Starting phenix.real_space_refine
on Sun Aug 24 00:17:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r04_53478/08_2025/9r04_53478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r04_53478/08_2025/9r04_53478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r04_53478/08_2025/9r04_53478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r04_53478/08_2025/9r04_53478.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r04_53478/08_2025/9r04_53478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r04_53478/08_2025/9r04_53478.map"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     283      5.49       5
     S      14      5.16       5
     C    8991      2.51       5
     N    3012      2.21       5
     O    3555      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 15855
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 789
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    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: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      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: "I"
      Number of atoms: 2891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2891
          Classifications: {'DNA': 142}
          Link IDs: {'rna3p': 141}
    Chain: "J"
      Number of atoms: 2928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 2928
          Classifications: {'DNA': 142}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 141}
    Chain: "K"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1017
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 165}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 575
          Unresolved non-hydrogen angles: 731
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11}
          Unresolved non-hydrogen planarities: 343
    Chain: "L"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1017
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 165}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 575
          Unresolved non-hydrogen angles: 731
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11}
          Unresolved non-hydrogen planarities: 343
    Chain: "M"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1017
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 165}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 575
          Unresolved non-hydrogen angles: 731
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11}
          Unresolved non-hydrogen planarities: 343
    Chain: "N"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1017
          Classifications: {'peptide': 200}
          Incomplete info: {'truncation_to_alanine': 165}
          Link IDs: {'PTRANS': 14, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 575
          Unresolved non-hydrogen angles: 731
          Unresolved non-hydrogen dihedrals: 474
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11}
          Unresolved non-hydrogen planarities: 343
  Time building chain proxies: 3.96, per 1000 atoms: 0.25
  Number of scatterers: 15855
  At special positions: 0
  Unit cell: (157.08, 121.44, 166.32, 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      14     16.00
     P     283     15.00
     O    3555      8.00
     N    3012      7.00
     C    8991      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 572.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2896

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 16 sheets defined
      40.9% alpha, 14.9% beta
      142 base pairs and 268 stacking pairs defined.
    Time for finding SS restraints: 2.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 58
    Processing helix  chain 'A' and resid 64 through 78
      removed outlier: 4.207A  pdb=" N   ASP A  78 " --> pdb=" O   GLU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 115
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'B' and resid 25 through 30
    Processing helix  chain 'B' and resid 31 through 42
    Processing helix  chain 'B' and resid 49 through 77
      removed outlier: 4.248A  pdb=" N   GLU B  53 " --> pdb=" O   GLY B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 94
      removed outlier: 4.170A  pdb=" N   GLN B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 23
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 74
      removed outlier: 3.975A  pdb=" N   VAL C  50 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'D' and resid 38 through 50
    Processing helix  chain 'D' and resid 56 through 85
    Processing helix  chain 'D' and resid 91 through 103
    Processing helix  chain 'D' and resid 104 through 125
    Processing helix  chain 'E' and resid 45 through 58
    Processing helix  chain 'E' and resid 66 through 80
      removed outlier: 4.182A  pdb=" N   ASP E  78 " --> pdb=" O   GLU E  74 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   PHE E  79 " --> pdb=" O   ILE E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
    Processing helix  chain 'E' and resid 121 through 132
    Processing helix  chain 'F' and resid 26 through 30
    Processing helix  chain 'F' and resid 31 through 42
    Processing helix  chain 'F' and resid 50 through 77
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 3.847A  pdb=" N   GLN F  94 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 23
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 74
      removed outlier: 3.946A  pdb=" N   VAL G  50 " --> pdb=" O   ALA G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 91
    Processing helix  chain 'G' and resid 93 through 98
    Processing helix  chain 'G' and resid 113 through 117
    Processing helix  chain 'H' and resid 38 through 48
    Processing helix  chain 'H' and resid 56 through 85
    Processing helix  chain 'H' and resid 91 through 103
      removed outlier: 3.516A  pdb=" N   ARG H 100 " --> pdb=" O   GLN H  96 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 125
    Processing helix  chain 'K' and resid 176 through 182
    Processing helix  chain 'K' and resid 277 through 289
    Processing helix  chain 'L' and resid 176 through 182
    Processing helix  chain 'L' and resid 277 through 289
    Processing helix  chain 'M' and resid 165 through 169
    Processing helix  chain 'M' and resid 176 through 182
    Processing helix  chain 'M' and resid 277 through 289
    Processing helix  chain 'N' and resid 176 through 182
    Processing helix  chain 'N' and resid 277 through 289
    Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 99
    Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 103
      removed outlier: 6.706A  pdb=" N   THR C 102 " --> pdb=" O   TYR F  99 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 84 through 85
      removed outlier: 6.843A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA7, first strand: chain 'G' and resid 43 through 44
      removed outlier: 6.800A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 78 through 79
    Processing sheet with id=AA9, first strand: chain 'K' and resid 110 through 112
    Processing sheet with id=AB1, first strand: chain 'K' and resid 124 through 127
      removed outlier: 3.896A  pdb=" N   ILE K 251 " --> pdb=" O   VAL K 272 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ALA K 161 " --> pdb=" O   HIS K 214 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   HIS K 214 " --> pdb=" O   ALA K 161 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 110 through 113
    Processing sheet with id=AB3, first strand: chain 'L' and resid 124 through 127
      removed outlier: 3.802A  pdb=" N   ILE L 251 " --> pdb=" O   VAL L 272 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   ALA L 161 " --> pdb=" O   HIS L 214 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   HIS L 214 " --> pdb=" O   ALA L 161 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 110 through 112
    Processing sheet with id=AB5, first strand: chain 'M' and resid 124 through 127
      removed outlier: 3.917A  pdb=" N   ILE M 251 " --> pdb=" O   VAL M 272 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   ALA M 161 " --> pdb=" O   HIS M 214 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   HIS M 214 " --> pdb=" O   ALA M 161 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'N' and resid 110 through 113
    Processing sheet with id=AB7, first strand: chain 'N' and resid 124 through 127
      removed outlier: 6.431A  pdb=" N   LEU N 257 " --> pdb=" O   LEU N 265 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ARG N 267 " --> pdb=" O   ILE N 255 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ILE N 255 " --> pdb=" O   ARG N 267 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   SER N 269 " --> pdb=" O   THR N 253 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   THR N 253 " --> pdb=" O   SER N 269 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   GLU N 271 " --> pdb=" O   ILE N 251 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ILE N 251 " --> pdb=" O   GLU N 271 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   ALA N 161 " --> pdb=" O   HIS N 214 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   HIS N 214 " --> pdb=" O   ALA N 161 " (cutoff:3.500A)

