Starting phenix.real_space_refine
on Sun Jun 15 09:14:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8haj_34592/06_2025/8haj_34592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8haj_34592/06_2025/8haj_34592.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8haj_34592/06_2025/8haj_34592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8haj_34592/06_2025/8haj_34592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8haj_34592/06_2025/8haj_34592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8haj_34592/06_2025/8haj_34592.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

  Symmetric amino acids flipped. Time to flip 113 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17214
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 819
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 735
          Classifications: {'peptide': 92}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'ALY:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 673
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 730
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "I"
      Number of atoms: 3362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3362
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
    Chain: "J"
      Number of atoms: 3320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 3320
          Classifications: {'DNA': 162}
          Link IDs: {'rna3p': 161}
    Chain: "K"
      Number of atoms: 4403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4403
          Classifications: {'peptide': 533}
          Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 499}
          Chain breaks: 3
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA C  14 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA C  14 " occ=0.00
  Time building chain proxies: 9.64, per 1000 atoms: 0.56
  Number of scatterers: 17214
  At special positions: 0
  Unit cell: (107.31, 163.17, 122.01, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P     326     15.00
     O    3843      8.00
     N    3138      7.00
     C    9860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.92
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 14 sheets defined
      60.7% alpha, 6.5% beta
      115 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 6.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.669A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.794A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.016A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   HIS B  75 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.581A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.507A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.542A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.586A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.883A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 121 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.810A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLU F  74 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   HIS F  75 " --> pdb=" O   THR F  71 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.367A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
      removed outlier: 3.552A  pdb=" N   GLN H  44 " --> pdb=" O   LYS H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'K' and resid 1051 through 1068
      removed outlier: 4.161A  pdb=" N   GLN K1056 " --> pdb=" O   GLU K1052 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ALA K1057 " --> pdb=" O   GLU K1053 " (cutoff:3.500A)
      Proline residue:  K1060  - end of helix
    Processing helix  chain 'K' and resid 1072 through 1077
      removed outlier: 4.399A  pdb=" N   GLN K1077 " --> pdb=" O   LEU K1073 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1088 through 1093
    Processing helix  chain 'K' and resid 1098 through 1109
    Processing helix  chain 'K' and resid 1113 through 1132
      removed outlier: 3.775A  pdb=" N   TYR K1117 " --> pdb=" O   GLU K1113 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1136 through 1159
      removed outlier: 3.596A  pdb=" N   GLU K1152 " --> pdb=" O   VAL K1148 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ASP K1154 " --> pdb=" O   GLU K1150 " (cutoff:3.500A)
      Proline residue:  K1155  - end of helix
    Processing helix  chain 'K' and resid 1201 through 1208
      removed outlier: 3.584A  pdb=" N   PHE K1205 " --> pdb=" O   CYS K1201 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ASN K1206 " --> pdb=" O   GLU K1202 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU K1207 " --> pdb=" O   LYS K1203 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE K1208 " --> pdb=" O   CYS K1204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 1201 through 1208'
    Processing helix  chain 'K' and resid 1272 through 1279
    Processing helix  chain 'K' and resid 1296 through 1314
    Processing helix  chain 'K' and resid 1336 through 1343
    Processing helix  chain 'K' and resid 1406 through 1429
      removed outlier: 4.100A  pdb=" N   THR K1411 " --> pdb=" O   LYS K1407 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ALA K1412 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS K1427 " --> pdb=" O   GLU K1423 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1459 through 1477
    Processing helix  chain 'K' and resid 1486 through 1493
    Processing helix  chain 'K' and resid 1497 through 1501
    Processing helix  chain 'K' and resid 1507 through 1519
      removed outlier: 3.881A  pdb=" N   ASN K1511 " --> pdb=" O   ASP K1507 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1579 through 1591
    Processing helix  chain 'K' and resid 1626 through 1638
      removed outlier: 3.915A  pdb=" N   PHE K1630 " --> pdb=" O   GLY K1626 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1643 through 1664
      removed outlier: 4.048A  pdb=" N   GLN K1663 " --> pdb=" O   HIS K1659 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.161A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 7.018A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.062A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.950A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.239A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 1175 through 1176
      removed outlier: 4.151A  pdb=" N   LEU K1175 " --> pdb=" O   ILE K1185 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1192 through 1194
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1244 through 1246
    Processing sheet with id=AB5, first strand: chain 'K' and resid 1321 through 1334
      removed outlier: 6.893A  pdb=" N   ALA K1359 " --> pdb=" O   VAL K1326 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   ALA K1328 " --> pdb=" O   THR K1357 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR K1357 " --> pdb=" O   ALA K1328 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   ASP K1330 " --> pdb=" O   TYR K1355 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   TYR K1355 " --> pdb=" O   ASP K1330 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   THR K1332 " --> pdb=" O   PHE K1353 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   PHE K1353 " --> pdb=" O   THR K1332 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE K1374 " --> pdb=" O   ALA K1362 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   GLU K1364 " --> pdb=" O   CYS K1372 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   CYS K1372 " --> pdb=" O   GLU K1364 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ILE K1366 " --> pdb=" O   ASP K1370 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   ASP K1370 " --> pdb=" O   ILE K1366 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   HIS K1377 " --> pdb=" O   SER K1396 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   TRP K1436 " --> pdb=" O   ILE K1395 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   TYR K1397 " --> pdb=" O   TRP K1436 " (cutoff:3.500A)

