER K1581 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   GLU F  74 "
            pdb=" NH2 ARG H  89 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.282 3.040
  ... (remaining 145975 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 19 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and ((resid 28 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 29 through 121))
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and resid 10 through 169)
  selection = (chain 'J' and resid 10 through 169)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     19.670
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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   0.044  18223  Z= 0.151
  Angle     :  0.604   8.661  26005  Z= 0.369
  Chirality :  0.034   0.151   2893
  Planarity :  0.004   0.061   2182
  Dihedral  : 24.856 163.816   7764
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.23), residues: 1276
  helix:  1.37 (0.19), residues: 761
  sheet:  0.14 (0.61), residues: 65
  loop :  0.06 (0.28), residues: 450

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (18223)
  covalent geometry    : angle       0.60443 (26005)
  hydrogen bonds       : bond        0.14477 (  865)
  hydrogen bonds       : angle       5.51504 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9156 (tp30) cc_final: 0.8689 (tt0)
REVERT: D   34 TYR cc_start: 0.9157 (m-10) cc_final: 0.8885 (m-80)
REVERT: G   78 ILE cc_start: 0.9124 (mt) cc_final: 0.8806 (mm)
REVERT: K 1129 TRP cc_start: 0.7371 (m-10) cc_final: 0.7169 (m-10)
REVERT: K 1478 ARG cc_start: 0.4409 (mmp-170) cc_final: 0.3607 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1167
  time to fit residues: 17.7646
Evaluate side-chains
  63 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0670
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.0970
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    3.0322

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

Flipped N/Q/H residues before XYZ refinement:
E  39 HIS
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1132 ASN
K1236 ASN
K1379 GLN
K1661 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.058022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.039764 restraints weight = 220145.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.040519 restraints weight = 126122.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.041222 restraints weight = 91125.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.041753 restraints weight = 68216.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.041890 restraints weight = 56193.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  18223  Z= 0.209
  Angle     :  0.607   7.082  26005  Z= 0.353
  Chirality :  0.037   0.144   2893
  Planarity :  0.005   0.061   2182
  Dihedral  : 28.389 168.567   5103
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  2.30 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.23), residues: 1276
  helix:  1.89 (0.18), residues: 773
  sheet:  0.21 (0.61), residues: 65
  loop :  0.22 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.032   0.001   ARG K1055 
 TYR   0.020   0.002   TYR F  72 
 PHE   0.019   0.002   PHE K1508 
 TRP   0.017   0.002   TRP K1122 
 HIS   0.013   0.002   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (18223)
  covalent geometry    : angle       0.60720 (26005)
  hydrogen bonds       : bond        0.07202 (  865)
  hydrogen bonds       : angle       3.59875 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9514 (tp30) cc_final: 0.9184 (tt0)
REVERT: A  106 ASP cc_start: 0.9033 (t0) cc_final: 0.8703 (m-30)
REVERT: G   78 ILE cc_start: 0.9102 (mt) cc_final: 0.8894 (mm)
REVERT: H   99 LEU cc_start: 0.8216 (tp) cc_final: 0.7970 (tp)
REVERT: K 1157 MET cc_start: 0.3660 (ttp) cc_final: 0.2784 (ttt)
REVERT: K 1254 MET cc_start: 0.0872 (tpt) cc_final: -0.0973 (ptp)
REVERT: K 1478 ARG cc_start: 0.5731 (mmp-170) cc_final: 0.5214 (tpm170)
  outliers start: 5
  outliers final: 1
  residues processed: 83
  average time/residue: 0.1182
  time to fit residues: 15.9698
Evaluate side-chains
  60 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 78 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 99 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 72 optimal weight:    5.9990
   chunk 116 optimal weight:   20.0000
   chunk 41 optimal weight:    2.9990
   chunk 106 optimal weight:   20.0000
   chunk 67 optimal weight:    0.7980
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
H  92 GLN
K1227 ASN
K1236 ASN