    617 hydrogen bonds defined for protein.
    1746 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      360 hydrogen bonds
      720 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      268 stacking parallelities
  Total time for adding SS restraints: 3.19

  Time building geometry restraints manager: 1.91 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: 2493
        1.33 -     1.45: 5221
        1.45 -     1.57: 8399
        1.57 -     1.69: 562
        1.69 -     1.81: 24
  Bond restraints: 16699
  Sorted by residual:
  bond pdb=" C5'  DG I  40 "
       pdb=" C4'  DG I  40 "
    ideal  model  delta    sigma   weight residual
    1.518  1.475  0.043 2.00e-02 2.50e+03 4.65e+00
  bond pdb=" C5'  DT J  50 "
       pdb=" C4'  DT J  50 "
    ideal  model  delta    sigma   weight residual
    1.518  1.477  0.041 2.00e-02 2.50e+03 4.30e+00
  bond pdb=" C5'  DT I  38 "
       pdb=" C4'  DT I  38 "
    ideal  model  delta    sigma   weight residual
    1.518  1.480  0.038 2.00e-02 2.50e+03 3.62e+00
  bond pdb=" C5'  DC J  49 "
       pdb=" C4'  DC J  49 "
    ideal  model  delta    sigma   weight residual
    1.518  1.481  0.037 2.00e-02 2.50e+03 3.46e+00
  bond pdb=" C5'  DA I  39 "
       pdb=" C4'  DA I  39 "
    ideal  model  delta    sigma   weight residual
    1.518  1.481  0.037 2.00e-02 2.50e+03 3.45e+00
  ... (remaining 16694 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 20125
        1.43 -     2.86: 2981
        2.86 -     4.30: 667
        4.30 -     5.73: 167
        5.73 -     7.16: 38
  Bond angle restraints: 23978
  Sorted by residual:
  angle pdb=" O3'  DA I 120 "
        pdb=" C3'  DA I 120 "
        pdb=" C2'  DA I 120 "
      ideal   model   delta    sigma   weight residual
     111.50  118.66   -7.16 1.50e+00 4.44e-01 2.28e+01
  angle pdb=" O3'  DT I  58 "
        pdb=" C3'  DT I  58 "
        pdb=" C2'  DT I  58 "
      ideal   model   delta    sigma   weight residual
     111.50  118.45   -6.95 1.50e+00 4.44e-01 2.14e+01
  angle pdb=" O3'  DT I  68 "
        pdb=" C3'  DT I  68 "
        pdb=" C2'  DT I  68 "
      ideal   model   delta    sigma   weight residual
     111.50  118.41   -6.91 1.50e+00 4.44e-01 2.13e+01
  angle pdb=" O3'  DT J  58 "
        pdb=" C3'  DT J  58 "
        pdb=" C2'  DT J  58 "
      ideal   model   delta    sigma   weight residual
     111.50  118.36   -6.86 1.50e+00 4.44e-01 2.09e+01
  angle pdb=" O3'  DA J  80 "
        pdb=" C3'  DA J  80 "
        pdb=" C2'  DA J  80 "
      ideal   model   delta    sigma   weight residual
     111.50  118.32   -6.82 1.50e+00 4.44e-01 2.07e+01
  ... (remaining 23973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.64: 7017
       16.64 -    33.27: 812
       33.27 -    49.91: 962
       49.91 -    66.54: 512
       66.54 -    83.18: 12
  Dihedral angle restraints: 9315
    sinusoidal: 4849
      harmonic: 4466
  Sorted by residual:
  dihedral pdb=" CA  ARG E  43 "
           pdb=" C   ARG E  43 "
           pdb=" N   PRO E  44 "
           pdb=" CA  PRO E  44 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.24  -26.76     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  ARG A  84 "
           pdb=" C   ARG A  84 "
           pdb=" N   PHE A  85 "
           pdb=" CA  PHE A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.52  -23.48     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  TYR E  42 "
           pdb=" C   TYR E  42 "
           pdb=" N   ARG E  43 "
           pdb=" CA  ARG E  43 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.27   22.73     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 9312 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1626
       0.046 -    0.093: 764
       0.093 -    0.139: 314
       0.139 -    0.185: 94
       0.185 -    0.232: 18
  Chirality restraints: 2816
  Sorted by residual:
  chirality pdb=" CA  SER N 121 "
            pdb=" N   SER N 121 "
            pdb=" C   SER N 121 "
            pdb=" CB  SER N 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  ARG K 248 "
            pdb=" N   ARG K 248 "
            pdb=" C   ARG K 248 "
            pdb=" CB  ARG K 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" C3'  DG J  95 "
            pdb=" C4'  DG J  95 "
            pdb=" O3'  DG J  95 "
            pdb=" C2'  DG J  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.43   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 2813 not shown)

  Planarity restraints: 2173
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT J  28 "    0.062 2.00e-02 2.50e+03   2.90e-02 2.10e+01
        pdb=" N1   DT J  28 "   -0.059 2.00e-02 2.50e+03
        pdb=" C2   DT J  28 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DT J  28 "   -0.012 2.00e-02 2.50e+03
        pdb=" N3   DT J  28 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DT J  28 "    0.008 2.00e-02 2.50e+03
        pdb=" O4   DT J  28 "    0.023 2.00e-02 2.50e+03
        pdb=" C5   DT J  28 "   -0.005 2.00e-02 2.50e+03
        pdb=" C7   DT J  28 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DT J  28 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I 119 "   -0.056 2.00e-02 2.50e+03   2.74e-02 1.69e+01
        pdb=" N1   DC I 119 "    0.051 2.00e-02 2.50e+03
        pdb=" C2   DC I 119 "    0.008 2.00e-02 2.50e+03
        pdb=" O2   DC I 119 "    0.008 2.00e-02 2.50e+03
        pdb=" N3   DC I 119 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I 119 "    0.004 2.00e-02 2.50e+03
        pdb=" N4   DC I 119 "   -0.029 2.00e-02 2.50e+03
        pdb=" C5   DC I 119 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DC I 119 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  48 "    0.049 2.00e-02 2.50e+03   2.49e-02 1.40e+01
        pdb=" N1   DC J  48 "   -0.050 2.00e-02 2.50e+03
        pdb=" C2   DC J  48 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DC J  48 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DC J  48 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DC J  48 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC J  48 "    0.025 2.00e-02 2.50e+03
        pdb=" C5   DC J  48 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DC J  48 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2170 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 272
        2.66 -     3.22: 14167
        3.22 -     3.78: 26892
        3.78 -     4.34: 35243
        4.34 -     4.90: 49930
  Nonbonded interactions: 126504
  Sorted by model distance:
  nonbonded pdb=" N   GLU F  53 "
            pdb=" OE1 GLU F  53 "
     model   vdw
     2.101 3.120
  nonbonded pdb=" OG  SER C  19 "
            pdb=" O   LEU C  24 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" N4   DC I 119 "
            pdb=" O4   DT J  28 "
     model   vdw
     2.402 3.120
  nonbonded pdb=" OG  SER D  88 "
            pdb=" O3'  DA I  39 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" OG1 THR D  91 "
            pdb=" OE1 GLU D  94 "
     model   vdw
     2.488 3.040
  ... (remaining 126499 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'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 18 through 119)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