    587 hydrogen bonds defined for protein.
    1731 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      278 hydrogen bonds
      548 hydrogen bond angles
      0 basepair planarities
      115 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 8.02

  Time building geometry restraints manager: 4.75 seconds

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

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

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

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

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 2064
       0.030 -    0.060: 608
       0.060 -    0.091: 149
       0.091 -    0.121: 61
       0.121 -    0.151: 11
  Chirality restraints: 2893
  Sorted by residual:
  chirality pdb=" CA  PRO E 121 "
            pdb=" N   PRO E 121 "
            pdb=" C   PRO E 121 "
            pdb=" CB  PRO E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" CA  ILE B  46 "
            pdb=" N   ILE B  46 "
            pdb=" C   ILE B  46 "
            pdb=" CB  ILE B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.50e-01
  chirality pdb=" P    DA J  60 "
            pdb=" OP1  DA J  60 "
            pdb=" OP2  DA J  60 "
            pdb=" O5'  DA J  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 2890 not shown)

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:          0.570
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     43.580
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  18223  Z= 0.151
  Angle     :  0.604   8.661  26005  Z= 0.369
  Chirality :  0.034   0.151   2893
  Planarity :  0.004   0.061   2182
  Dihedral  : 24.856 163.816   7764
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.23), residues: 1276
  helix:  1.37 (0.19), residues: 761
  sheet:  0.14 (0.61), residues: 65
  loop :  0.06 (0.28), residues: 450

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

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

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9156 (tp30) cc_final: 0.8689 (tt0)
REVERT: D   34 TYR cc_start: 0.9157 (m-10) cc_final: 0.8885 (m-80)
REVERT: G   78 ILE cc_start: 0.9124 (mt) cc_final: 0.8806 (mm)
REVERT: K 1129 TRP cc_start: 0.7371 (m-10) cc_final: 0.7169 (m-10)
REVERT: K 1478 ARG cc_start: 0.4409 (mmp-170) cc_final: 0.3607 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.2700
  time to fit residues: 40.8696
Evaluate side-chains
  63 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:    9.9990
   chunk 119 optimal weight:    0.5980
   chunk 66 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 80 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9980
   chunk 123 optimal weight:    8.9990
   chunk 47 optimal weight:    0.6980
   chunk 75 optimal weight:    8.9990
   chunk 92 optimal weight:    6.9990
   chunk 143 optimal weight:    0.8980
   overall best weight:    2.0382

