Starting phenix.real_space_refine
on Sun Aug 24 04:43:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ham_34596/08_2025/8ham_34596.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ham_34596/08_2025/8ham_34596.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2025/8ham_34596.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2025/8ham_34596.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2025/8ham_34596.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ham_34596/08_2025/8ham_34596.map"
  }
  resolution = 4.5
  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=   0.004
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     330      5.49       5
     S      46      5.16       5
     C    9835      2.51       5
     N    3130      2.21       5
     O    3836      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 135 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: 17177
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 720
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ALY:plan-2': 2, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 12
    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: 3384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 3384
          Classifications: {'DNA': 165}
          Link IDs: {'rna3p': 164}
    Chain: "J"
      Number of atoms: 3381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 3381
          Classifications: {'DNA': 165}
          Link IDs: {'rna3p': 164}
    Chain: "K"
      Number of atoms: 4302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 4302
          Classifications: {'peptide': 517}
          Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 484}
          Chain breaks: 4
  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: 4.04, per 1000 atoms: 0.24
  Number of scatterers: 17177
  At special positions: 0
  Unit cell: (101.43, 161.7, 124.95, 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      46     16.00
     P     330     15.00
     O    3836      8.00
     N    3130      7.00
     C    9835      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: 1.28
  Conformation dependent library (CDL) restraints added in 465.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2428

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 14 sheets defined
      62.0% alpha, 7.5% beta
      129 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 2.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.775A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.705A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLU B  63 " --> pdb=" O   LYS B  59 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.356A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.533A  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 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.686A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.559A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.561A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    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: 4.342A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.943A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'K' and resid 1088 through 1104
      Proline residue:  K1096  - end of helix
      removed outlier: 3.514A  pdb=" N   GLN K1104 " --> pdb=" O   ALA K1100 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1108 through 1112
    Processing helix  chain 'K' and resid 1124 through 1129
      removed outlier: 3.510A  pdb=" N   ILE K1128 " --> pdb=" O   ASP K1124 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1134 through 1145
    Processing helix  chain 'K' and resid 1149 through 1168
      removed outlier: 4.061A  pdb=" N   TYR K1153 " --> pdb=" O   GLU K1149 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1172 through 1197
      removed outlier: 4.353A  pdb=" N   ASP K1190 " --> pdb=" O   GLU K1186 " (cutoff:3.500A)
      Proline residue:  K1191  - end of helix
    Processing helix  chain 'K' and resid 1238 through 1244
    Processing helix  chain 'K' and resid 1292 through 1296
    Processing helix  chain 'K' and resid 1308 through 1316
    Processing helix  chain 'K' and resid 1332 through 1350
    Processing helix  chain 'K' and resid 1372 through 1380
    Processing helix  chain 'K' and resid 1443 through 1464
      removed outlier: 4.474A  pdb=" N   THR K1447 " --> pdb=" O   ARG K1443 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ALA K1448 " --> pdb=" O   CYS K1444 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1495 through 1513
    Processing helix  chain 'K' and resid 1522 through 1530
    Processing helix  chain 'K' and resid 1533 through 1537
    Processing helix  chain 'K' and resid 1543 through 1554
      removed outlier: 4.115A  pdb=" N   ASN K1547 " --> pdb=" O   ASP K1543 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1617 through 1629
    Processing helix  chain 'K' and resid 1664 through 1675
    Processing helix  chain 'K' and resid 1680 through 1698
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.712A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.768A  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: 7.294A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.540A  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: 7.122A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 1205 through 1206
      removed outlier: 3.526A  pdb=" N   ASP K1276 " --> pdb=" O   PHE K1206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1234 through 1237
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1280 through 1282
    Processing sheet with id=AB5, first strand: chain 'K' and resid 1357 through 1370
      removed outlier: 6.529A  pdb=" N   ALA K1395 " --> pdb=" O   VAL K1362 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   SER K1364 " --> pdb=" O   THR K1393 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   THR K1393 " --> pdb=" O   SER K1364 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   ASP K1366 " --> pdb=" O   TYR K1391 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TYR K1391 " --> pdb=" O   ASP K1366 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   THR K1368 " --> pdb=" O   PHE K1389 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   PHE K1389 " --> pdb=" O   THR K1368 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU K1396 " --> pdb=" O   MET K1412 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE K1410 " --> pdb=" O   ALA K1398 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   GLU K1400 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   CYS K1408 " --> pdb=" O   GLU K1400 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ILE K1402 " --> pdb=" O   ASP K1406 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   ASP K1406 " --> pdb=" O   ILE K1402 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLN K1415 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   ILE K1431 " --> pdb=" O   GLN K1415 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   TYR K1417 " --> pdb=" O   VAL K1429 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL K1429 " --> pdb=" O   TYR K1417 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   TRP K1472 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   TYR K1433 " --> pdb=" O   TRP K1472 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASP K1518 " --> pdb=" O   HIS K1636 " (cutoff:3.500A)

    605 hydrogen bonds defined for protein.