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=1.00 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:             1.100
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.630
  Find NCS groups from input model:        0.200
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
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      :  0.008   0.043  16699  Z= 0.396
  Angle     :  1.169   7.161  23978  Z= 0.718
  Chirality :  0.064   0.232   2816
  Planarity :  0.010   0.098   2173
  Dihedral  : 25.010  83.176   6419
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 0.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.09 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  3.35 %
    Favored  : 96.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.06 (0.20), residues: 1528
  helix: -0.84 (0.17), residues: 600
  sheet:  1.15 (0.30), residues: 276
  loop :  0.48 (0.23), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  18 
 TYR   0.037   0.003   TYR D  41 
 PHE   0.029   0.005   PHE A  79 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.019   0.003   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00773 (16699)
  covalent geometry    : angle       1.16877 (23978)
  hydrogen bonds       : bond        0.13808 (  977)
  hydrogen bonds       : angle       6.41728 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 302
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ARG cc_start: 0.5262 (OUTLIER) cc_final: 0.4854 (tpt90)
REVERT: A   61 LEU cc_start: 0.8893 (mt) cc_final: 0.7604 (mp)
REVERT: A  106 GLU cc_start: 0.9034 (tt0) cc_final: 0.8679 (tp30)
REVERT: B   45 LYS cc_start: 0.8398 (tttt) cc_final: 0.7952 (ttmm)
REVERT: B   50 LEU cc_start: 0.9251 (mt) cc_final: 0.8777 (mp)
REVERT: B   64 GLU cc_start: 0.8933 (tt0) cc_final: 0.8547 (pt0)
REVERT: C   75 LYS cc_start: 0.8754 (mttt) cc_final: 0.8446 (mmtt)
REVERT: C   79 ILE cc_start: 0.9260 (mt) cc_final: 0.9046 (mm)
REVERT: C   96 LYS cc_start: 0.9154 (tttp) cc_final: 0.8820 (ttpt)
REVERT: C  100 ARG cc_start: 0.8032 (mmt-90) cc_final: 0.7778 (mmm-85)
REVERT: C  102 THR cc_start: 0.8865 (m) cc_final: 0.8332 (p)
REVERT: D   41 TYR cc_start: 0.9090 (m-80) cc_final: 0.8713 (m-80)
REVERT: D   60 MET cc_start: 0.8863 (tpp) cc_final: 0.8574 (tpp)
REVERT: D   63 MET cc_start: 0.9039 (mmm) cc_final: 0.8768 (mmp)
REVERT: D   94 GLU cc_start: 0.9186 (mp0) cc_final: 0.8927 (mp0)
REVERT: E   68 PHE cc_start: 0.8118 (t80) cc_final: 0.7670 (t80)
REVERT: E   81 THR cc_start: 0.8252 (p) cc_final: 0.7250 (p)
REVERT: E  121 MET cc_start: 0.8069 (mmm) cc_final: 0.7734 (mmm)
REVERT: F   45 LYS cc_start: 0.9200 (tttt) cc_final: 0.8572 (pttm)
REVERT: F   64 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8931 (mt-10)
REVERT: F   86 ASP cc_start: 0.7663 (m-30) cc_final: 0.7444 (m-30)
REVERT: F   94 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8755 (mm110)
REVERT: F  101 PHE cc_start: 0.8363 (m-80) cc_final: 0.8126 (m-80)
REVERT: G   18 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.7905 (mtm110)
REVERT: G   26 PHE cc_start: 0.8826 (m-80) cc_final: 0.8168 (m-80)
REVERT: G   51 TYR cc_start: 0.9132 (t80) cc_final: 0.8906 (t80)
REVERT: G  105 GLN cc_start: 0.7875 (mp10) cc_final: 0.7512 (mp10)
REVERT: H   48 GLN cc_start: 0.8448 (mt0) cc_final: 0.8170 (mt0)
REVERT: H   52 ASP cc_start: 0.9297 (p0) cc_final: 0.8977 (p0)
REVERT: H   83 HIS cc_start: 0.8374 (t70) cc_final: 0.7959 (t70)
REVERT: H   94 GLU cc_start: 0.8939 (mp0) cc_final: 0.8686 (mp0)
REVERT: H   96 GLN cc_start: 0.8472 (tm130) cc_final: 0.7994 (tm-30)
REVERT: H  100 ARG cc_start: 0.8844 (mtt-85) cc_final: 0.8474 (mpp80)
REVERT: H  103 LEU cc_start: 0.9459 (mt) cc_final: 0.9259 (mp)
REVERT: H  107 LEU cc_start: 0.9072 (mt) cc_final: 0.8518 (mt)
  outliers start: 4
  outliers final: 1
  residues processed: 305
  average time/residue: 0.1383
  time to fit residues: 59.9865
Evaluate side-chains
  214 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 212
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:   30.0000
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:   40.0000
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:   30.0000
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:   50.0000
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  76 HIS
E  69 GLN
E  86 GLN
** F  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  25 GLN
G  32 HIS
G  39 ASN
H  96 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.115152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.077479 restraints weight = 66795.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.079323 restraints weight = 30838.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.080452 restraints weight = 19765.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.081175 restraints weight = 15573.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.081527 restraints weight = 13671.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.102  16699  Z= 0.286
  Angle     :  0.710   8.054  23978  Z= 0.396
  Chirality :  0.043   0.270   2816
  Planarity :  0.005   0.058   2173
  Dihedral  : 28.759  81.890   4750
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.57 (0.21), residues: 1528
  helix:  1.46 (0.20), residues: 615
  sheet:  0.95 (0.29), residues: 324