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1132 ASN
K1236 ASN
K1261 HIS
K1661 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.059830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.041254 restraints weight = 218403.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.042396 restraints weight = 124759.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.042747 restraints weight = 81084.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  18223  Z= 0.165
  Angle     :  0.558   7.019  26005  Z= 0.327
  Chirality :  0.035   0.148   2893
  Planarity :  0.005   0.058   2182
  Dihedral  : 28.271 167.466   5103
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.22 %
    Favored  : 97.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.23), residues: 1276
  helix:  1.92 (0.19), residues: 774
  sheet:  0.18 (0.62), residues: 65
  loop :  0.18 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP K1466 
 HIS   0.011   0.001   HIS E 113 
 PHE   0.017   0.001   PHE K1508 
 TYR   0.015   0.001   TYR F  72 
 ARG   0.005   0.000   ARG K1055 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05632 (  865)
  hydrogen bonds       : angle       3.58035 ( 2279)
  covalent geometry    : bond        0.00349 (18223)
  covalent geometry    : angle       0.55789 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9483 (tp30) cc_final: 0.9185 (tt0)
REVERT: A  106 ASP cc_start: 0.8977 (t0) cc_final: 0.8676 (m-30)
REVERT: E   67 PHE cc_start: 0.8908 (t80) cc_final: 0.8366 (t80)
REVERT: E   92 LEU cc_start: 0.9418 (mp) cc_final: 0.9152 (tt)
REVERT: G   78 ILE cc_start: 0.9101 (mt) cc_final: 0.8886 (mm)
REVERT: G   89 ASN cc_start: 0.9225 (m-40) cc_final: 0.8958 (m-40)
REVERT: H   99 LEU cc_start: 0.8266 (tp) cc_final: 0.7988 (tp)
REVERT: K 1478 ARG cc_start: 0.5520 (mmp-170) cc_final: 0.4883 (tpm170)
  outliers start: 2
  outliers final: 2
  residues processed: 85
  average time/residue: 0.2505
  time to fit residues: 35.1631
Evaluate side-chains
  62 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   chunk 64 optimal weight:    0.0020
   chunk 4 optimal weight:    7.9990
   chunk 31 optimal weight:   10.0000
   chunk 152 optimal weight:   20.0000
   chunk 91 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 80 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   overall best weight:    2.1792

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
K1236 ASN
K1261 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.057976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.039785 restraints weight = 220473.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.040577 restraints weight = 125130.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.041047 restraints weight = 84702.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18223  Z= 0.164
  Angle     :  0.557   6.893  26005  Z= 0.326
  Chirality :  0.034   0.168   2893
  Planarity :  0.005   0.056   2182
  Dihedral  : 28.510 170.391   5103
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.23), residues: 1276
  helix:  2.00 (0.18), residues: 773
  sheet:  0.30 (0.68), residues: 55
  loop :  0.23 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K1466 
 HIS   0.006   0.001   HIS E 113 
 PHE   0.021   0.001   PHE K1508 
 TYR   0.018   0.002   TYR G  39 
 ARG   0.005   0.000   ARG D  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04772 (  865)
  hydrogen bonds       : angle       3.46208 ( 2279)
  covalent geometry    : bond        0.00353 (18223)
  covalent geometry    : angle       0.55702 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.9521 (tp30) cc_final: 0.9102 (tt0)
REVERT: A  106 ASP cc_start: 0.9082 (t0) cc_final: 0.8833 (m-30)
REVERT: B   97 LEU cc_start: 0.8496 (tp) cc_final: 0.8257 (tp)
REVERT: K 1157 MET cc_start: 0.4062 (ttt) cc_final: 0.2335 (ttt)
REVERT: K 1254 MET cc_start: 0.0423 (tpt) cc_final: -0.1558 (ptp)
REVERT: K 1478 ARG cc_start: 0.5438 (mmp-170) cc_final: 0.4879 (tpm170)
REVERT: K 1624 MET cc_start: -0.1520 (mmt) cc_final: -0.2250 (mmt)
REVERT: K 1652 MET cc_start: 0.6157 (tmm) cc_final: 0.5643 (ppp)
REVERT: K 1654 MET cc_start: 0.4867 (mmp) cc_final: 0.3827 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.2724
  time to fit residues: 34.4332
Evaluate side-chains
  58 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 61 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 135 optimal weight:    9.9990
   chunk 148 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   chunk 112 optimal weight:    7.9990
   chunk 145 optimal weight:   10.0000
   chunk 150 optimal weight:    0.6980
   overall best weight:    5.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN
K1227 ASN
K1236 ASN
K1379 GLN
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1591 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.052168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.034777 restraints weight = 230126.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.035494 restraints weight = 132431.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.036083 restraints weight = 94431.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066  18223  Z= 0.321
  Angle     :  0.731  10.232  26005  Z= 0.417
  Chirality :  0.041   0.233   2893
  Planarity :  0.007   0.060   2182
  Dihedral  : 29.261 170.483   5103
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 19.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.23), residues: 1276
  helix:  1.47 (0.18), residues: 772
  sheet:  0.13 (0.67), residues: 60
  loop :  0.22 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP K1122 
 HIS   0.011   0.002   HIS G  82 
 PHE   0.027   0.003   PHE D  62 
 TYR   0.023   0.003   TYR K1355 
 ARG   0.010   0.001   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10818 (  865)
  hydrogen bonds       : angle       4.07358 ( 2279)
  covalent geometry    : bond        0.00707 (18223)
  covalent geometry    : angle       0.73092 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9122 (t0) cc_final: 0.8848 (m-30)
REVERT: K 1124 MET cc_start: 0.6595 (ttm) cc_final: 0.6309 (ttm)
REVERT: K 1157 MET cc_start: 0.4127 (ttt) cc_final: 0.2698 (ttt)
REVERT: K 1254 MET cc_start: 0.2194 (tpt) cc_final: -0.0892 (ptp)
REVERT: K 1478 ARG cc_start: 0.5480 (mmp-170) cc_final: 0.4898 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2673
  time to fit residues: 30.2093
Evaluate side-chains
  48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 1.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 147 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 131 optimal weight:    9.9990
   chunk 106 optimal weight:    4.9990
   chunk 91 optimal weight:    6.9990
   chunk 124 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 137 optimal weight:    0.0270
   chunk 25 optimal weight:    5.9990
   overall best weight:    1.7444

