Starting phenix.real_space_refine
on Sat Oct 11 12:04:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wt6_37827/10_2025/8wt6_37827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wt6_37827/10_2025/8wt6_37827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wt6_37827/10_2025/8wt6_37827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wt6_37827/10_2025/8wt6_37827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wt6_37827/10_2025/8wt6_37827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wt6_37827/10_2025/8wt6_37827.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.071
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: 6
    Type Number    sf(0)   Gaussians
     P     234      5.49       5
     Mg      2      5.21       5
     S      48      5.16       5
     C    8431      2.51       5
     N    2726      2.21       5
     O    3302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14743
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "A"
      Number of atoms: 2420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2420
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 12, 'TRANS': 293}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2514
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 318, 2503
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 318, 2503
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 305}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 2540
    Chain: "C"
      Number of atoms: 2411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2411
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 12, 'TRANS': 292}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2498
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 12, 'TRANS': 304}
    Chain: "E"
      Number of atoms: 1275
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 59, 1252
          Classifications: {'RNA': 59}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 23, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 16, 'rna3p': 42}
      Conformer: "B"
        Number of residues, atoms: 59, 1252
          Classifications: {'RNA': 59}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 12, 'rna3p_pur': 23, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 16, 'rna3p': 42}
          bond proxies already assigned to first conformer: 1369
    Chain: "F"
      Number of atoms: 1443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 1443
          Classifications: {'RNA': 68}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 27, 'rna3p_pyr': 28}
          Link IDs: {'rna2p': 13, 'rna3p': 54}
    Chain: "G"
      Number of atoms: 509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 509
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 558
          Classifications: {'DNA': 27}
          Link IDs: {'rna3p': 26}
    Chain: "I"
      Number of atoms: 507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 507
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 602
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG B 221 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 221 " occ=0.50
    residue:
      pdb=" P  A  G E  75 " occ=0.50
      ... (44 atoms not shown)
      pdb=" C4 B  G E  75 " occ=0.50
  Time building chain proxies: 4.09, per 1000 atoms: 0.28
  Number of scatterers: 14743
  At special positions: 0
  Unit cell: (119.52, 123.314, 115.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      48     16.00
     P     234     15.00
     Mg      2     11.99
     O    3302      8.00
     N    2726      7.00
     C    8431      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: 1.22
  Conformation dependent library (CDL) restraints added in 540.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2334

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 8 sheets defined
      68.4% alpha, 9.3% beta
      87 base pairs and 138 stacking pairs defined.
    Time for finding SS restraints: 2.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 50
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 84 through 95
      removed outlier: 3.827A  pdb=" N   GLY A  88 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 117
    Processing helix  chain 'A' and resid 125 through 155
      removed outlier: 4.112A  pdb=" N   GLU A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   THR A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 187
    Processing helix  chain 'A' and resid 188 through 200
    Processing helix  chain 'A' and resid 205 through 217
      removed outlier: 3.539A  pdb=" N   ALA A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 232
      removed outlier: 3.566A  pdb=" N   PHE A 228 " --> pdb=" O   HIS A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 262
      removed outlier: 3.591A  pdb=" N   ALA A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 274 through 287
      removed outlier: 3.715A  pdb=" N   ASN A 287 " --> pdb=" O   ARG A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 317 through 321
    Processing helix  chain 'B' and resid 36 through 50
    Processing helix  chain 'B' and resid 66 through 77
    Processing helix  chain 'B' and resid 84 through 95
      removed outlier: 3.714A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
    Processing helix  chain 'B' and resid 125 through 155
      removed outlier: 3.769A  pdb=" N   GLU B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   THR B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 158
      No H-bonds generated for 'chain 'B' and resid 156 through 158'
    Processing helix  chain 'B' and resid 159 through 188
      removed outlier: 3.623A  pdb=" N   ASP B 188 " --> pdb=" O   LEU B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 200
    Processing helix  chain 'B' and resid 205 through 217