    1785 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      310 hydrogen bonds
      620 hydrogen bond angles
      0 basepair planarities
      129 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 3.98

  Time building geometry restraints manager: 1.85 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: 3318
        1.33 -     1.45: 5725
        1.45 -     1.57: 8432
        1.57 -     1.69: 658
        1.69 -     1.81: 68
  Bond restraints: 18201
  Sorted by residual:
  bond pdb=" NZ  ALY B  16 "
       pdb=" CH  ALY B  16 "
    ideal  model  delta    sigma   weight residual
    1.343  1.385 -0.042 2.00e-02 2.50e+03 4.45e+00
  bond pdb=" NZ  ALY B  12 "
       pdb=" CH  ALY B  12 "
    ideal  model  delta    sigma   weight residual
    1.343  1.384 -0.041 2.00e-02 2.50e+03 4.19e+00
  bond pdb=" C3'  DT I 136 "
       pdb=" O3'  DT I 136 "
    ideal  model  delta    sigma   weight residual
    1.422  1.471 -0.049 3.00e-02 1.11e+03 2.70e+00
  bond pdb=" C   LEU D 101 "
       pdb=" N   LEU D 102 "
    ideal  model  delta    sigma   weight residual
    1.329  1.352 -0.024 1.60e-02 3.91e+03 2.20e+00
  bond pdb=" C3'  DA J  59 "
       pdb=" O3'  DA J  59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.69e+00
  ... (remaining 18196 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 25591
        2.07 -     4.14: 381
        4.14 -     6.22: 17
        6.22 -     8.29: 4
        8.29 -    10.36: 1
  Bond angle restraints: 25994
  Sorted by residual:
  angle pdb=" CA  LEU K1507 "
        pdb=" CB  LEU K1507 "
        pdb=" CG  LEU K1507 "
      ideal   model   delta    sigma   weight residual
     116.30  105.94   10.36 3.50e+00 8.16e-02 8.76e+00
  angle pdb=" C   ASN B  64 "
        pdb=" N   VAL B  65 "
        pdb=" CA  VAL B  65 "
      ideal   model   delta    sigma   weight residual
     122.97  120.31    2.66 9.80e-01 1.04e+00 7.38e+00
  angle pdb=" C   PHE K1544 "
        pdb=" N   TRP K1545 "
        pdb=" CA  TRP K1545 "
      ideal   model   delta    sigma   weight residual
     120.09  123.41   -3.32 1.25e+00 6.40e-01 7.04e+00
  angle pdb=" CB  MET K1290 "
        pdb=" CG  MET K1290 "
        pdb=" SD  MET K1290 "
      ideal   model   delta    sigma   weight residual
     112.70  120.41   -7.71 3.00e+00 1.11e-01 6.60e+00
  angle pdb=" C   LEU D 101 "
        pdb=" N   LEU D 102 "
        pdb=" CA  LEU D 102 "
      ideal   model   delta    sigma   weight residual
     120.49  116.91    3.58 1.42e+00 4.96e-01 6.35e+00
  ... (remaining 25989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.73: 8639
       34.73 -    69.46: 1510
       69.46 -   104.19: 30
      104.19 -   138.92: 2
      138.92 -   173.65: 2
  Dihedral angle restraints: 10183
    sinusoidal: 6423
      harmonic: 3760
  Sorted by residual:
  dihedral pdb=" CA  LYS B  20 "
           pdb=" C   LYS B  20 "
           pdb=" N   VAL B  21 "
           pdb=" CA  VAL B  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.44  -28.56     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  MET K1412 "
           pdb=" C   MET K1412 "
           pdb=" N   HIS K1413 "
           pdb=" CA  HIS K1413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ILE F  29 "
           pdb=" C   ILE F  29 "
           pdb=" N   THR F  30 "
           pdb=" CA  THR F  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.83  -20.17     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 10180 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 2234
       0.034 -    0.069: 512
       0.069 -    0.103: 98
       0.103 -    0.137: 41
       0.137 -    0.172: 1
  Chirality restraints: 2886
  Sorted by residual:
  chirality pdb=" CA  ILE K1635 "
            pdb=" N   ILE K1635 "
            pdb=" C   ILE K1635 "
            pdb=" CB  ILE K1635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.36e-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   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CB  VAL B  43 "
            pdb=" CA  VAL B  43 "
            pdb=" CG1 VAL B  43 "
            pdb=" CG2 VAL B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 2883 not shown)

  Planarity restraints: 2162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO D 103 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E 120 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO E 121 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO E 121 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 121 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  30 "   -0.007 2.00e-02 2.50e+03   1.12e-02 2.84e+00
        pdb=" N1   DC J  30 "    0.007 2.00e-02 2.50e+03
        pdb=" C2   DC J  30 "   -0.026 2.00e-02 2.50e+03
        pdb=" O2   DC J  30 "    0.013 2.00e-02 2.50e+03
        pdb=" N3   DC J  30 "    0.011 2.00e-02 2.50e+03
        pdb=" C4   DC J  30 "   -0.002 2.00e-02 2.50e+03