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

Flipped N/Q/H residues before XYZ refinement:
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1230 GLN
K1236 ASN
K1261 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.054119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.036515 restraints weight = 228286.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.037201 restraints weight = 128168.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.037643 restraints weight = 86648.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  18223  Z= 0.161
  Angle     :  0.591   7.850  26005  Z= 0.342
  Chirality :  0.036   0.235   2893
  Planarity :  0.004   0.054   2182
  Dihedral  : 29.376 174.433   5103
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.77 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.23), residues: 1276
  helix:  1.82 (0.18), residues: 771
  sheet:  0.05 (0.67), residues: 60
  loop :  0.17 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K1122 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.037   0.002   PHE E 104 
 TYR   0.026   0.001   TYR A  99 
 ARG   0.004   0.000   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04457 (  865)
  hydrogen bonds       : angle       3.63362 ( 2279)
  covalent geometry    : bond        0.00346 (18223)
  covalent geometry    : angle       0.59063 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 1.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9093 (t0) cc_final: 0.8872 (m-30)
REVERT: A  120 MET cc_start: 0.8138 (ppp) cc_final: 0.7922 (ppp)
REVERT: B   63 GLU cc_start: 0.8900 (pm20) cc_final: 0.8505 (pm20)
REVERT: D   56 MET cc_start: 0.9343 (tmm) cc_final: 0.8977 (tpp)
REVERT: K 1097 MET cc_start: 0.6024 (mmm) cc_final: 0.5798 (ppp)
REVERT: K 1157 MET cc_start: 0.4603 (ttt) cc_final: 0.3152 (ttt)
REVERT: K 1254 MET cc_start: 0.1012 (tpt) cc_final: -0.0861 (ptp)
REVERT: K 1478 ARG cc_start: 0.5550 (mmp-170) cc_final: 0.4976 (tpm170)
  outliers start: 2
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2932
  time to fit residues: 37.5146
Evaluate side-chains
  55 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 93 optimal weight:    7.9990
   chunk 150 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 113 optimal weight:    0.0570
   chunk 82 optimal weight:    7.9990
   chunk 146 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 9 optimal weight:   20.0000
   chunk 78 optimal weight:    7.9990
   chunk 145 optimal weight:    6.9990
   overall best weight:    2.9502