      removed outlier: 3.508A  pdb=" N   ALA B 210 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 233
      removed outlier: 3.704A  pdb=" N   PHE B 228 " --> pdb=" O   HIS B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 263
      removed outlier: 3.567A  pdb=" N   ARG B 260 " --> pdb=" O   HIS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 274
    Processing helix  chain 'B' and resid 274 through 287
    Processing helix  chain 'B' and resid 290 through 313
    Processing helix  chain 'B' and resid 317 through 321
    Processing helix  chain 'C' and resid 36 through 50
    Processing helix  chain 'C' and resid 66 through 76
    Processing helix  chain 'C' and resid 84 through 95
      removed outlier: 3.739A  pdb=" N   GLY C  88 " --> pdb=" O   ASN C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 117
    Processing helix  chain 'C' and resid 125 through 153
      removed outlier: 3.790A  pdb=" N   GLU C 153 " --> pdb=" O   LEU C 149 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 188
      removed outlier: 3.558A  pdb=" N   ASP C 188 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 188 through 200
    Processing helix  chain 'C' and resid 205 through 217
    Processing helix  chain 'C' and resid 224 through 232
      removed outlier: 3.723A  pdb=" N   PHE C 228 " --> pdb=" O   HIS C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 262
      removed outlier: 3.576A  pdb=" N   ALA C 262 " --> pdb=" O   SER C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
    Processing helix  chain 'C' and resid 274 through 287
      removed outlier: 3.600A  pdb=" N   ASN C 287 " --> pdb=" O   ARG C 283 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 290 through 313
    Processing helix  chain 'C' and resid 317 through 321
    Processing helix  chain 'D' and resid 36 through 50
    Processing helix  chain 'D' and resid 66 through 77
    Processing helix  chain 'D' and resid 84 through 95
      removed outlier: 3.670A  pdb=" N   GLY D  88 " --> pdb=" O   ASN D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 117
    Processing helix  chain 'D' and resid 125 through 155
      removed outlier: 3.956A  pdb=" N   GLU D 153 " --> pdb=" O   LEU D 149 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   THR D 154 " --> pdb=" O   ASN D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 156 through 158
      No H-bonds generated for 'chain 'D' and resid 156 through 158'
    Processing helix  chain 'D' and resid 159 through 187
    Processing helix  chain 'D' and resid 188 through 199
    Processing helix  chain 'D' and resid 205 through 217
      removed outlier: 3.570A  pdb=" N   ALA D 210 " --> pdb=" O   GLU D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 224 through 233
      removed outlier: 3.537A  pdb=" N   PHE D 228 " --> pdb=" O   HIS D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 263
      removed outlier: 3.584A  pdb=" N   LEU D 263 " --> pdb=" O   LEU D 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 263 through 274
      removed outlier: 3.549A  pdb=" N   SER D 272 " --> pdb=" O   MET D 268 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR D 274 " --> pdb=" O   ALA D 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 274 through 287
    Processing helix  chain 'D' and resid 290 through 313
    Processing helix  chain 'D' and resid 317 through 321
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34
      removed outlier: 6.480A  pdb=" N   HIS A   6 " --> pdb=" O   HIS A  56 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   CYS A  58 " --> pdb=" O   HIS A   6 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ILE A   8 " --> pdb=" O   CYS A  58 " (cutoff:3.500A)
      removed outlier: 8.446A  pdb=" N   GLU A  60 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 8.275A  pdb=" N   ILE A  10 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 34
      removed outlier: 6.775A  pdb=" N   HIS B   6 " --> pdb=" O   HIS B  56 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   CYS B  58 " --> pdb=" O   HIS B   6 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ILE B   8 " --> pdb=" O   CYS B  58 " (cutoff:3.500A)
      removed outlier: 8.621A  pdb=" N   GLU B  60 " --> pdb=" O   ILE B   8 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   ILE B  10 " --> pdb=" O   GLU B  60 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237
      removed outlier: 3.796A  pdb=" N   ARG B 250 " --> pdb=" O   ARG B 237 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 241
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34
      removed outlier: 6.520A  pdb=" N   HIS C   6 " --> pdb=" O   HIS C  56 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   CYS C  58 " --> pdb=" O   HIS C   6 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ILE C   8 " --> pdb=" O   CYS C  58 " (cutoff:3.500A)
      removed outlier: 8.465A  pdb=" N   GLU C  60 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   ILE C  10 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 34
      removed outlier: 6.673A  pdb=" N   HIS D   6 " --> pdb=" O   HIS D  56 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   CYS D  58 " --> pdb=" O   HIS D   6 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ILE D   8 " --> pdb=" O   CYS D  58 " (cutoff:3.500A)
      removed outlier: 8.477A  pdb=" N   GLU D  60 " --> pdb=" O   ILE D   8 " (cutoff:3.500A)
      removed outlier: 8.288A  pdb=" N   ILE D  10 " --> pdb=" O   GLU D  60 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 236 through 237
      removed outlier: 3.776A  pdb=" N   ARG D 250 " --> pdb=" O   ARG D 237 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 240 through 241

    672 hydrogen bonds defined for protein.