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.053222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.035667 restraints weight = 229354.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.036399 restraints weight = 129036.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 73)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.037096 restraints weight = 91048.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.037348 restraints weight = 68475.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.037607 restraints weight = 58735.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.109  18223  Z= 0.300
  Angle     :  0.690   8.951  26005  Z= 0.399
  Chirality :  0.039   0.216   2893
  Planarity :  0.006   0.060   2182
  Dihedral  : 29.167 169.817   5103
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.88 %
    Favored  : 95.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.23), residues: 1276
  helix:  1.58 (0.18), residues: 772
  sheet:  0.38 (0.69), residues: 55
  loop :  0.28 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  40 
 TYR   0.033   0.003   TYR K1191 
 PHE   0.024   0.003   PHE K1508 
 TRP   0.011   0.002   TRP K1122 
 HIS   0.014   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 (18223)
  covalent geometry    : angle       0.69033 (26005)
  hydrogen bonds       : bond        0.08001 (  865)
  hydrogen bonds       : angle       4.01150 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   63 GLU cc_start: 0.9157 (pm20) cc_final: 0.8809 (pm20)
REVERT: E   41 TYR cc_start: 0.8530 (m-80) cc_final: 0.8259 (m-80)
REVERT: K 1157 MET cc_start: 0.3974 (ttp) cc_final: 0.3105 (ttm)
REVERT: K 1254 MET cc_start: 0.2008 (tpt) cc_final: -0.1043 (ptp)
REVERT: K 1478 ARG cc_start: 0.5516 (mmp-170) cc_final: 0.4995 (tpm170)
REVERT: K 1624 MET cc_start: -0.2026 (mmt) cc_final: -0.2812 (mmt)
REVERT: K 1652 MET cc_start: 0.7137 (tmm) cc_final: 0.6575 (ppp)
REVERT: K 1654 MET cc_start: 0.5747 (mmp) cc_final: 0.4884 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 75
  average time/residue: 0.1275
  time to fit residues: 15.4164
Evaluate side-chains
  55 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 136 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0770
   chunk 7 optimal weight:    5.9990
   overall best weight:    1.1744

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

Flipped N/Q/H residues before XYZ refinement:
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1230 GLN
K1261 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.055115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.037216 restraints weight = 226066.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.038073 restraints weight = 126254.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.038484 restraints weight = 83919.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.039144 restraints weight = 66329.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.039258 restraints weight = 56635.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18223  Z= 0.144
  Angle     :  0.572   7.271  26005  Z= 0.332
  Chirality :  0.035   0.192   2893
  Planarity :  0.004   0.054   2182
  Dihedral  : 29.138 173.817   5103
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.23), residues: 1276
  helix:  1.92 (0.18), residues: 771
  sheet:  0.40 (0.70), residues: 55
  loop :  0.21 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.027   0.001   TYR A  99 
 PHE   0.039   0.001   PHE E 104 
 TRP   0.007   0.001   TRP K1649 
 HIS   0.006   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (18223)
  covalent geometry    : angle       0.57185 (26005)
  hydrogen bonds       : bond        0.04176 (  865)
  hydrogen bonds       : angle       3.52213 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   56 MET cc_start: 0.9463 (tmm) cc_final: 0.9172 (tpp)
REVERT: K 1097 MET cc_start: 0.6208 (mmm) cc_final: 0.6005 (ppp)
REVERT: K 1157 MET cc_start: 0.4928 (ttp) cc_final: 0.4129 (ttm)
REVERT: K 1254 MET cc_start: 0.1588 (tpt) cc_final: -0.0338 (ptp)
REVERT: K 1478 ARG cc_start: 0.5862 (mmp-170) cc_final: 0.5318 (tpm170)
REVERT: K 1652 MET cc_start: 0.6479 (tmm) cc_final: 0.6220 (ppp)
REVERT: K 1654 MET cc_start: 0.5697 (mmp) cc_final: 0.5295 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1241
  time to fit residues: 15.7965
Evaluate side-chains
  55 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 135 optimal weight:    0.3980
   chunk 91 optimal weight:    7.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1261 HIS
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1591 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.054939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.037134 restraints weight = 224029.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.037828 restraints weight = 125716.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.038588 restraints weight = 88398.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.038797 restraints weight = 66024.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.039167 restraints weight = 55914.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  18223  Z= 0.150