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1236 ASN
K1261 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.053090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.035646 restraints weight = 227308.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.036370 restraints weight = 128635.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.036790 restraints weight = 85213.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.4336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  18223  Z= 0.200
  Angle     :  0.602   8.267  26005  Z= 0.349
  Chirality :  0.036   0.176   2893
  Planarity :  0.005   0.057   2182
  Dihedral  : 29.322 171.101   5103
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.23), residues: 1276
  helix:  1.95 (0.18), residues: 769
  sheet:  0.05 (0.66), residues: 60
  loop :  0.06 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1466 
 HIS   0.005   0.001   HIS E 113 
 PHE   0.019   0.002   PHE A 104 
 TYR   0.019   0.002   TYR K1585 
 ARG   0.017   0.001   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06179 (  865)
  hydrogen bonds       : angle       3.63125 ( 2279)
  covalent geometry    : bond        0.00438 (18223)
  covalent geometry    : angle       0.60175 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 1.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9140 (t0) cc_final: 0.8886 (m-30)
REVERT: K 1157 MET cc_start: 0.4828 (ttt) cc_final: 0.3810 (ttt)
REVERT: K 1254 MET cc_start: 0.1493 (tpt) cc_final: -0.0385 (ptp)
REVERT: K 1478 ARG cc_start: 0.5558 (mmp-170) cc_final: 0.4991 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.2733
  time to fit residues: 31.4683
Evaluate side-chains
  56 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 157 optimal weight:    8.9990
   chunk 113 optimal weight:    1.9990
   chunk 128 optimal weight:    5.9990
   chunk 139 optimal weight:    7.9990
   chunk 72 optimal weight:    5.9990
   chunk 141 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 101 optimal weight:    7.9990
   chunk 103 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
E 125 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1236 ASN
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.049783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.032914 restraints weight = 237060.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.033508 restraints weight = 143633.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.034079 restraints weight = 100976.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.5754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.065  18223  Z= 0.330
  Angle     :  0.741  10.055  26005  Z= 0.424
  Chirality :  0.042   0.185   2893
  Planarity :  0.007   0.065   2182
  Dihedral  : 30.106 170.319   5103
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 23.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.23), residues: 1276
  helix:  1.33 (0.18), residues: 769
  sheet: -0.46 (0.65), residues: 60
  loop : -0.27 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K1122 
 HIS   0.008   0.002   HIS K1255 
 PHE   0.021   0.003   PHE K1301 
 TYR   0.027   0.002   TYR A  99 
 ARG   0.007   0.001   ARG E 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10143 (  865)
  hydrogen bonds       : angle       4.33562 ( 2279)
  covalent geometry    : bond        0.00717 (18223)
  covalent geometry    : angle       0.74083 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 ASP cc_start: 0.9246 (t0) cc_final: 0.8879 (m-30)
REVERT: B   63 GLU cc_start: 0.9035 (pm20) cc_final: 0.8777 (pm20)
REVERT: D   68 GLU cc_start: 0.9397 (tt0) cc_final: 0.8984 (tm-30)
REVERT: K 1157 MET cc_start: 0.4556 (ttt) cc_final: 0.3795 (ttm)
REVERT: K 1254 MET cc_start: 0.2649 (tpt) cc_final: 0.0510 (ptp)
REVERT: K 1478 ARG cc_start: 0.5458 (mmp-170) cc_final: 0.5048 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.2723
  time to fit residues: 28.8721
Evaluate side-chains
  50 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 154 optimal weight:    0.9980
   chunk 153 optimal weight:    4.9990
   chunk 117 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 120 optimal weight:    6.9990
   chunk 46 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 HIS
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1236 ASN
K1261 HIS
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.048489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.030543 restraints weight = 222153.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.031485 restraints weight = 122127.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 75)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.032214 restraints weight = 84190.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.5633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  18223  Z= 0.186
  Angle     :  0.622   6.765  26005  Z= 0.359
  Chirality :  0.037   0.188   2893
  Planarity :  0.005   0.054   2182
  Dihedral  : 30.160 175.226   5103
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.23), residues: 1276
  helix:  1.69 (0.18), residues: 761
  sheet: -0.02 (0.69), residues: 54
  loop : -0.24 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP K1466 
 HIS   0.010   0.001   HIS K1415 
 PHE   0.018   0.001   PHE K1508 
 TYR   0.022   0.002   TYR A  99 
 ARG   0.008   0.001   ARG C  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05102 (  865)
  hydrogen bonds       : angle       3.93841 ( 2279)
  covalent geometry    : bond        0.00402 (18223)
  covalent geometry    : angle       0.62222 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.323 
Fit side-chains
REVERT: D   56 MET cc_start: 0.9025 (tmm) cc_final: 0.8737 (tpp)
REVERT: K 1097 MET cc_start: 0.6163 (mmm) cc_final: 0.5960 (ppp)
REVERT: K 1157 MET cc_start: 0.4198 (ttt) cc_final: 0.3627 (ttm)
REVERT: K 1254 MET cc_start: 0.3339 (tpt) cc_final: 0.1546 (ptp)
REVERT: K 1478 ARG cc_start: 0.5678 (mmp-170) cc_final: 0.5240 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.3071
  time to fit residues: 30.2425
Evaluate side-chains
  47 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 135 optimal weight:   30.0000
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9980
   chunk 124 optimal weight:    8.9990
   chunk 75 optimal weight:   10.0000
   chunk 155 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
C  38 ASN
D 106 HIS
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1236 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.051124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.034020 restraints weight = 232532.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.034716 restraints weight = 132731.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.035410 restraints weight = 85896.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.5840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  18223  Z= 0.209
  Angle     :  0.624   7.098  26005  Z= 0.359
  Chirality :  0.037   0.199   2893
  Planarity :  0.005   0.055   2182
  Dihedral  : 30.051 172.322   5103
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 15.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.62 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.23), residues: 1276
  helix:  1.67 (0.18), residues: 767
  sheet: -0.00 (0.71), residues: 54
  loop : -0.16 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP K1466 
 HIS   0.007   0.001   HIS D 106 
 PHE   0.018   0.002   PHE K1508 
 TYR   0.023   0.002   TYR A  99 
 ARG   0.004   0.000   ARG F  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06250 (  865)
  hydrogen bonds       : angle       3.86245 ( 2279)
  covalent geometry    : bond        0.00455 (18223)
  covalent geometry    : angle       0.62353 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
REVERT: D   56 MET cc_start: 0.9218 (tmm) cc_final: 0.8937 (tpp)
REVERT: D  102 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9069 (mm-30)
REVERT: K 1097 MET cc_start: 0.5955 (mmm) cc_final: 0.5630 (ppp)
REVERT: K 1157 MET cc_start: 0.4156 (ttt) cc_final: 0.3540 (ttm)
REVERT: K 1254 MET cc_start: 0.3176 (tpt) cc_final: 0.1376 (ptp)
REVERT: K 1478 ARG cc_start: 0.5720 (mmp-170) cc_final: 0.5269 (tpp-160)
REVERT: K 1588 MET cc_start: -0.0868 (mmp) cc_final: -0.1105 (mmp)
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2815
  time to fit residues: 27.5121
Evaluate side-chains
  50 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 101 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 64 optimal weight:   20.0000
   chunk 42 optimal weight:    4.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1236 ASN
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1464 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.050232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.033374 restraints weight = 231508.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.034040 restraints weight = 132818.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.034497 restraints weight = 88101.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.6305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  18223  Z= 0.251
  Angle     :  0.663   9.155  26005  Z= 0.382
  Chirality :  0.038   0.198   2893
  Planarity :  0.005   0.056   2182
  Dihedral  : 30.200 172.224   5103
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 19.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.23), residues: 1276
  helix:  1.44 (0.18), residues: 773
  sheet: -0.24 (0.69), residues: 54
  loop : -0.43 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K1122 
 HIS   0.008   0.002   HIS K1415 
 PHE   0.019   0.002   PHE K1508 
 TYR   0.026   0.002   TYR A  99 
 ARG   0.005   0.001   ARG C  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07511 (  865)
  hydrogen bonds       : angle       4.06197 ( 2279)
  covalent geometry    : bond        0.00545 (18223)
  covalent geometry    : angle       0.66341 (26005)