    1974 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      220 hydrogen bonds
      424 hydrogen bond angles
      0 basepair planarities
      87 basepair parallelities
      140 stacking parallelities
  Total time for adding SS restraints: 2.69

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3123
        1.34 -     1.46: 5359
        1.46 -     1.57: 6479
        1.57 -     1.69: 459
        1.69 -     1.81: 84
  Bond restraints: 15504
  Sorted by residual:
  bond pdb=" C   ILE C 201 "
       pdb=" N   PRO C 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.359 -0.026 1.01e-02 9.80e+03 6.41e+00
  bond pdb=" O5'   C F 176 "
       pdb=" C5'   C F 176 "
    ideal  model  delta    sigma   weight residual
    1.420  1.458 -0.038 1.50e-02 4.44e+03 6.31e+00
  bond pdb=" O5'   G E  53 "
       pdb=" C5'   G E  53 "
    ideal  model  delta    sigma   weight residual
    1.420  1.457 -0.037 1.50e-02 4.44e+03 6.16e+00
  bond pdb=" O5'   G E  41 "
       pdb=" C5'   G E  41 "
    ideal  model  delta    sigma   weight residual
    1.420  1.456 -0.036 1.50e-02 4.44e+03 5.84e+00
  bond pdb=" C   ILE D 201 "
       pdb=" N   PRO D 202 "
    ideal  model  delta    sigma   weight residual
    1.333  1.358 -0.024 1.01e-02 9.80e+03 5.70e+00
  ... (remaining 15499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 19192
        2.01 -     4.02: 2510
        4.02 -     6.03: 252
        6.03 -     8.04: 22
        8.04 -    10.05: 4
  Bond angle restraints: 21980
  Sorted by residual:
  angle pdb=" O3'   U F 132 "
        pdb=" P     G F 133 "
        pdb=" O5'   G F 133 "
      ideal   model   delta    sigma   weight residual
     104.00  114.05  -10.05 1.50e+00 4.44e-01 4.49e+01
  angle pdb=" O3'  DG J  32 "
        pdb=" P    DT J  33 "
        pdb=" O5'  DT J  33 "
      ideal   model   delta    sigma   weight residual
     104.00   95.56    8.44 1.50e+00 4.44e-01 3.17e+01
  angle pdb=" O3'  DA H  21 "
        pdb=" P    DT H  22 "
        pdb=" O5'  DT H  22 "
      ideal   model   delta    sigma   weight residual
     104.00   95.72    8.28 1.50e+00 4.44e-01 3.04e+01
  angle pdb=" O3'  DA I  24 "
        pdb=" P    DT I  25 "
        pdb=" O5'  DT I  25 "
      ideal   model   delta    sigma   weight residual
     104.00   95.81    8.19 1.50e+00 4.44e-01 2.98e+01
  angle pdb=" O3'  DA G  26 "
        pdb=" P    DC G  27 "
        pdb=" O5'  DC G  27 "
      ideal   model   delta    sigma   weight residual
     104.00   96.69    7.31 1.50e+00 4.44e-01 2.37e+01
  ... (remaining 21975 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.82: 8658
       34.82 -    69.63: 606
       69.63 -   104.45: 53
      104.45 -   139.27: 0
      139.27 -   174.09: 1
  Dihedral angle restraints: 9318
    sinusoidal: 5712
      harmonic: 3606
  Sorted by residual:
  dihedral pdb=" O4'   U F 159 "
           pdb=" C1'   U F 159 "
           pdb=" N1    U F 159 "
           pdb=" C2    U F 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   46.09 -174.09     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   C E  42 "
           pdb=" C2'   C E  42 "
           pdb=" C1'   C E  42 "
           pdb=" C3'   C E  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -9.61   34.61     1      8.00e+00 1.56e-02 2.65e+01
  dihedral pdb=" C4'   C E  42 "
           pdb=" O4'   C E  42 "
           pdb=" C1'   C E  42 "
           pdb=" C2'   C E  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -29.14   32.14     1      8.00e+00 1.56e-02 2.30e+01
  ... (remaining 9315 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.130: 2253
       0.130 -    0.261: 288
       0.261 -    0.391: 0
       0.391 -    0.521: 0
       0.521 -    0.652: 8
  Chirality restraints: 2549
  Sorted by residual:
  chirality pdb=" P    DA I  18 "
            pdb=" OP1  DA I  18 "
            pdb=" OP2  DA I  18 "
            pdb=" O5'  DA I  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.00   -0.65 2.00e-01 2.50e+01 1.06e+01
  chirality pdb=" P    DG I   5 "
            pdb=" OP1  DG I   5 "
            pdb=" OP2  DG I   5 "