  Angle     :  0.567   6.931  26005  Z= 0.330
  Chirality :  0.035   0.177   2893
  Planarity :  0.005   0.061   2182
  Dihedral  : 29.005 171.932   5103
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.23), residues: 1276
  helix:  2.07 (0.18), residues: 767
  sheet:  0.32 (0.69), residues: 55
  loop :  0.07 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E 134 
 TYR   0.022   0.001   TYR A  99 
 PHE   0.019   0.001   PHE K1508 
 TRP   0.017   0.001   TRP K1466 
 HIS   0.009   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (18223)
  covalent geometry    : angle       0.56690 (26005)
  hydrogen bonds       : bond        0.04460 (  865)
  hydrogen bonds       : angle       3.45349 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: B   63 GLU cc_start: 0.8962 (pm20) cc_final: 0.8595 (pm20)
REVERT: D   56 MET cc_start: 0.9444 (tmm) cc_final: 0.9122 (tpp)
REVERT: K 1157 MET cc_start: 0.5060 (ttp) cc_final: 0.4459 (ttm)
REVERT: K 1254 MET cc_start: 0.2199 (tpt) cc_final: 0.0421 (ptp)
REVERT: K 1478 ARG cc_start: 0.5882 (mmp-170) cc_final: 0.5348 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0925
  time to fit residues: 11.2647
Evaluate side-chains
  52 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 130 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 48 optimal weight:   20.0000
   chunk 45 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   chunk 83 optimal weight:    8.9990
   chunk 99 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 105 optimal weight:   20.0000
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1261 HIS
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.052498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.034871 restraints weight = 233345.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.035674 restraints weight = 136218.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.036008 restraints weight = 90502.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.036543 restraints weight = 71586.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.036668 restraints weight = 60843.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  18223  Z= 0.241
  Angle     :  0.631   6.582  26005  Z= 0.365
  Chirality :  0.038   0.230   2893
  Planarity :  0.005   0.053   2182
  Dihedral  : 29.261 170.317   5103
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.23), residues: 1276
  helix:  1.87 (0.18), residues: 770
  sheet: -0.03 (0.65), residues: 60
  loop : -0.02 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  40 
 TYR   0.022   0.002   TYR A  99 
 PHE   0.018   0.002   PHE K1508 
 TRP   0.015   0.002   TRP K1466 
 HIS   0.008   0.002   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (18223)
  covalent geometry    : angle       0.63104 (26005)
  hydrogen bonds       : bond        0.07679 (  865)
  hydrogen bonds       : angle       3.77446 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: B   63 GLU cc_start: 0.8934 (pm20) cc_final: 0.8607 (pm20)
REVERT: K 1157 MET cc_start: 0.5297 (ttp) cc_final: 0.4869 (ttm)
REVERT: K 1254 MET cc_start: 0.2076 (tpt) cc_final: 0.0142 (ptp)
REVERT: K 1478 ARG cc_start: 0.5683 (mmp-170) cc_final: 0.5158 (tpm170)
REVERT: K 1624 MET cc_start: -0.2134 (mmt) cc_final: -0.2454 (mmt)
REVERT: K 1654 MET cc_start: 0.6597 (tpt) cc_final: 0.6360 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1166
  time to fit residues: 11.7091
Evaluate side-chains
  50 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 144 optimal weight:    1.9990
   chunk 141 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 54 optimal weight:    8.9990
   chunk 107 optimal weight:   20.0000
   chunk 111 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1261 HIS
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.052405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.035042 restraints weight = 230866.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.036006 restraints weight = 126989.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.036334 restraints weight = 84811.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.036653 restraints weight = 67432.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.037071 restraints weight = 57688.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  18223  Z= 0.207
  Angle     :  0.617   8.634  26005  Z= 0.357
  Chirality :  0.037   0.166   2893
  Planarity :  0.005   0.053   2182
  Dihedral  : 29.587 172.369   5103
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.23), residues: 1276
  helix:  1.86 (0.18), residues: 764