  loop :  0.85 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  50 
 TYR   0.028   0.002   TYR H  43 
 PHE   0.012   0.002   PHE D  71 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.010   0.002   HIS E 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00626 (16699)
  covalent geometry    : angle       0.71024 (23978)
  hydrogen bonds       : bond        0.06675 (  977)
  hydrogen bonds       : angle       4.22626 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8334 (mp0) cc_final: 0.8049 (mp0)
REVERT: A  121 MET cc_start: 0.7733 (mtm) cc_final: 0.7337 (mtm)
REVERT: B   45 LYS cc_start: 0.9280 (tttt) cc_final: 0.8710 (ttmm)
REVERT: B   67 ILE cc_start: 0.9623 (mt) cc_final: 0.9398 (mt)
REVERT: C   39 ASN cc_start: 0.6884 (m-40) cc_final: 0.6446 (t0)
REVERT: C   57 GLU cc_start: 0.8684 (pp20) cc_final: 0.8363 (pp20)
REVERT: C  100 ARG cc_start: 0.8125 (mmt-90) cc_final: 0.7803 (mmm-85)
REVERT: D   41 TYR cc_start: 0.8974 (m-80) cc_final: 0.8755 (m-80)
REVERT: D   60 MET cc_start: 0.8828 (tpp) cc_final: 0.8460 (tpp)
REVERT: D   73 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8415 (mtp180)
REVERT: E   74 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8305 (tm-30)
REVERT: E  121 MET cc_start: 0.8477 (mmm) cc_final: 0.8130 (mmm)
REVERT: F   45 LYS cc_start: 0.9225 (tttt) cc_final: 0.8868 (tmtt)
REVERT: F   51 ILE cc_start: 0.9072 (mm) cc_final: 0.8686 (mm)
REVERT: F   64 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8905 (mt-10)
REVERT: F   65 ASN cc_start: 0.8676 (t0) cc_final: 0.8201 (t0)
REVERT: F   94 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8495 (mm-40)
REVERT: G   26 PHE cc_start: 0.8987 (m-80) cc_final: 0.8587 (m-80)
REVERT: G   91 ASP cc_start: 0.9129 (t70) cc_final: 0.8753 (t0)
REVERT: G   93 GLU cc_start: 0.9003 (mp0) cc_final: 0.8077 (mt-10)
REVERT: G  111 ASN cc_start: 0.8873 (t0) cc_final: 0.8659 (t0)
REVERT: H   52 ASP cc_start: 0.9031 (p0) cc_final: 0.8665 (p0)
REVERT: H   63 MET cc_start: 0.8851 (mmt) cc_final: 0.8218 (mmm)
REVERT: H   83 HIS cc_start: 0.8105 (t70) cc_final: 0.7761 (t70)
REVERT: H   90 ILE cc_start: 0.9307 (mm) cc_final: 0.9090 (mm)
REVERT: H   94 GLU cc_start: 0.8964 (mp0) cc_final: 0.8575 (mp0)
REVERT: H  107 LEU cc_start: 0.9014 (mt) cc_final: 0.8512 (mt)
REVERT: H  114 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8450 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1129
  time to fit residues: 39.6812
Evaluate side-chains
  180 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 177 optimal weight:    0.6980
   chunk 158 optimal weight:   30.0000
   chunk 168 optimal weight:    1.9990
   chunk 125 optimal weight:   50.0000
   chunk 106 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 143 optimal weight:   20.0000
   chunk 140 optimal weight:    0.0980
   chunk 25 optimal weight:    8.9990
   chunk 175 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  32 HIS
G  39 ASN
H  50 HIS
H  85 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.117541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.079818 restraints weight = 67073.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.081781 restraints weight = 29841.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.082972 restraints weight = 18674.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.083680 restraints weight = 14520.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.083997 restraints weight = 12725.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16699  Z= 0.159
  Angle     :  0.598   7.123  23978  Z= 0.344
  Chirality :  0.040   0.200   2816
  Planarity :  0.004   0.045   2173
  Dihedral  : 27.677  78.299   4750
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.18 (0.21), residues: 1528
  helix:  2.22 (0.21), residues: 613
  sheet:  1.11 (0.29), residues: 324
  loop :  0.97 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C  72 
 TYR   0.015   0.001   TYR H  41 
 PHE   0.012   0.001   PHE A  68 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.006   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (16699)
  covalent geometry    : angle       0.59753 (23978)
  hydrogen bonds       : bond        0.04334 (  977)
  hydrogen bonds       : angle       3.57742 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 PHE cc_start: 0.8724 (m-80) cc_final: 0.8504 (m-10)
REVERT: B   45 LYS cc_start: 0.9245 (tttt) cc_final: 0.8895 (ttmt)
REVERT: B   50 LEU cc_start: 0.8746 (mp) cc_final: 0.8307 (mp)
REVERT: B   51 ILE cc_start: 0.9296 (mt) cc_final: 0.9005 (mt)
REVERT: B   54 GLU cc_start: 0.9038 (tp30) cc_final: 0.8835 (tp30)
REVERT: B   61 VAL cc_start: 0.9515 (t) cc_final: 0.9195 (t)
REVERT: B   64 GLU cc_start: 0.8595 (tt0) cc_final: 0.8355 (pt0)
REVERT: C   39 ASN cc_start: 0.6881 (m-40) cc_final: 0.6285 (t0)
REVERT: C   85 GLN cc_start: 0.8780 (tp40) cc_final: 0.8537 (tm-30)
REVERT: C   93 GLU cc_start: 0.8621 (mp0) cc_final: 0.8408 (mp0)
REVERT: C   96 LYS cc_start: 0.9360 (tttp) cc_final: 0.8833 (tmmt)
REVERT: C  100 ARG cc_start: 0.8149 (mmt-90) cc_final: 0.7761 (mmm-85)
REVERT: D   40 ILE cc_start: 0.9458 (mp) cc_final: 0.9240 (tp)
REVERT: D   60 MET cc_start: 0.8879 (tpp) cc_final: 0.8296 (tpp)
REVERT: D   73 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8354 (mtp180)