            pdb=" O5'  DG I   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.99   -0.64 2.00e-01 2.50e+01 1.04e+01
  chirality pdb=" P    DG J  12 "
            pdb=" OP1  DG J  12 "
            pdb=" OP2  DG J  12 "
            pdb=" O5'  DG J  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.99   -0.64 2.00e-01 2.50e+01 1.03e+01
  ... (remaining 2546 not shown)

  Planarity restraints: 1975
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F 157 "   -0.071 2.00e-02 2.50e+03   2.87e-02 2.27e+01
        pdb=" N9    A F 157 "    0.046 2.00e-02 2.50e+03
        pdb=" C8    A F 157 "    0.016 2.00e-02 2.50e+03
        pdb=" N7    A F 157 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    A F 157 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    A F 157 "   -0.016 2.00e-02 2.50e+03
        pdb=" N6    A F 157 "   -0.028 2.00e-02 2.50e+03
        pdb=" N1    A F 157 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A F 157 "    0.006 2.00e-02 2.50e+03
        pdb=" N3    A F 157 "    0.015 2.00e-02 2.50e+03
        pdb=" C4    A F 157 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U F 132 "    0.040 2.00e-02 2.50e+03   2.08e-02 9.72e+00
        pdb=" N1    U F 132 "   -0.043 2.00e-02 2.50e+03
        pdb=" C2    U F 132 "   -0.012 2.00e-02 2.50e+03
        pdb=" O2    U F 132 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    U F 132 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    U F 132 "    0.010 2.00e-02 2.50e+03
        pdb=" O4    U F 132 "    0.008 2.00e-02 2.50e+03
        pdb=" C5    U F 132 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U F 132 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  26 "    0.040 2.00e-02 2.50e+03   1.96e-02 9.64e+00
        pdb=" N1   DT I  26 "   -0.042 2.00e-02 2.50e+03
        pdb=" C2   DT I  26 "   -0.009 2.00e-02 2.50e+03
        pdb=" O2   DT I  26 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I  26 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DT I  26 "    0.008 2.00e-02 2.50e+03
        pdb=" O4   DT I  26 "    0.015 2.00e-02 2.50e+03
        pdb=" C5   DT I  26 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT I  26 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6   DT I  26 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1972 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 15
        2.27 -     2.92: 5204
        2.92 -     3.58: 21840
        3.58 -     4.24: 39791
        4.24 -     4.90: 60500
  Nonbonded interactions: 127350
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 241 "
            pdb=" P    DT I  21 "
     model   vdw
     1.607 3.400
  nonbonded pdb=" OG  SER D 241 "
            pdb=" P    DA G  26 "
     model   vdw
     1.609 3.400
  nonbonded pdb=" OE2 GLU C  60 "
            pdb="MG    MG C 401 "
     model   vdw
     1.856 2.170
  nonbonded pdb="MG    MG C 401 "
            pdb=" O   HOH C 502 "
     model   vdw
     1.908 2.170
  nonbonded pdb="MG    MG A 401 "
            pdb=" O   HOH G 101 "
     model   vdw
     1.965 2.170
  ... (remaining 127345 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 99 or (resid 100 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 101 through 220 or resid 222 through 321))
  selection = (chain 'B' and (resid 5 through 220 or resid 222 through 238 or resid 251 throug \ 
h 321))
  selection = (chain 'C' and (resid 5 through 99 or (resid 100 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 101 through 220 or resid 222 through 321))
  selection = (chain 'D' and (resid 5 through 99 or (resid 100 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 101 through 220 or resid 222 through 238 or r \ 
esid 251 through 321))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.390
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
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  15504  Z= 0.482
  Angle     :  1.365  10.051  21980  Z= 0.875
  Chirality :  0.083   0.652   2549
  Planarity :  0.005   0.044   1975
  Dihedral  : 19.929 174.086   6984
  Min Nonbonded Distance : 1.607

Molprobity Statistics.