  sheet: -0.06 (0.65), residues: 60
  loop : -0.07 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  49 
 TYR   0.022   0.002   TYR A  99 
 PHE   0.017   0.001   PHE K1508 
 TRP   0.010   0.001   TRP K1122 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (18223)
  covalent geometry    : angle       0.61721 (26005)
  hydrogen bonds       : bond        0.05400 (  865)
  hydrogen bonds       : angle       3.86122 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   56 MET cc_start: 0.9343 (tmm) cc_final: 0.8989 (tpp)
REVERT: K 1157 MET cc_start: 0.5315 (ttp) cc_final: 0.4827 (ttm)
REVERT: K 1254 MET cc_start: 0.3713 (tpt) cc_final: 0.1868 (ptp)
REVERT: K 1478 ARG cc_start: 0.5778 (mmp-170) cc_final: 0.5260 (tpm170)
REVERT: K 1624 MET cc_start: -0.1368 (mmt) cc_final: -0.2518 (mmt)
REVERT: K 1652 MET cc_start: 0.6692 (ppp) cc_final: 0.6347 (ppp)
REVERT: K 1654 MET cc_start: 0.6216 (tpt) cc_final: 0.5886 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1297
  time to fit residues: 13.5436
Evaluate side-chains
  49 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 114 optimal weight:   20.0000
   chunk 56 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 111 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1261 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.048542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.030500 restraints weight = 224731.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.031562 restraints weight = 124856.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.032109 restraints weight = 83661.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.032602 restraints weight = 65519.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.032900 restraints weight = 54891.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.5215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  18223  Z= 0.211
  Angle     :  0.614   8.708  26005  Z= 0.355
  Chirality :  0.036   0.177   2893
  Planarity :  0.005   0.054   2182
  Dihedral  : 29.663 171.525   5103
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.23), residues: 1276
  helix:  1.85 (0.18), residues: 771
  sheet: -0.16 (0.66), residues: 60
  loop : -0.11 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  20 
 TYR   0.024   0.002   TYR A  99 
 PHE   0.018   0.002   PHE K1508 
 TRP   0.009   0.001   TRP K1122 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (18223)
  covalent geometry    : angle       0.61402 (26005)
  hydrogen bonds       : bond        0.06177 (  865)
  hydrogen bonds       : angle       3.81333 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K 1157 MET cc_start: 0.5531 (ttp) cc_final: 0.4991 (ttm)
REVERT: K 1254 MET cc_start: 0.2881 (tpt) cc_final: 0.0953 (ptp)
REVERT: K 1478 ARG cc_start: 0.5607 (mmp-170) cc_final: 0.5067 (tpm170)
REVERT: K 1652 MET cc_start: 0.7079 (ppp) cc_final: 0.6766 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1195
  time to fit residues: 12.1432
Evaluate side-chains
  48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 101 optimal weight:    6.9990
   chunk 152 optimal weight:    1.9990
   chunk 129 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:   20.0000
   chunk 83 optimal weight:    7.9990
   chunk 114 optimal weight:   20.0000
   chunk 119 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 106 HIS
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.050951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.033847 restraints weight = 234439.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.034567 restraints weight = 133822.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.034975 restraints weight = 90265.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 63)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.035546 restraints weight = 68761.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.035652 restraints weight = 58083.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.5739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  18223  Z= 0.242
  Angle     :  0.649   8.430  26005  Z= 0.373
  Chirality :  0.038   0.181   2893
  Planarity :  0.005   0.054   2182
  Dihedral  : 29.868 171.904   5103
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.23), residues: 1276
  helix:  1.61 (0.18), residues: 771
  sheet: -0.05 (0.69), residues: 54
  loop : -0.23 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  35 
 TYR   0.023   0.002   TYR A  99 
 PHE   0.018   0.002   PHE K1508 
 TRP   0.014   0.002   TRP K1649 
 HIS   0.007   0.002   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 (18223)
  covalent geometry    : angle       0.64941 (26005)
  hydrogen bonds       : bond        0.06960 (  865)
  hydrogen bonds       : angle       4.02273 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.9318 (ttp) cc_final: 0.8855 (tmm)
