Starting phenix.real_space_refine
on Sun Jun  8 01:47:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i0n_35104/06_2025/8i0n_35104.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i0n_35104/06_2025/8i0n_35104.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i0n_35104/06_2025/8i0n_35104.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i0n_35104/06_2025/8i0n_35104.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i0n_35104/06_2025/8i0n_35104.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i0n_35104/06_2025/8i0n_35104.cif"
  }
  resolution = 3.26
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.040
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      10      5.49       5
     S      32      5.16       5
     C    5798      2.51       5
     N    1546      2.21       5
     O    1755      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9141
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2775
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 28, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 78
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 75
    Chain: "B"
      Number of atoms: 2767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2767
          Classifications: {'peptide': 362}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 28, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 80
    Chain: "H"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 908
          Classifications: {'peptide': 117}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113}
    Chain: "I"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 908
          Classifications: {'peptide': 117}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 804
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "M"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 799
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "U"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 90
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'TPO:plan-1': 3}
          Unresolved non-hydrogen planarities: 3
    Chain: "V"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 90
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Planarities with less than four sites: {'TPO:plan-1': 3}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 5.95, per 1000 atoms: 0.65
  Number of scatterers: 9141
  At special positions: 0
  Unit cell: (113.436, 168.104, 84.7354, 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      32     16.00
     P      10     15.00
     O    1755      8.00
     N    1546      7.00
     C    5798      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  25 " - pdb=" SG  CYS I  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  24 " - pdb=" SG  CYS M  89 " distance=2.03

  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: 2.28
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2228

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 22 sheets defined
      5.6% alpha, 47.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 109
      removed outlier: 3.686A  pdb=" N   ARG A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 161
      No H-bonds generated for 'chain 'A' and resid 159 through 161'
    Processing helix  chain 'A' and resid 278 through 282
      removed outlier: 4.114A  pdb=" N   ARG A 282 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 94
      removed outlier: 3.912A  pdb=" N   LYS B  94 " --> pdb=" O   PRO B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 109
      removed outlier: 3.700A  pdb=" N   ARG B 103 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 278 through 282
      removed outlier: 4.108A  pdb=" N   ARG B 282 " --> pdb=" O   ALA B 279 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 4.176A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 65 through 68
      removed outlier: 3.640A  pdb=" N   LYS I  68 " --> pdb=" O   ASP I  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 65 through 68'
    Processing helix  chain 'I' and resid 77 through 79
      No H-bonds generated for 'chain 'I' and resid 77 through 79'
    Processing helix  chain 'I' and resid 90 through 94
      removed outlier: 4.142A  pdb=" N   THR I  94 " --> pdb=" O   ALA I  91 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 80 through 84
      removed outlier: 4.260A  pdb=" N   PHE M  84 " --> pdb=" O   PRO M  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28
      removed outlier: 3.742A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 10.117A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL A  55 " --> pdb=" O   ASN A  83 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ASN A  83 " --> pdb=" O   VAL A  55 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU A  57 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   CYS A  59 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28
      removed outlier: 3.742A  pdb=" N   TYR A 144 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LYS A 170 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 10.117A  pdb=" N   VAL A 142 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   CYS A 140 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 189
    Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208
      removed outlier: 4.215A  pdb=" N   TYR A 321 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   LEU A 351 " --> pdb=" O   VAL A 319 " (cutoff:3.500A)
      removed outlier: 9.280A  pdb=" N   VAL A 319 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ILE A 231 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   GLU A 257 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ILE A 233 " --> pdb=" O   MET A 255 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   MET A 255 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   VAL A 235 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   TYR A 249 " --> pdb=" O   ALA A 239 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 117
    Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.750A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 10.142A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   VAL B  55 " --> pdb=" O   ASN B  83 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ASN B  83 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU B  57 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   CYS B  59 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28
      removed outlier: 3.750A  pdb=" N   TYR B 144 " --> pdb=" O   ILE B 168 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   LYS B 170 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 10.142A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   CYS B 140 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 183 through 189
    Processing sheet with id=AB1, first strand: chain 'B' and resid 207 through 208
      removed outlier: 3.518A  pdb=" N   PHE B 349 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   TYR B 321 " --> pdb=" O   PHE B 349 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   LEU B 351 " --> pdb=" O   VAL B 319 " (cutoff:3.500A)
      removed outlier: 9.318A  pdb=" N   VAL B 319 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ILE B 231 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   GLU B 257 " --> pdb=" O   ILE B 231 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   ILE B 233 " --> pdb=" O   MET B 255 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   MET B 255 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL B 235 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TYR B 249 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.892A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TYR H 112 " --> pdb=" O   ARG H 101 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 63
      removed outlier: 6.892A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   SER H  53 " --> pdb=" O   ILE H  37 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ILE H  37 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   SER H  55 " --> pdb=" O   SER H  35 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   SER H  35 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'I' and resid 6 through 10
    Processing sheet with id=AB6, first strand: chain 'I' and resid 60 through 63
      removed outlier: 6.885A  pdb=" N   TRP I  39 " --> pdb=" O   VAL I  51 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   SER I  53 " --> pdb=" O   ILE I  37 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ILE I  37 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   SER I  55 " --> pdb=" O   SER I  35 " (cutoff:3.500A)
      removed outlier: 8.773A  pdb=" N   SER I  35 " --> pdb=" O   SER I  55 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   TYR I 112 " --> pdb=" O   ARG I 101 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'I' and resid 60 through 63
      removed outlier: 6.885A  pdb=" N   TRP I  39 " --> pdb=" O   VAL I  51 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   SER I  53 " --> pdb=" O   ILE I  37 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   ILE I  37 " --> pdb=" O   SER I  53 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   SER I  55 " --> pdb=" O   SER I  35 " (cutoff:3.500A)
      removed outlier: 8.773A  pdb=" N   SER I  35 " --> pdb=" O   SER I  55 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 5 through 8
    Processing sheet with id=AB9, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.505A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.874A  pdb=" N   THR L  98 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'M' and resid 5 through 8
    Processing sheet with id=AC3, first strand: chain 'M' and resid 11 through 13
      removed outlier: 6.484A  pdb=" N   VAL M  34 " --> pdb=" O   TYR M  50 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   TYR M  50 " --> pdb=" O   VAL M  34 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   TRP M  36 " --> pdb=" O   LEU M  48 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'M' and resid 11 through 13
      removed outlier: 3.838A  pdb=" N   THR M  98 " --> pdb=" O   GLN M  91 " (cutoff:3.500A)