  All-atom Clashscore : 0.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  2.47 %
    Favored  : 97.13 %
  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: -1.54 (0.20), residues: 1237
  helix: -0.78 (0.15), residues: 786
  sheet: -0.88 (0.37), residues: 160
  loop : -1.21 (0.30), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.003   ARG A 300 
 TYR   0.024   0.003   TYR B 264 
 PHE   0.024   0.004   PHE A 231 
 TRP   0.037   0.009   TRP D 169 
 HIS   0.012   0.002   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00795 (15504)
  covalent geometry    : angle       1.36474 (21980)
  hydrogen bonds       : bond        0.20172 (  892)
  hydrogen bonds       : angle       6.42089 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 LYS cc_start: 0.9418 (mttm) cc_final: 0.9211 (mtmm)
REVERT: B   71 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8372 (mt-10)
REVERT: C  265 MET cc_start: 0.9357 (mmm) cc_final: 0.9029 (mmt)
REVERT: D  105 ASP cc_start: 0.8265 (t70) cc_final: 0.8041 (p0)
REVERT: D  287 ASN cc_start: 0.9065 (t0) cc_final: 0.8504 (t0)
REVERT: D  307 TYR cc_start: 0.9076 (t80) cc_final: 0.8660 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 106
  average time/residue: 1.0068
  time to fit residues: 113.2873
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   60 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 139 GLN
B  93 GLN
B  99 ASN
B 139 GLN
D  99 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.081569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.054216 restraints weight = 47271.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.2575 rms_B_bonded: 2.42
r_work: 0.2378 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2378
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2387 r_free = 0.2387    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2387 r_free = 0.2387    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15504  Z= 0.183
  Angle     :  0.588   7.238  21980  Z= 0.332
  Chirality :  0.040   0.237   2549
  Planarity :  0.004   0.039   1975
  Dihedral  : 22.014 173.577   4558
  Min Nonbonded Distance : 1.757

Molprobity Statistics.
  All-atom Clashscore : 2.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  7.21 %
    Favored  : 92.09 %
  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:  1.69 (0.23), residues: 1237
  helix:  2.00 (0.17), residues: 794
  sheet: -0.29 (0.39), residues: 164
  loop : -0.47 (0.34), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  27 
 TYR   0.016   0.002   TYR B 215 
 PHE   0.016   0.002   PHE C 280 
 TRP   0.021   0.002   TRP D  46 
 HIS   0.005   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (15504)
  covalent geometry    : angle       0.58810 (21980)
  hydrogen bonds       : bond        0.05990 (  892)
  hydrogen bonds       : angle       3.99138 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 HIS cc_start: 0.8708 (m-70) cc_final: 0.8495 (m-70)
REVERT: A  221 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8358 (ttm-80)
REVERT: A  258 SER cc_start: 0.9336 (m) cc_final: 0.8965 (t)
REVERT: B   27 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7866 (mtm110)
REVERT: B   51 LYS cc_start: 0.9396 (mttm) cc_final: 0.9191 (mtmm)
REVERT: D  105 ASP cc_start: 0.7754 (t70) cc_final: 0.7175 (p0)
REVERT: D  287 ASN cc_start: 0.8805 (t0) cc_final: 0.8526 (t160)
  outliers start: 7
  outliers final: 0
  residues processed: 84
  average time/residue: 0.8378
  time to fit residues: 75.7225
Evaluate side-chains
  75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 128 optimal weight:    6.9990
   chunk 127 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 100 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 79 optimal weight:    0.6980
   chunk 132 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN
D  99 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.078228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.050936 restraints weight = 47650.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.2540 rms_B_bonded: 2.45
r_work: 0.2339 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.2202 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2213 r_free = 0.2213    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2213 r_free = 0.2213    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.052  15504  Z= 0.355
  Angle     :  0.621   7.315  21980  Z= 0.346
  Chirality :  0.045   0.266   2549
  Planarity :  0.005   0.045   1975
  Dihedral  : 22.066 172.257   4554
  Min Nonbonded Distance : 1.726

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  8.20 %
    Favored  : 91.11 %
  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:  2.06 (0.24), residues: 1237
  helix:  2.31 (0.18), residues: 793
  sheet: -0.38 (0.37), residues: 176
  loop : -0.24 (0.37), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 320 
 TYR   0.015   0.002   TYR D 215 
 PHE   0.018   0.002   PHE B 231 
 TRP   0.021   0.003   TRP D  46 
 HIS   0.005   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00797 (15504)
  covalent geometry    : angle       0.62149 (21980)
  hydrogen bonds       : bond        0.06659 (  892)
  hydrogen bonds       : angle       3.89441 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8742 (ttp80) cc_final: 0.8342 (ttm-80)
REVERT: A  258 SER cc_start: 0.9354 (m) cc_final: 0.9010 (t)