REVERT: E   74 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8364 (tm-30)
REVERT: E  108 THR cc_start: 0.9513 (m) cc_final: 0.9289 (m)
REVERT: F   45 LYS cc_start: 0.9142 (tttt) cc_final: 0.8684 (tptp)
REVERT: F   65 ASN cc_start: 0.8665 (t0) cc_final: 0.8230 (t0)
REVERT: F   75 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8874 (tm-30)
REVERT: F   86 ASP cc_start: 0.8604 (m-30) cc_final: 0.8340 (m-30)
REVERT: F   94 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8402 (mm-40)
REVERT: G   26 PHE cc_start: 0.8813 (m-80) cc_final: 0.8477 (m-80)
REVERT: G  111 ASN cc_start: 0.8984 (t0) cc_final: 0.8680 (t0)
REVERT: H   52 ASP cc_start: 0.8983 (p0) cc_final: 0.8551 (p0)
REVERT: H   63 MET cc_start: 0.8844 (mmt) cc_final: 0.8236 (mmm)
REVERT: H   83 HIS cc_start: 0.8106 (t70) cc_final: 0.7705 (t70)
REVERT: H   94 GLU cc_start: 0.8942 (mp0) cc_final: 0.8677 (mp0)
REVERT: H  107 LEU cc_start: 0.9062 (mt) cc_final: 0.8600 (mt)
REVERT: H  114 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8055 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1080
  time to fit residues: 38.5107
Evaluate side-chains
  189 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 20 optimal weight:    0.3980
   chunk 65 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 105 optimal weight:   30.0000
   chunk 36 optimal weight:   20.0000
   chunk 112 optimal weight:   50.0000
   chunk 24 optimal weight:    0.9990
   chunk 111 optimal weight:    5.9990
   chunk 110 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 88 optimal weight:   20.0000
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
H  50 HIS
H  96 GLN
H 110 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.118312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.079509 restraints weight = 68241.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.081486 restraints weight = 30649.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.082720 restraints weight = 19569.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.083460 restraints weight = 15340.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.083827 restraints weight = 13556.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.3767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16699  Z= 0.147
  Angle     :  0.568   7.232  23978  Z= 0.328
  Chirality :  0.039   0.225   2816
  Planarity :  0.004   0.036   2173
  Dihedral  : 27.359  77.778   4750
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.35 (0.21), residues: 1528
  helix:  2.42 (0.21), residues: 609
  sheet:  1.15 (0.29), residues: 324
  loop :  1.03 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  72 
 TYR   0.011   0.001   TYR E  55 
 PHE   0.015   0.001   PHE E  68 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.008   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (16699)
  covalent geometry    : angle       0.56832 (23978)
  hydrogen bonds       : bond        0.04060 (  977)
  hydrogen bonds       : angle       3.43823 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8578 (mp0) cc_final: 0.8358 (mp0)
REVERT: A   85 PHE cc_start: 0.8680 (m-80) cc_final: 0.8442 (m-10)
REVERT: B   45 LYS cc_start: 0.9345 (tttt) cc_final: 0.8880 (ttmt)
REVERT: C   39 ASN cc_start: 0.6943 (m-40) cc_final: 0.6158 (t0)
REVERT: C   92 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8578 (tm-30)
REVERT: C   96 LYS cc_start: 0.9319 (tttp) cc_final: 0.8790 (ttpt)
REVERT: D   60 MET cc_start: 0.8774 (tpp) cc_final: 0.8335 (tpp)
REVERT: D   73 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8362 (mtp180)
REVERT: E   74 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8505 (tm-30)
REVERT: E  104 LEU cc_start: 0.9315 (tp) cc_final: 0.9084 (tp)
REVERT: F   51 ILE cc_start: 0.8892 (mm) cc_final: 0.8633 (mm)
REVERT: F   64 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8743 (mt-10)
REVERT: F   75 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8753 (tm-30)
REVERT: F   86 ASP cc_start: 0.8645 (m-30) cc_final: 0.8395 (m-30)
REVERT: F   89 TYR cc_start: 0.8569 (m-10) cc_final: 0.8161 (m-10)
REVERT: F   94 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8346 (mm-40)
REVERT: G   26 PHE cc_start: 0.8853 (m-80) cc_final: 0.8382 (m-80)
REVERT: G  111 ASN cc_start: 0.8985 (t0) cc_final: 0.8704 (t0)
REVERT: H   43 TYR cc_start: 0.8412 (p90) cc_final: 0.7962 (p90)
REVERT: H   52 ASP cc_start: 0.8931 (p0) cc_final: 0.8445 (p0)
REVERT: H   63 MET cc_start: 0.8729 (mmt) cc_final: 0.8082 (mmm)
REVERT: H   83 HIS cc_start: 0.8041 (t70) cc_final: 0.7659 (t70)
REVERT: H   90 ILE cc_start: 0.9597 (mt) cc_final: 0.9217 (mt)
REVERT: H   94 GLU cc_start: 0.8787 (mp0) cc_final: 0.8521 (mp0)
REVERT: H  103 LEU cc_start: 0.9471 (mp) cc_final: 0.9254 (mp)
REVERT: H  114 GLU cc_start: 0.8553 (mm-30) cc_final: 0.7972 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1103
  time to fit residues: 38.4941
Evaluate side-chains
  197 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 105 optimal weight:   20.0000
   chunk 106 optimal weight:    9.9990
   chunk 151 optimal weight:   10.0000
   chunk 139 optimal weight:   20.0000
   chunk 173 optimal weight:   40.0000
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0770
   chunk 114 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0060
   overall best weight:    4.2160