        pdb=" N4   DC J  30 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5   DC J  30 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DC J  30 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2159 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3218
        2.79 -     3.32: 16302
        3.32 -     3.84: 34004
        3.84 -     4.37: 38628
        4.37 -     4.90: 55646
  Nonbonded interactions: 147798
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN E 108 "
            pdb=" O   GLY F  42 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" N   GLY C  44 "
            pdb=" O   ILE D  89 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" NE2 HIS A 113 "
            pdb=" OD1 ASP E 123 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" NH2 ARG G  35 "
            pdb=" OP2  DT I 129 "
     model   vdw
     2.309 3.120
  ... (remaining 147793 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 31 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 32 through 124))
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and resid 10 through 171)
  selection = (chain 'J' and resid 10 through 171)
}

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:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     18.820
  Find NCS groups from input model:        0.220
  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:             0.010
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
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   0.049  18201  Z= 0.145
  Angle     :  0.565  10.362  25994  Z= 0.351
  Chirality :  0.033   0.172   2886
  Planarity :  0.004   0.047   2162
  Dihedral  : 25.163 173.648   7755
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.23), residues: 1258
  helix:  1.94 (0.18), residues: 772
  sheet:  0.25 (0.61), residues: 77
  loop :  0.68 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 129 
 TYR   0.016   0.001   TYR K1227 
 PHE   0.024   0.001   PHE K1410 
 TRP   0.007   0.001   TRP K1472 
 HIS   0.009   0.001   HIS K1451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (18201)
  covalent geometry    : angle       0.56453 (25994)
  hydrogen bonds       : bond        0.12581 (  915)
  hydrogen bonds       : angle       5.04066 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: A  124 ILE cc_start: 0.9712 (mt) cc_final: 0.9507 (tp)
REVERT: B   84 MET cc_start: 0.7405 (tpp) cc_final: 0.7030 (mmm)
REVERT: D   59 MET cc_start: 0.9014 (tpp) cc_final: 0.8581 (tpp)
REVERT: K 1502 TRP cc_start: 0.4260 (t60) cc_final: 0.3669 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1248
  time to fit residues: 11.0494
Evaluate side-chains
  42 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    9.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    5.9990
   overall best weight:    5.7588

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
E  39 HIS
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN
G  38 ASN
K1113 GLN
K1291 HIS
K1310 ASN
K1415 GLN
** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.059167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.038337 restraints weight = 167382.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.038133 restraints weight = 89728.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.038525 restraints weight = 60546.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.038724 restraints weight = 51140.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.038803 restraints weight = 47802.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060  18201  Z= 0.375
  Angle     :  0.810  12.246  25994  Z= 0.455
  Chirality :  0.045   0.167   2886
  Planarity :  0.006   0.058   2162
  Dihedral  : 29.942 170.796   5132
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 17.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.96 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    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:  1.46 (0.23), residues: 1258
  helix:  1.36 (0.17), residues: 783
  sheet:  0.34 (0.60), residues: 78
  loop :  0.55 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F  35 
 TYR   0.022   0.002   TYR K1539 
 PHE   0.033   0.003   PHE G  25 
 TRP   0.016   0.002   TRP K1545 
 HIS   0.012   0.003   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00807 (18201)
  covalent geometry    : angle       0.80991 (25994)
  hydrogen bonds       : bond        0.08286 (  915)
  hydrogen bonds       : angle       4.39227 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8566 (mtm) cc_final: 0.8213 (mtp)
REVERT: C   56 GLU cc_start: 0.8491 (tt0) cc_final: 0.7721 (tt0)
REVERT: D   59 MET cc_start: 0.9442 (tpp) cc_final: 0.9118 (tpp)
REVERT: F   84 MET cc_start: 0.8413 (tpp) cc_final: 0.8054 (tpp)
REVERT: H   61 ILE cc_start: 0.9555 (mm) cc_final: 0.9265 (mm)
REVERT: H   62 MET cc_start: 0.9429 (tpt) cc_final: 0.9178 (tpp)