REVERT: B   27 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8003 (mtm110)
REVERT: B   51 LYS cc_start: 0.9406 (mttm) cc_final: 0.9182 (mtmm)
REVERT: D  103 THR cc_start: 0.8758 (m) cc_final: 0.8549 (t)
REVERT: D  105 ASP cc_start: 0.8075 (t0) cc_final: 0.7379 (p0)
REVERT: D  287 ASN cc_start: 0.8851 (t0) cc_final: 0.8517 (t160)
  outliers start: 7
  outliers final: 1
  residues processed: 79
  average time/residue: 0.8802
  time to fit residues: 74.6199
Evaluate side-chains
  73 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 99 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN
D 256 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.081778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.054782 restraints weight = 41350.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2603 rms_B_bonded: 2.27
r_work: 0.2414 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2279 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2287 r_free = 0.2287    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2287 r_free = 0.2287    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15504  Z= 0.149
  Angle     :  0.509   7.452  21980  Z= 0.290
  Chirality :  0.037   0.228   2549
  Planarity :  0.004   0.046   1975
  Dihedral  : 21.957 172.761   4554
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  8.89 %
    Favored  : 90.42 %
  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:  2.42 (0.24), residues: 1237
  helix:  2.60 (0.18), residues: 794
  sheet: -0.12 (0.39), residues: 162
  loop : -0.24 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.015   0.001   TYR B  74 
 PHE   0.011   0.001   PHE C 280 
 TRP   0.016   0.002   TRP D  46 
 HIS   0.004   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (15504)
  covalent geometry    : angle       0.50940 (21980)
  hydrogen bonds       : bond        0.04827 (  892)
  hydrogen bonds       : angle       3.68530 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8334 (ttm-80)
REVERT: A  258 SER cc_start: 0.9284 (m) cc_final: 0.8953 (t)
REVERT: B   27 ARG cc_start: 0.8276 (mtm-85) cc_final: 0.7839 (mtm110)
REVERT: B   51 LYS cc_start: 0.9311 (mttm) cc_final: 0.9088 (mtmm)
REVERT: D  287 ASN cc_start: 0.8736 (t0) cc_final: 0.8423 (t160)
  outliers start: 7
  outliers final: 1
  residues processed: 83
  average time/residue: 0.8203
  time to fit residues: 73.6357
Evaluate side-chains
  76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 95 optimal weight:    0.1980
   chunk 2 optimal weight:    6.9990
   chunk 70 optimal weight:    0.8980
   chunk 33 optimal weight:    7.9990
   chunk 120 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 140 optimal weight:    4.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.080888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.053723 restraints weight = 41641.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.2581 rms_B_bonded: 2.28
r_work: 0.2389 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2254 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2291 r_free = 0.2291    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2291 r_free = 0.2291    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15504  Z= 0.187
  Angle     :  0.515   6.776  21980  Z= 0.291
  Chirality :  0.038   0.240   2549
  Planarity :  0.004   0.047   1975
  Dihedral  : 21.896 173.010   4554
  Min Nonbonded Distance : 1.822

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  9.58 %
    Favored  : 89.92 %
  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:  2.54 (0.24), residues: 1237
  helix:  2.68 (0.18), residues: 794
  sheet: -0.13 (0.38), residues: 162
  loop : -0.11 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  27 
 TYR   0.014   0.001   TYR B 307 
 PHE   0.013   0.002   PHE B 112 
 TRP   0.014   0.002   TRP D  46 
 HIS   0.004   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (15504)
  covalent geometry    : angle       0.51513 (21980)
  hydrogen bonds       : bond        0.05033 (  892)
  hydrogen bonds       : angle       3.65023 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.462 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8390 (ttm-80)
REVERT: A  258 SER cc_start: 0.9279 (m) cc_final: 0.8948 (t)
REVERT: B   27 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7837 (mtm110)
REVERT: B   51 LYS cc_start: 0.9313 (mttm) cc_final: 0.9099 (mtmm)
  outliers start: 5
  outliers final: 2
  residues processed: 77
  average time/residue: 0.8221
  time to fit residues: 68.3203
Evaluate side-chains
  75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 138 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.081123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.054157 restraints weight = 37856.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.2591 rms_B_bonded: 2.17
r_work: 0.2404 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2271 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2271
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2306
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2306 r_free = 0.2306    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2306 r_free = 0.2306    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  15504  Z= 0.177
  Angle     :  0.509   6.579  21980  Z= 0.288
  Chirality :  0.038   0.232   2549