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

Flipped N/Q/H residues before XYZ refinement:
A 114 HIS
B  94 GLN
** F  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  25 GLN
H  48 GLN
H  50 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.112183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.074832 restraints weight = 68132.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.076533 restraints weight = 31940.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.077609 restraints weight = 20830.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.078227 restraints weight = 16521.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.078588 restraints weight = 14690.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.131  16699  Z= 0.290
  Angle     :  0.677   7.408  23978  Z= 0.387
  Chirality :  0.043   0.255   2816
  Planarity :  0.005   0.058   2173
  Dihedral  : 27.473  81.478   4750
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.94 (0.21), residues: 1528
  helix:  1.85 (0.20), residues: 620
  sheet:  0.87 (0.29), residues: 336
  loop :  1.13 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 117 
 TYR   0.038   0.002   TYR H  41 
 PHE   0.020   0.002   PHE G  26 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.009   0.003   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 (16699)
  covalent geometry    : angle       0.67682 (23978)
  hydrogen bonds       : bond        0.06606 (  977)
  hydrogen bonds       : angle       3.81411 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 PHE cc_start: 0.8670 (m-80) cc_final: 0.8465 (m-10)
REVERT: B   60 LYS cc_start: 0.9243 (ttmt) cc_final: 0.8614 (ttmt)
REVERT: B   61 VAL cc_start: 0.9563 (t) cc_final: 0.9223 (t)
REVERT: B   63 LEU cc_start: 0.9535 (tp) cc_final: 0.9236 (tp)
REVERT: B   67 ILE cc_start: 0.9638 (mt) cc_final: 0.9435 (mt)
REVERT: B   85 MET cc_start: 0.8759 (mmm) cc_final: 0.8509 (mmt)
REVERT: C   57 GLU cc_start: 0.8811 (pp20) cc_final: 0.8544 (pp20)
REVERT: C   96 LYS cc_start: 0.9301 (tttp) cc_final: 0.9015 (tptt)
REVERT: D   60 MET cc_start: 0.8860 (tpp) cc_final: 0.8275 (tpp)
REVERT: D   73 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8335 (mtp180)
REVERT: D   85 ASN cc_start: 0.9023 (t0) cc_final: 0.8723 (t0)
REVERT: E   74 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8451 (tm-30)
REVERT: E  121 MET cc_start: 0.8640 (mmm) cc_final: 0.8346 (mmm)
REVERT: F   64 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8842 (mt-10)
REVERT: F   75 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8863 (tm-30)
REVERT: F   94 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8285 (mm-40)
REVERT: G   62 GLU cc_start: 0.8458 (tp30) cc_final: 0.8223 (tp30)
REVERT: G  111 ASN cc_start: 0.8909 (t0) cc_final: 0.8666 (t0)
REVERT: H   63 MET cc_start: 0.8835 (mmt) cc_final: 0.8209 (mmm)
REVERT: H   83 HIS cc_start: 0.8060 (t70) cc_final: 0.7658 (t70)
REVERT: H   90 ILE cc_start: 0.9513 (mt) cc_final: 0.9259 (mt)
REVERT: H   94 GLU cc_start: 0.9010 (mp0) cc_final: 0.8731 (mp0)
REVERT: H  114 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7961 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0969
  time to fit residues: 29.9128
Evaluate side-chains
  169 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 126 optimal weight:   20.0000
   chunk 100 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 175 optimal weight:    7.9990
   chunk 116 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 170 optimal weight:   50.0000
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
D 110 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.115470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.076451 restraints weight = 68334.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.078263 restraints weight = 31473.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.079418 restraints weight = 20278.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.080073 restraints weight = 16122.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.080433 restraints weight = 14396.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.4753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  16699  Z= 0.162
  Angle     :  0.581   7.013  23978  Z= 0.336
  Chirality :  0.039   0.292   2816
  Planarity :  0.004   0.041   2173
  Dihedral  : 27.373  78.647   4750
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.24 (0.21), residues: 1528
  helix:  2.23 (0.20), residues: 621
  sheet:  0.93 (0.29), residues: 336
  loop :  1.17 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  72 
 TYR   0.026   0.001   TYR H  41 
 PHE   0.022   0.001   PHE E 105 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.008   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (16699)
  covalent geometry    : angle       0.58060 (23978)
  hydrogen bonds       : bond        0.04074 (  977)
  hydrogen bonds       : angle       3.43523 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.7984 (mt) cc_final: 0.7658 (mp)
REVERT: A   85 PHE cc_start: 0.8612 (m-80) cc_final: 0.8411 (m-10)
REVERT: B   45 LYS cc_start: 0.9349 (tttt) cc_final: 0.8890 (ttmt)
REVERT: B   60 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8585 (ttmt)
REVERT: B   61 VAL cc_start: 0.9471 (t) cc_final: 0.9258 (m)
REVERT: B   85 MET cc_start: 0.8598 (mmm) cc_final: 0.8282 (mmt)
REVERT: C   96 LYS cc_start: 0.9300 (tttp) cc_final: 0.9013 (tptt)
REVERT: D   60 MET cc_start: 0.8817 (tpp) cc_final: 0.8395 (tpp)
REVERT: D   73 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8412 (mtp180)
REVERT: D   85 ASN cc_start: 0.9008 (t0) cc_final: 0.8674 (t0)
REVERT: D  101 LEU cc_start: 0.9327 (mt) cc_final: 0.9031 (mt)
REVERT: E   61 LEU cc_start: 0.8975 (mt) cc_final: 0.8661 (mt)
REVERT: E   74 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8448 (tm-30)
REVERT: E  106 GLU cc_start: 0.8684 (pt0) cc_final: 0.8074 (pp20)
REVERT: E  107 ASP cc_start: 0.8868 (m-30) cc_final: 0.7710 (m-30)
REVERT: E  121 MET cc_start: 0.8580 (mmm) cc_final: 0.8271 (mmm)
REVERT: F   86 ASP cc_start: 0.8548 (m-30) cc_final: 0.8263 (m-30)
REVERT: F   94 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8228 (mm-40)
REVERT: G   88 ILE cc_start: 0.9294 (mt) cc_final: 0.9031 (mm)
REVERT: G  111 ASN cc_start: 0.8932 (t0) cc_final: 0.8651 (t0)
REVERT: H   63 MET cc_start: 0.8771 (mmt) cc_final: 0.8256 (mmm)
REVERT: H   83 HIS cc_start: 0.7982 (t70) cc_final: 0.7606 (t70)
REVERT: H   90 ILE cc_start: 0.9390 (mt) cc_final: 0.9133 (mt)
REVERT: H   94 GLU cc_start: 0.8796 (mp0) cc_final: 0.8559 (mp0)
REVERT: H  114 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7615 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1084
  time to fit residues: 36.0907
Evaluate side-chains
  185 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 96 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 122 optimal weight:   50.0000
   chunk 156 optimal weight:   50.0000
   chunk 43 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 123 optimal weight:    0.0670
   chunk 118 optimal weight:   40.0000
   overall best weight:    0.7320