REVERT: D   56 MET cc_start: 0.9259 (tmm) cc_final: 0.8968 (tpp)
REVERT: D  102 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9086 (mm-30)
REVERT: K 1097 MET cc_start: 0.3297 (mmp) cc_final: 0.3065 (ppp)
REVERT: K 1157 MET cc_start: 0.4984 (ttp) cc_final: 0.4565 (ttm)
REVERT: K 1254 MET cc_start: 0.3270 (tpt) cc_final: 0.1512 (ptp)
REVERT: K 1478 ARG cc_start: 0.5818 (mmp-170) cc_final: 0.5327 (tpm170)
REVERT: K 1654 MET cc_start: 0.6568 (mtt) cc_final: 0.6342 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1080
  time to fit residues: 11.3319
Evaluate side-chains
  49 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 127 optimal weight:    0.6980
   chunk 64 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 46 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 7 optimal weight:    0.4980
   chunk 94 optimal weight:    6.9990
   chunk 135 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    3.4386

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
E 125 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.051088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.033966 restraints weight = 232955.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.034643 restraints weight = 133689.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.035311 restraints weight = 88720.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.035547 restraints weight = 68303.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.035741 restraints weight = 58852.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.5977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  18223  Z= 0.206
  Angle     :  0.626  10.256  26005  Z= 0.359
  Chirality :  0.037   0.177   2893
  Planarity :  0.005   0.052   2182
  Dihedral  : 29.953 173.227   5103
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.23), residues: 1276
  helix:  1.72 (0.18), residues: 770
  sheet: -0.12 (0.70), residues: 54
  loop : -0.24 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  42 
 TYR   0.022   0.002   TYR A  99 
 PHE   0.018   0.002   PHE K1508 
 TRP   0.008   0.001   TRP K1122 
 HIS   0.012   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (18223)
  covalent geometry    : angle       0.62599 (26005)
  hydrogen bonds       : bond        0.05573 (  865)
  hydrogen bonds       : angle       3.94252 ( 2279)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.9419 (ttp) cc_final: 0.8979 (tmm)
REVERT: D   56 MET cc_start: 0.9277 (tmm) cc_final: 0.9003 (tpp)
REVERT: K 1097 MET cc_start: 0.4456 (mmp) cc_final: 0.4107 (ppp)
REVERT: K 1157 MET cc_start: 0.4909 (ttp) cc_final: 0.4506 (ttm)
REVERT: K 1254 MET cc_start: 0.3405 (tpt) cc_final: 0.1746 (ptp)
REVERT: K 1478 ARG cc_start: 0.5842 (mmp-170) cc_final: 0.5345 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1066
  time to fit residues: 10.2615
Evaluate side-chains
  49 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 118 optimal weight:    9.9990
   chunk 145 optimal weight:    1.9990
   chunk 113 optimal weight:    9.9990
   chunk 112 optimal weight:    5.9990
   chunk 125 optimal weight:    0.8980
   chunk 9 optimal weight:   20.0000
   chunk 83 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 142 optimal weight:    2.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.047191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.029549 restraints weight = 219988.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.030548 restraints weight = 123364.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.031089 restraints weight = 83583.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.031554 restraints weight = 66117.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.031822 restraints weight = 55632.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.6174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  18223  Z= 0.203
  Angle     :  0.619   7.428  26005  Z= 0.356
  Chirality :  0.037   0.179   2893
  Planarity :  0.005   0.052   2182
  Dihedral  : 29.942 172.533   5103
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.23), residues: 1276
  helix:  1.73 (0.18), residues: 770
  sheet: -0.26 (0.68), residues: 54
  loop : -0.25 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  35 
 TYR   0.021   0.002   TYR A  99 
 PHE   0.018   0.002   PHE K1508 
 TRP   0.008   0.001   TRP K1122 
 HIS   0.006   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (18223)
  covalent geometry    : angle       0.61894 (26005)
  hydrogen bonds       : bond        0.06011 (  865)
  hydrogen bonds       : angle       3.88816 ( 2279)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2999.19 seconds
wall clock time: 52 minutes 31.03 seconds (3151.03 seconds total)