REVERT: K 1502 TRP cc_start: 0.4815 (t60) cc_final: 0.4506 (t60)
  outliers start: 2
  outliers final: 1
  residues processed: 47
  average time/residue: 0.1214
  time to fit residues: 9.6647
Evaluate side-chains
  34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 113 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   chunk 121 optimal weight:   40.0000
   chunk 128 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
E 108 ASN
K1146 GLN
K1413 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.059820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.039059 restraints weight = 166258.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 73)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.038974 restraints weight = 88770.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.039297 restraints weight = 59888.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.039567 restraints weight = 49418.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.039584 restraints weight = 45162.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  18201  Z= 0.186
  Angle     :  0.580   7.902  25994  Z= 0.341
  Chirality :  0.035   0.153   2886
  Planarity :  0.004   0.050   2162
  Dihedral  : 29.799 170.649   5132
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.24), residues: 1258
  helix:  2.07 (0.18), residues: 781
  sheet:  0.44 (0.59), residues: 76
  loop :  0.64 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  23 
 TYR   0.017   0.001   TYR K1102 
 PHE   0.020   0.002   PHE H  65 
 TRP   0.007   0.001   TRP K1545 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (18201)
  covalent geometry    : angle       0.57978 (25994)
  hydrogen bonds       : bond        0.04632 (  915)
  hydrogen bonds       : angle       3.56391 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8543 (mtm) cc_final: 0.8027 (mtp)
REVERT: D   59 MET cc_start: 0.9357 (tpp) cc_final: 0.9055 (tpp)
REVERT: H   59 MET cc_start: 0.8785 (tpp) cc_final: 0.8561 (tpp)
REVERT: H   61 ILE cc_start: 0.9533 (mm) cc_final: 0.9208 (mm)
REVERT: H   62 MET cc_start: 0.9384 (tpt) cc_final: 0.9147 (tpp)
REVERT: K 1502 TRP cc_start: 0.4789 (t60) cc_final: 0.4227 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1224
  time to fit residues: 8.9324
Evaluate side-chains
  31 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 140 optimal weight:   40.0000
   chunk 133 optimal weight:    9.9990
   chunk 89 optimal weight:   20.0000
   chunk 25 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 154 optimal weight:   40.0000
   chunk 6 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 152 optimal weight:    0.0010
   chunk 1 optimal weight:    0.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    1.9992

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

Flipped N/Q/H residues before XYZ refinement:
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1451 HIS
** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.059756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.038843 restraints weight = 165972.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 62)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.038889 restraints weight = 89045.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.039286 restraints weight = 59643.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.039434 restraints weight = 49577.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.039585 restraints weight = 45843.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  18201  Z= 0.173
  Angle     :  0.559   9.130  25994  Z= 0.330
  Chirality :  0.034   0.158   2886
  Planarity :  0.004   0.045   2162
  Dihedral  : 29.624 167.782   5132
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.24), residues: 1258
  helix:  2.24 (0.18), residues: 784
  sheet:  0.22 (0.57), residues: 77
  loop :  0.71 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  35 
 TYR   0.010   0.001   TYR K1102 
 PHE   0.015   0.001   PHE K1410 
 TRP   0.006   0.001   TRP K1545 
 HIS   0.006   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (18201)
  covalent geometry    : angle       0.55879 (25994)
  hydrogen bonds       : bond        0.04225 (  915)
  hydrogen bonds       : angle       3.34094 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8696 (mtm) cc_final: 0.7908 (mtp)
REVERT: D   59 MET cc_start: 0.9394 (tpp) cc_final: 0.9141 (tpp)
REVERT: E  106 ASP cc_start: 0.9151 (m-30) cc_final: 0.8875 (m-30)
REVERT: E  110 CYS cc_start: 0.9183 (m) cc_final: 0.8926 (m)
REVERT: F   84 MET cc_start: 0.8122 (tpp) cc_final: 0.7881 (tpp)
REVERT: H   61 ILE cc_start: 0.9481 (mm) cc_final: 0.9199 (mm)
REVERT: H   62 MET cc_start: 0.9422 (tpt) cc_final: 0.9189 (tpp)
REVERT: K 1385 MET cc_start: 0.7573 (tmm) cc_final: 0.7297 (ptm)
REVERT: K 1502 TRP cc_start: 0.4780 (t60) cc_final: 0.4572 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1281