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.116412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.077425 restraints weight = 67930.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.079336 restraints weight = 31182.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.080494 restraints weight = 20239.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.081162 restraints weight = 16071.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.081387 restraints weight = 14326.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.4956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16699  Z= 0.147
  Angle     :  0.570   7.386  23978  Z= 0.332
  Chirality :  0.038   0.280   2816
  Planarity :  0.004   0.039   2173
  Dihedral  : 27.056  75.694   4750
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.30 (0.22), residues: 1528
  helix:  2.25 (0.21), residues: 619
  sheet:  1.04 (0.29), residues: 332
  loop :  1.21 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  36 
 TYR   0.022   0.001   TYR H  41 
 PHE   0.009   0.001   PHE E 105 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.006   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (16699)
  covalent geometry    : angle       0.57019 (23978)
  hydrogen bonds       : bond        0.03900 (  977)
  hydrogen bonds       : angle       3.32514 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 GLU cc_start: 0.8643 (mp0) cc_final: 0.8247 (mp0)
REVERT: A   85 PHE cc_start: 0.8591 (m-80) cc_final: 0.8369 (m-10)
REVERT: B   45 LYS cc_start: 0.9340 (tttt) cc_final: 0.8888 (ttmt)
REVERT: B   60 LYS cc_start: 0.9299 (ttmt) cc_final: 0.8702 (tttt)
REVERT: B   64 GLU cc_start: 0.8548 (pm20) cc_final: 0.7991 (pm20)
REVERT: B   75 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7950 (tm-30)
REVERT: C   96 LYS cc_start: 0.9374 (tttp) cc_final: 0.9019 (tptt)
REVERT: D   60 MET cc_start: 0.8818 (tpp) cc_final: 0.8399 (tpp)
REVERT: D   73 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8409 (mtp180)
REVERT: D   85 ASN cc_start: 0.8973 (t0) cc_final: 0.8595 (t0)
REVERT: D  107 LEU cc_start: 0.8968 (mm) cc_final: 0.8510 (mm)
REVERT: E   61 LEU cc_start: 0.8978 (mt) cc_final: 0.8698 (mt)
REVERT: E   74 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8533 (tm-30)
REVERT: E  106 GLU cc_start: 0.8590 (pt0) cc_final: 0.7944 (pp20)
REVERT: E  107 ASP cc_start: 0.8767 (m-30) cc_final: 0.7613 (m-30)
REVERT: E  121 MET cc_start: 0.8665 (mmm) cc_final: 0.8414 (mmm)
REVERT: F   32 LYS cc_start: 0.9080 (pptt) cc_final: 0.8784 (ptpp)
REVERT: F   64 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8761 (mt-10)
REVERT: H   52 ASP cc_start: 0.8945 (p0) cc_final: 0.8433 (p0)
REVERT: H   63 MET cc_start: 0.8766 (mmt) cc_final: 0.8226 (mmm)
REVERT: H   83 HIS cc_start: 0.7944 (t70) cc_final: 0.7623 (t70)
REVERT: H   96 GLN cc_start: 0.9044 (tt0) cc_final: 0.8837 (pt0)
REVERT: H  106 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7484 (tm-30)
REVERT: H  107 LEU cc_start: 0.9052 (mt) cc_final: 0.8410 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.0984
  time to fit residues: 33.0128
Evaluate side-chains
  179 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 135 optimal weight:    0.0270
   chunk 142 optimal weight:   40.0000
   chunk 123 optimal weight:    0.7980
   chunk 36 optimal weight:   20.0000
   chunk 27 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 105 optimal weight:   40.0000
   chunk 166 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.6840

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

Flipped N/Q/H residues before XYZ refinement:
D 110 HIS
F  76 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.117145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.077748 restraints weight = 69299.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.079674 restraints weight = 32072.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.080894 restraints weight = 20723.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.081564 restraints weight = 16375.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.081684 restraints weight = 14549.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.5118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16699  Z= 0.142
  Angle     :  0.565   9.157  23978  Z= 0.327
  Chirality :  0.038   0.297   2816
  Planarity :  0.004   0.045   2173
  Dihedral  : 26.874  71.025   4750
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.30 (0.21), residues: 1528
  helix:  2.17 (0.20), residues: 619
  sheet:  1.14 (0.29), residues: 332
  loop :  1.23 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  36 
 TYR   0.021   0.001   TYR H  41 
 PHE   0.008   0.001   PHE E  68 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.005   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (16699)
  covalent geometry    : angle       0.56480 (23978)
  hydrogen bonds       : bond        0.03764 (  977)
  hydrogen bonds       : angle       3.31928 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.9332 (tttt) cc_final: 0.8908 (ttmt)
REVERT: B   75 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8007 (tm-30)
REVERT: C   96 LYS cc_start: 0.9297 (tttp) cc_final: 0.9050 (tptt)
REVERT: D   60 MET cc_start: 0.8785 (tpp) cc_final: 0.8346 (tpp)
REVERT: D   85 ASN cc_start: 0.9028 (t0) cc_final: 0.8700 (t0)
REVERT: E   74 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8620 (tm-30)
REVERT: E  104 LEU cc_start: 0.9378 (tp) cc_final: 0.9073 (tp)
REVERT: E  106 GLU cc_start: 0.8554 (pt0) cc_final: 0.7889 (pp20)
REVERT: E  107 ASP cc_start: 0.8771 (m-30) cc_final: 0.7664 (m-30)
REVERT: E  116 LYS cc_start: 0.9461 (mtpt) cc_final: 0.9187 (mmtt)
REVERT: E  121 MET cc_start: 0.8606 (mmm) cc_final: 0.8359 (mmm)
REVERT: F   32 LYS cc_start: 0.9033 (pptt) cc_final: 0.8740 (ptpp)
REVERT: F   64 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8741 (mt-10)
REVERT: G   88 ILE cc_start: 0.9270 (mt) cc_final: 0.9065 (mm)
REVERT: H   83 HIS cc_start: 0.7942 (t70) cc_final: 0.7598 (t70)
REVERT: H   90 ILE cc_start: 0.8894 (mt) cc_final: 0.8601 (mt)
REVERT: H  106 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7236 (tm-30)
REVERT: H  107 LEU cc_start: 0.8963 (mt) cc_final: 0.8194 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1127
  time to fit residues: 36.6204
Evaluate side-chains
  178 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 104 optimal weight:   40.0000
   chunk 95 optimal weight:    5.9990
   chunk 166 optimal weight:    9.9990
   chunk 175 optimal weight:    0.0870
   chunk 102 optimal weight:    0.6980
   chunk 157 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 82 optimal weight:    8.9990
   chunk 150 optimal weight:   10.0000
   overall best weight:    1.6560