  Planarity :  0.004   0.046   1975
  Dihedral  : 21.889 173.128   4554
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.78 %
    Favored  : 89.62 %
  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:  2.59 (0.24), residues: 1237
  helix:  2.71 (0.18), residues: 794
  sheet: -0.06 (0.38), residues: 162
  loop : -0.13 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 221 
 TYR   0.016   0.001   TYR B  74 
 PHE   0.012   0.002   PHE B 112 
 TRP   0.014   0.002   TRP D  46 
 HIS   0.004   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (15504)
  covalent geometry    : angle       0.50901 (21980)
  hydrogen bonds       : bond        0.04905 (  892)
  hydrogen bonds       : angle       3.63095 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.437 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8272 (ttm-80)
REVERT: A  258 SER cc_start: 0.9283 (m) cc_final: 0.8955 (t)
REVERT: B   27 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.7801 (mtm110)
REVERT: B   51 LYS cc_start: 0.9310 (mttm) cc_final: 0.9093 (mtmm)
  outliers start: 6
  outliers final: 2
  residues processed: 78
  average time/residue: 0.8064
  time to fit residues: 68.0754
Evaluate side-chains
  76 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 131 optimal weight:    6.9990
   chunk 92 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 132 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B  93 GLN
B 139 GLN
D  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.082630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.055494 restraints weight = 47546.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.2619 rms_B_bonded: 2.40
r_work: 0.2425 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2425
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2462 r_free = 0.2462    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2462 r_free = 0.2462    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15504  Z= 0.141
  Angle     :  0.488   6.073  21980  Z= 0.277
  Chirality :  0.036   0.227   2549
  Planarity :  0.004   0.047   1975
  Dihedral  : 21.833 173.203   4554
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 10.28 %
    Favored  : 89.43 %
  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:  2.73 (0.24), residues: 1237
  helix:  2.80 (0.18), residues: 795
  sheet:  0.11 (0.38), residues: 160
  loop : -0.11 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  27 
 TYR   0.013   0.001   TYR C 307 
 PHE   0.011   0.001   PHE B 112 
 TRP   0.013   0.001   TRP D  46 
 HIS   0.003   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (15504)
  covalent geometry    : angle       0.48797 (21980)
  hydrogen bonds       : bond        0.04401 (  892)
  hydrogen bonds       : angle       3.52270 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8255 (ttm-80)
REVERT: A  258 SER cc_start: 0.9212 (m) cc_final: 0.8876 (t)
  outliers start: 3
  outliers final: 1
  residues processed: 79
  average time/residue: 0.7981
  time to fit residues: 68.2661
Evaluate side-chains
  75 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 107 optimal weight:    0.5980
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.081712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.054193 restraints weight = 53474.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.2592 rms_B_bonded: 2.56
r_work: 0.2390 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15504  Z= 0.179
  Angle     :  0.505   5.630  21980  Z= 0.284
  Chirality :  0.037   0.230   2549
  Planarity :  0.004   0.050   1975
  Dihedral  : 21.828 173.209   4554
  Min Nonbonded Distance : 1.793

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 10.87 %
    Favored  : 88.83 %
  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:  2.72 (0.24), residues: 1237
  helix:  2.80 (0.18), residues: 795
  sheet:  0.11 (0.38), residues: 160
  loop : -0.12 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  27 
 TYR   0.014   0.001   TYR C 307 
 PHE   0.013   0.002   PHE B 112 
 TRP   0.012   0.002   TRP D  46 
 HIS   0.004   0.001   HIS D 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (15504)
  covalent geometry    : angle       0.50504 (21980)
  hydrogen bonds       : bond        0.04741 (  892)
  hydrogen bonds       : angle       3.54139 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8289 (ttm-80)
REVERT: A  258 SER cc_start: 0.9218 (m) cc_final: 0.8883 (t)
REVERT: B   27 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7797 (mtp-110)
  outliers start: 3
  outliers final: 2
  residues processed: 75
  average time/residue: 0.8341
  time to fit residues: 67.6589
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Chi-restraints excluded: chain D residue  158 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 41 optimal weight:    0.0010
   chunk 1 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9980
   chunk 140 optimal weight:    4.9990
   chunk 110 optimal weight:    0.0670
   chunk 59 optimal weight:    6.9990
   chunk 81 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 123 optimal weight:    6.9990
   overall best weight:    0.4924

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN
D 287 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.083029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.055785 restraints weight = 45490.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.2628 rms_B_bonded: 2.38