  time to fit residues: 9.0349
Evaluate side-chains
  33 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 127 optimal weight:    7.9990
   chunk 119 optimal weight:    8.9990
   chunk 46 optimal weight:    0.6980
   chunk 129 optimal weight:   20.0000
   chunk 154 optimal weight:   30.0000
   chunk 2 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 96 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
F  25 ASN
K1628 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.057685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.037057 restraints weight = 168387.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.036774 restraints weight = 92707.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.037095 restraints weight = 63575.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.037275 restraints weight = 53123.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.037320 restraints weight = 48982.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.5228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085  18201  Z= 0.336
  Angle     :  0.719   9.595  25994  Z= 0.409
  Chirality :  0.041   0.160   2886
  Planarity :  0.005   0.040   2162
  Dihedral  : 30.278 166.573   5132
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    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:  1.73 (0.23), residues: 1258
  helix:  1.69 (0.18), residues: 783
  sheet:  0.02 (0.58), residues: 77
  loop :  0.45 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  35 
 TYR   0.013   0.002   TYR C  39 
 PHE   0.023   0.002   PHE G  25 
 TRP   0.012   0.001   TRP K1545 
 HIS   0.013   0.002   HIS K1451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00729 (18201)
  covalent geometry    : angle       0.71930 (25994)
  hydrogen bonds       : bond        0.07035 (  915)
  hydrogen bonds       : angle       4.12809 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8308 (mt-10)
REVERT: A  120 MET cc_start: 0.8546 (mtm) cc_final: 0.7828 (mtp)
REVERT: D   59 MET cc_start: 0.9367 (tpp) cc_final: 0.9144 (tpp)
REVERT: F   84 MET cc_start: 0.8288 (tpp) cc_final: 0.7658 (tpp)
REVERT: H   61 ILE cc_start: 0.9598 (mm) cc_final: 0.9304 (mm)
REVERT: H   62 MET cc_start: 0.9420 (tpt) cc_final: 0.9092 (tpp)
REVERT: K 1385 MET cc_start: 0.7153 (tmm) cc_final: 0.6881 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.1357
  time to fit residues: 8.2366
Evaluate side-chains
  30 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 128 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 98 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 79 optimal weight:    6.9990
   chunk 86 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
G  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.058875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.037921 restraints weight = 165612.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.037738 restraints weight = 91652.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.038066 restraints weight = 61748.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.038346 restraints weight = 51273.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.038363 restraints weight = 47199.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.5207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  18201  Z= 0.197
  Angle     :  0.591   7.824  25994  Z= 0.347
  Chirality :  0.036   0.144   2886
  Planarity :  0.004   0.047   2162
  Dihedral  : 30.219 170.668   5132
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.20 (0.24), residues: 1258
  helix:  2.12 (0.18), residues: 784
  sheet:  0.07 (0.59), residues: 77
  loop :  0.53 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  35 
 TYR   0.009   0.001   TYR C  57 
 PHE   0.018   0.002   PHE D  65 
 TRP   0.008   0.001   TRP K1502 
 HIS   0.007   0.001   HIS K1451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (18201)
  covalent geometry    : angle       0.59097 (25994)
  hydrogen bonds       : bond        0.04481 (  915)
  hydrogen bonds       : angle       3.52307 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.8706 (m-30) cc_final: 0.8405 (m-30)
REVERT: A  120 MET cc_start: 0.8504 (mtm) cc_final: 0.7937 (mtp)
REVERT: F   84 MET cc_start: 0.8244 (tpp) cc_final: 0.7680 (tpp)
REVERT: H   61 ILE cc_start: 0.9549 (mm) cc_final: 0.9275 (mm)
REVERT: H   62 MET cc_start: 0.9321 (tpt) cc_final: 0.9004 (tpp)
REVERT: K 1502 TRP cc_start: 0.5071 (t60) cc_final: 0.4806 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1265
  time to fit residues: 8.3492
Evaluate side-chains
  35 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 144 optimal weight:    2.9990
   chunk 137 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 38 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 95 optimal weight:    7.9990
   chunk 68 optimal weight:    0.8980