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

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
REVERT: D   56 MET cc_start: 0.9149 (tmm) cc_final: 0.8864 (tpp)
REVERT: K 1097 MET cc_start: 0.5635 (mmm) cc_final: 0.5309 (ptm)
REVERT: K 1157 MET cc_start: 0.4418 (ttt) cc_final: 0.3748 (ttm)
REVERT: K 1254 MET cc_start: 0.3176 (tpt) cc_final: 0.1315 (ptp)
REVERT: K 1478 ARG cc_start: 0.5674 (mmp-170) cc_final: 0.5241 (tpm170)
REVERT: K 1588 MET cc_start: -0.0513 (mmp) cc_final: -0.0723 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.2700
  time to fit residues: 25.3718
Evaluate side-chains
  48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 9 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 150 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 89 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9990
   chunk 82 optimal weight:    6.9990
   chunk 115 optimal weight:    4.9990
   chunk 8 optimal weight:    7.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1236 ASN
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.048893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.031059 restraints weight = 226060.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.032163 restraints weight = 123406.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.032815 restraints weight = 81524.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.6201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  18223  Z= 0.165
  Angle     :  0.608   8.619  26005  Z= 0.349
  Chirality :  0.036   0.186   2893
  Planarity :  0.004   0.053   2182
  Dihedral  : 30.077 174.279   5103
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 13.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.23), residues: 1276
  helix:  1.68 (0.18), residues: 768
  sheet: -0.14 (0.70), residues: 54
  loop : -0.18 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP K1122 
 HIS   0.008   0.001   HIS K1415 
 PHE   0.019   0.001   PHE K1508 
 TYR   0.021   0.001   TYR A  99 
 ARG   0.004   0.000   ARG K1137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04779 (  865)
  hydrogen bonds       : angle       3.77348 ( 2279)
  covalent geometry    : bond        0.00356 (18223)
  covalent geometry    : angle       0.60810 (26005)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5247.74 seconds
wall clock time: 91 minutes 51.11 seconds (5511.11 seconds total)