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

Flipped N/Q/H residues before XYZ refinement:
D 110 HIS
E  56 GLN
** F  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  94 GLN ** 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 = 0.4209 r_free = 0.4209 target = 0.115450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.078218 restraints weight = 67162.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.080061 restraints weight = 30806.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.081206 restraints weight = 19798.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.081869 restraints weight = 15437.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.082197 restraints weight = 13599.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.5325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  16699  Z= 0.168
  Angle     :  0.573   7.037  23978  Z= 0.335
  Chirality :  0.039   0.374   2816
  Planarity :  0.004   0.045   2173
  Dihedral  : 26.820  72.334   4750
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.35 (0.22), residues: 1528
  helix:  2.24 (0.21), residues: 616
  sheet:  1.11 (0.29), residues: 336
  loop :  1.28 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  36 
 TYR   0.024   0.001   TYR H  41 
 PHE   0.008   0.001   PHE A 105 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.005   0.001   HIS E 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (16699)
  covalent geometry    : angle       0.57349 (23978)
  hydrogen bonds       : bond        0.04166 (  977)
  hydrogen bonds       : angle       3.34497 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.7719 (tm-30) cc_final: 0.6710 (tm-30)
REVERT: B   45 LYS cc_start: 0.9352 (tttt) cc_final: 0.8737 (ttmm)
REVERT: B   89 TYR cc_start: 0.8411 (m-10) cc_final: 0.7701 (m-10)
REVERT: C   96 LYS cc_start: 0.9347 (tttp) cc_final: 0.9055 (tptt)
REVERT: D   60 MET cc_start: 0.8774 (tpp) cc_final: 0.8398 (tpp)
REVERT: D   85 ASN cc_start: 0.9056 (t0) cc_final: 0.8702 (t0)
REVERT: E   74 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8601 (tm-30)
REVERT: E  106 GLU cc_start: 0.8645 (pt0) cc_final: 0.8374 (pp20)
REVERT: E  116 LYS cc_start: 0.9474 (mtpt) cc_final: 0.9191 (mmtt)
REVERT: E  121 MET cc_start: 0.8581 (mmm) cc_final: 0.8321 (mmm)
REVERT: F   64 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8773 (mt-10)
REVERT: G   62 GLU cc_start: 0.8384 (tp30) cc_final: 0.8112 (tp30)
REVERT: H   63 MET cc_start: 0.8850 (mmt) cc_final: 0.8171 (mmm)
REVERT: H   83 HIS cc_start: 0.8035 (t70) cc_final: 0.7702 (t70)
REVERT: H  106 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7583 (tm-30)
REVERT: H  107 LEU cc_start: 0.9082 (mt) cc_final: 0.8440 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0986
  time to fit residues: 31.3080
Evaluate side-chains
  169 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 131 optimal weight:   20.0000
   chunk 139 optimal weight:   50.0000
   chunk 78 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 179 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 126 optimal weight:   30.0000
   chunk 49 optimal weight:    0.0770
   chunk 97 optimal weight:    6.9990
   overall best weight:    4.6146

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

Flipped N/Q/H residues before XYZ refinement:
D 110 HIS
** F  94 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 = 0.4148 r_free = 0.4148 target = 0.111262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.071475 restraints weight = 70866.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.073194 restraints weight = 33848.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.074276 restraints weight = 22460.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.074927 restraints weight = 18093.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.075045 restraints weight = 16224.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.5854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.135  16699  Z= 0.302
  Angle     :  0.703   9.100  23978  Z= 0.402
  Chirality :  0.044   0.346   2816
  Planarity :  0.005   0.051   2173
  Dihedral  : 27.269  78.428   4750
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.91 (0.21), residues: 1528
  helix:  1.66 (0.20), residues: 626
  sheet:  1.11 (0.29), residues: 324
  loop :  1.14 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  36 
 TYR   0.031   0.003   TYR G  51 
 PHE   0.019   0.002   PHE A  68 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.009   0.002   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00677 (16699)
  covalent geometry    : angle       0.70303 (23978)
  hydrogen bonds       : bond        0.06423 (  977)
  hydrogen bonds       : angle       3.94238 ( 2466)

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

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

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3056 Ramachandran restraints generated.
    1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   45 LYS cc_start: 0.9293 (tttt) cc_final: 0.8732 (ttmm)
REVERT: B   64 GLU cc_start: 0.8587 (pm20) cc_final: 0.8037 (pm20)
REVERT: B   89 TYR cc_start: 0.8537 (m-10) cc_final: 0.8083 (m-10)
REVERT: C   96 LYS cc_start: 0.9439 (tttp) cc_final: 0.9011 (tptt)
REVERT: D   60 MET cc_start: 0.8773 (tpp) cc_final: 0.8311 (tpp)
REVERT: D   85 ASN cc_start: 0.9137 (t0) cc_final: 0.8794 (t0)
REVERT: E   74 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8302 (tm-30)
REVERT: E  121 MET cc_start: 0.8522 (mmm) cc_final: 0.8290 (mmm)
REVERT: G   39 ASN cc_start: 0.7811 (t0) cc_final: 0.7349 (t0)
REVERT: H   63 MET cc_start: 0.8836 (mmt) cc_final: 0.8322 (mmm)
REVERT: H   83 HIS cc_start: 0.8001 (t70) cc_final: 0.7659 (t70)
REVERT: H  114 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7809 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.0963
  time to fit residues: 29.4072
Evaluate side-chains
  162 residues out of total 1346 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 164 optimal weight:   50.0000
   chunk 62 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 159 optimal weight:   30.0000
   chunk 82 optimal weight:    7.9990
   chunk 146 optimal weight:    0.2980
   chunk 52 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
D 110 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.114805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.075683 restraints weight = 69298.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.077566 restraints weight = 32095.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.078735 restraints weight = 20934.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.079316 restraints weight = 16669.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.079754 restraints weight = 15097.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.5935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  16699  Z= 0.156
  Angle     :  0.604   8.959  23978  Z= 0.351
  Chirality :  0.039   0.339   2816
  Planarity :  0.004   0.039   2173
  Dihedral  : 27.175  82.533   4750
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.24 (0.21), residues: 1528
  helix:  2.15 (0.21), residues: 617
  sheet:  1.17 (0.29), residues: 328
  loop :  1.12 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  36 
 TYR   0.030   0.001   TYR H  41 
 PHE   0.021   0.001   PHE A  68 
 TRP   0.000   0.000   TRP K 146 
 HIS   0.005   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (16699)
  covalent geometry    : angle       0.60387 (23978)
  hydrogen bonds       : bond        0.04025 (  977)
  hydrogen bonds       : angle       3.56601 ( 2466)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2923.76 seconds
wall clock time: 50 minutes 43.93 seconds (3043.93 seconds total)