   chunk 145 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.059794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.038847 restraints weight = 163239.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 67)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.038762 restraints weight = 84207.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.039129 restraints weight = 56153.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.039370 restraints weight = 45651.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.039400 restraints weight = 42225.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.5116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  18201  Z= 0.141
  Angle     :  0.550   7.457  25994  Z= 0.324
  Chirality :  0.034   0.145   2886
  Planarity :  0.004   0.050   2162
  Dihedral  : 29.921 169.756   5132
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.24), residues: 1258
  helix:  2.33 (0.18), residues: 784
  sheet:  0.48 (0.64), residues: 67
  loop :  0.51 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K1441 
 TYR   0.011   0.001   TYR C  57 
 PHE   0.018   0.001   PHE D  65 
 TRP   0.006   0.001   TRP K1472 
 HIS   0.006   0.001   HIS K1451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (18201)
  covalent geometry    : angle       0.55026 (25994)
  hydrogen bonds       : bond        0.03819 (  915)
  hydrogen bonds       : angle       3.16844 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8557 (mtm) cc_final: 0.8029 (mtp)
REVERT: E  106 ASP cc_start: 0.9059 (m-30) cc_final: 0.8796 (m-30)
REVERT: F   84 MET cc_start: 0.8230 (tpp) cc_final: 0.7598 (tpp)
REVERT: H   61 ILE cc_start: 0.9522 (mm) cc_final: 0.9239 (mm)
REVERT: K 1412 MET cc_start: 0.1515 (mpp) cc_final: 0.1315 (mpp)
REVERT: K 1502 TRP cc_start: 0.4914 (t60) cc_final: 0.4611 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1237
  time to fit residues: 10.0021
Evaluate side-chains
  37 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 79 optimal weight:    7.9990
   chunk 128 optimal weight:   20.0000
   chunk 81 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   chunk 56 optimal weight:    0.8980
   chunk 123 optimal weight:   20.0000
   chunk 68 optimal weight:    0.7980
   chunk 119 optimal weight:    8.9990
   overall best weight:    2.1384

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.059027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.038278 restraints weight = 165303.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 78)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.038090 restraints weight = 93838.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.038408 restraints weight = 64083.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.038630 restraints weight = 53375.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 56)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.038779 restraints weight = 48982.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.5362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  18201  Z= 0.178
  Angle     :  0.570   7.827  25994  Z= 0.334
  Chirality :  0.035   0.140   2886
  Planarity :  0.004   0.051   2162
  Dihedral  : 29.939 167.814   5132
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.24), residues: 1258
  helix:  2.32 (0.18), residues: 784
  sheet:  0.22 (0.60), residues: 77
  loop :  0.58 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  92 
 TYR   0.016   0.001   TYR H  40 
 PHE   0.016   0.001   PHE D  65 
 TRP   0.006   0.001   TRP K1502 
 HIS   0.006   0.001   HIS K1451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (18201)
  covalent geometry    : angle       0.56955 (25994)
  hydrogen bonds       : bond        0.04364 (  915)
  hydrogen bonds       : angle       3.31609 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8704 (mtm) cc_final: 0.7960 (mtp)
REVERT: B   97 LEU cc_start: 0.9347 (tp) cc_final: 0.9084 (tp)
REVERT: F   84 MET cc_start: 0.8381 (tpp) cc_final: 0.7712 (tpp)
REVERT: H   61 ILE cc_start: 0.9498 (mm) cc_final: 0.9265 (mm)
REVERT: K 1502 TRP cc_start: 0.5031 (t60) cc_final: 0.4805 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.1097
  time to fit residues: 7.8434
Evaluate side-chains
  35 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 113 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 149 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
G  38 ASN
K1698 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.057923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037256 restraints weight = 167860.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.037002 restraints weight = 90876.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.037314 restraints weight = 61963.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.037591 restraints weight = 51403.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.037612 restraints weight = 46888.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.5950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  18201  Z= 0.241