r_work: 0.2435 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2435
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2472 r_free = 0.2472    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2472 r_free = 0.2472    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  15504  Z= 0.117
  Angle     :  0.490   5.400  21980  Z= 0.278
  Chirality :  0.035   0.223   2549
  Planarity :  0.004   0.048   1975
  Dihedral  : 21.855 173.454   4554
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 11.46 %
    Favored  : 88.44 %
  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:  2.76 (0.24), residues: 1237
  helix:  2.83 (0.18), residues: 796
  sheet:  0.33 (0.39), residues: 148
  loop : -0.24 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  27 
 TYR   0.014   0.001   TYR C 307 
 PHE   0.009   0.001   PHE C 280 
 TRP   0.012   0.001   TRP D  46 
 HIS   0.002   0.000   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (15504)
  covalent geometry    : angle       0.49049 (21980)
  hydrogen bonds       : bond        0.04355 (  892)
  hydrogen bonds       : angle       3.50745 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.464 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8254 (ttm-80)
REVERT: A  258 SER cc_start: 0.9216 (m) cc_final: 0.8875 (t)
REVERT: B   27 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7721 (mtp-110)
  outliers start: 1
  outliers final: 1
  residues processed: 77
  average time/residue: 0.8160
  time to fit residues: 68.0326
Evaluate side-chains
  77 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  150 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 122 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 133 optimal weight:    7.9990
   chunk 14 optimal weight:    0.7980
   chunk 119 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
B 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.084192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.056913 restraints weight = 55310.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.2646 rms_B_bonded: 2.57
r_work: 0.2449 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2489
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2489 r_free = 0.2489    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2489 r_free = 0.2489    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2489
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15504  Z= 0.129
  Angle     :  0.480   6.258  21980  Z= 0.270
  Chirality :  0.035   0.221   2549
  Planarity :  0.004   0.047   1975
  Dihedral  : 21.794 172.969   4554
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 11.46 %
    Favored  : 88.34 %
  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:  2.91 (0.24), residues: 1237
  helix:  2.89 (0.18), residues: 799
  sheet:  0.49 (0.39), residues: 150
  loop : -0.10 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  27 
 TYR   0.013   0.001   TYR B 307 
 PHE   0.011   0.001   PHE B 112 
 TRP   0.011   0.001   TRP D  46 
 HIS   0.003   0.000   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (15504)
  covalent geometry    : angle       0.48006 (21980)
  hydrogen bonds       : bond        0.04123 (  892)
  hydrogen bonds       : angle       3.44581 ( 2398)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.489 
Fit side-chains
REVERT: A  221 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8468 (ttm-80)
REVERT: A  258 SER cc_start: 0.9202 (m) cc_final: 0.8875 (t)
REVERT: B   27 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.8016 (mtp-110)
REVERT: D  246 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8203 (tpp-160)
  outliers start: 2
  outliers final: 0
  residues processed: 80
  average time/residue: 0.8249
  time to fit residues: 71.4717
Evaluate side-chains
  78 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 121 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.082176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.054748 restraints weight = 52219.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.2629 rms_B_bonded: 2.51
r_work: 0.2428 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2437 r_free = 0.2437    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2437 r_free = 0.2437    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15504  Z= 0.178
  Angle     :  0.504   8.006  21980  Z= 0.281
  Chirality :  0.037   0.222   2549
  Planarity :  0.004   0.047   1975
  Dihedral  : 21.826 173.108   4554
  Min Nonbonded Distance : 1.817

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 11.36 %
    Favored  : 88.54 %
  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:  2.84 (0.24), residues: 1237
  helix:  2.85 (0.18), residues: 797
  sheet:  0.22 (0.38), residues: 162
  loop : -0.02 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  27 
 TYR   0.014   0.001   TYR C 307 
 PHE   0.013   0.002   PHE B 112 
 TRP   0.011   0.001   TRP C  46 
 HIS   0.004   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (15504)
  covalent geometry    : angle       0.50364 (21980)
  hydrogen bonds       : bond        0.04718 (  892)
  hydrogen bonds       : angle       3.49644 ( 2398)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5205.07 seconds
wall clock time: 89 minutes 24.96 seconds (5364.96 seconds total)