  Angle     :  0.629   9.626  25994  Z= 0.363
  Chirality :  0.037   0.148   2886
  Planarity :  0.005   0.051   2162
  Dihedral  : 30.300 170.291   5132
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.24), residues: 1258
  helix:  2.05 (0.18), residues: 789
  sheet:  0.46 (0.66), residues: 67
  loop :  0.38 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  35 
 TYR   0.012   0.001   TYR E  99 
 PHE   0.017   0.002   PHE H  65 
 TRP   0.010   0.001   TRP K1502 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (18201)
  covalent geometry    : angle       0.62939 (25994)
  hydrogen bonds       : bond        0.05303 (  915)
  hydrogen bonds       : angle       3.65476 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8579 (mtm) cc_final: 0.7995 (mtp)
REVERT: F   84 MET cc_start: 0.8188 (tpp) cc_final: 0.7551 (tpp)
REVERT: H   61 ILE cc_start: 0.9511 (mm) cc_final: 0.9225 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0903
  time to fit residues: 5.7358
Evaluate side-chains
  30 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 116 optimal weight:    0.7980
   overall best weight:    1.3588

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.058878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.038287 restraints weight = 165124.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.038084 restraints weight = 91118.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.038398 restraints weight = 62508.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.038652 restraints weight = 52260.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.038647 restraints weight = 47770.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.5838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  18201  Z= 0.153
  Angle     :  0.565   7.901  25994  Z= 0.331
  Chirality :  0.034   0.143   2886
  Planarity :  0.004   0.053   2162
  Dihedral  : 30.120 172.173   5132
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.24), residues: 1258
  helix:  2.33 (0.18), residues: 783
  sheet:  0.09 (0.61), residues: 77
  loop :  0.54 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  92 
 TYR   0.012   0.001   TYR C  57 
 PHE   0.015   0.001   PHE D  65 
 TRP   0.006   0.001   TRP K1676 
 HIS   0.006   0.001   HIS K1451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (18201)
  covalent geometry    : angle       0.56483 (25994)
  hydrogen bonds       : bond        0.03963 (  915)
  hydrogen bonds       : angle       3.25568 ( 2405)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8330 (mt-10)
REVERT: A  120 MET cc_start: 0.8809 (mtm) cc_final: 0.8118 (mtp)
REVERT: B   97 LEU cc_start: 0.9332 (tp) cc_final: 0.9087 (tp)
REVERT: F   84 MET cc_start: 0.8364 (tpp) cc_final: 0.7679 (tpp)
REVERT: G   61 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8111 (mm-30)
REVERT: H   61 ILE cc_start: 0.9399 (mm) cc_final: 0.9127 (mm)
REVERT: K 1375 MET cc_start: -0.1822 (ttt) cc_final: -0.2744 (mmm)
REVERT: K 1502 TRP cc_start: 0.4902 (t60) cc_final: 0.4670 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1166
  time to fit residues: 8.4563
Evaluate side-chains
  34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 123 optimal weight:   10.0000
   chunk 114 optimal weight:    0.4980
   chunk 138 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 130 optimal weight:   20.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.059032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.038449 restraints weight = 164803.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.038214 restraints weight = 93099.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.038565 restraints weight = 62559.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.038778 restraints weight = 50728.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.038805 restraints weight = 46902.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  18201  Z= 0.143
  Angle     :  0.562   8.963  25994  Z= 0.328
  Chirality :  0.034   0.149   2886
  Planarity :  0.004   0.054   2162
  Dihedral  : 30.062 171.280   5132
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.40 (0.24), residues: 1258
  helix:  2.30 (0.18), residues: 783
  sheet:  0.18 (0.61), residues: 77
  loop :  0.56 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG F  92 
 TYR   0.010   0.001   TYR C  57 
 PHE   0.018   0.001   PHE D  65 
 TRP   0.006   0.001   TRP K1472 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (18201)
  covalent geometry    : angle       0.56185 (25994)
  hydrogen bonds       : bond        0.03903 (  915)
  hydrogen bonds       : angle       3.20175 ( 2405)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3060.62 seconds
wall clock time: 53 minutes 43.84 seconds (3223.84 seconds total)