    397 hydrogen bonds defined for protein.
    1035 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.86

  Time building geometry restraints manager: 2.70 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: 1767
        1.33 -     1.45: 2226
        1.45 -     1.57: 5284
        1.57 -     1.69: 28
        1.69 -     1.81: 42
  Bond restraints: 9347
  Sorted by residual:
  bond pdb=" OG1 TPO V 339 "
       pdb=" P   TPO V 339 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.05e+01
  bond pdb=" OG1 TPO U 339 "
       pdb=" P   TPO U 339 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" OG1 TPO V 336 "
       pdb=" P   TPO V 336 "
    ideal  model  delta    sigma   weight residual
    1.717  1.607  0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" OG1 TPO U 336 "
       pdb=" P   TPO U 336 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" OG1 TPO V 342 "
       pdb=" P   TPO V 342 "
    ideal  model  delta    sigma   weight residual
    1.717  1.616  0.101 2.00e-02 2.50e+03 2.56e+01
  ... (remaining 9342 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 12561
        2.52 -     5.04: 138
        5.04 -     7.55: 20
        7.55 -    10.07: 8
       10.07 -    12.59: 6
  Bond angle restraints: 12733
  Sorted by residual:
  angle pdb=" N   PRO B 360 "
        pdb=" CA  PRO B 360 "
        pdb=" C   PRO B 360 "
      ideal   model   delta    sigma   weight residual
     110.70  103.37    7.33 1.22e+00 6.72e-01 3.61e+01
  angle pdb=" CB  TPO V 339 "
        pdb=" OG1 TPO V 339 "
        pdb=" P   TPO V 339 "
      ideal   model   delta    sigma   weight residual
     119.31  106.72   12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" CB  TPO U 339 "
        pdb=" OG1 TPO U 339 "
        pdb=" P   TPO U 339 "
      ideal   model   delta    sigma   weight residual
     119.31  107.13   12.18 3.00e+00 1.11e-01 1.65e+01
  angle pdb=" CB  TPO V 336 "
        pdb=" OG1 TPO V 336 "
        pdb=" P   TPO V 336 "
      ideal   model   delta    sigma   weight residual
     119.31  107.38   11.93 3.00e+00 1.11e-01 1.58e+01
  angle pdb=" OG1 TPO U 342 "
        pdb=" P   TPO U 342 "
        pdb=" O1P TPO U 342 "
      ideal   model   delta    sigma   weight residual
     100.43  112.33  -11.90 3.00e+00 1.11e-01 1.57e+01
  ... (remaining 12728 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 5117
       17.97 -    35.94: 389
       35.94 -    53.90: 77
       53.90 -    71.87: 20
       71.87 -    89.84: 16
  Dihedral angle restraints: 5619
    sinusoidal: 2151
      harmonic: 3468
  Sorted by residual:
  dihedral pdb=" CA  GLU A 364 "
           pdb=" C   GLU A 364 "
           pdb=" N   VAL A 365 "
           pdb=" CA  VAL A 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.83  -16.17     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CB  GLU B 206 "
           pdb=" CG  GLU B 206 "
           pdb=" CD  GLU B 206 "
           pdb=" OE1 GLU B 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.52  -87.52     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CA  GLU B 364 "
           pdb=" C   GLU B 364 "
           pdb=" N   VAL B 365 "
           pdb=" CA  VAL B 365 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.07  -15.93     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 5616 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1040
       0.040 -    0.080: 260
       0.080 -    0.121: 131
       0.121 -    0.161: 18
       0.161 -    0.201: 1
  Chirality restraints: 1450
  Sorted by residual:
  chirality pdb=" CA  PRO B 360 "
            pdb=" N   PRO B 360 "
            pdb=" C   PRO B 360 "
            pdb=" CB  PRO B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.92   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  VAL A  84 "
            pdb=" N   VAL A  84 "
            pdb=" C   VAL A  84 "
            pdb=" CB  VAL A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  ILE A 318 "
            pdb=" N   ILE A 318 "
            pdb=" C   ILE A 318 "
            pdb=" CB  ILE A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  ... (remaining 1447 not shown)

  Planarity restraints: 1622
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 359 "    0.015 2.00e-02 2.50e+03   3.00e-02 8.99e+00
        pdb=" C   GLU A 359 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLU A 359 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PRO A 360 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 337 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.74e+00
        pdb=" C   ASP A 337 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A 337 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU A 338 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 359 "    0.009 2.00e-02 2.50e+03   1.70e-02 2.90e+00
        pdb=" C   GLU B 359 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLU B 359 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PRO B 360 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1619 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2245
        2.80 -     3.32: 7626
        3.32 -     3.85: 14136
        3.85 -     4.37: 15956
        4.37 -     4.90: 30113
  Nonbonded interactions: 70076
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B  76 "
            pdb=" OD1 ASP B  78 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" N   GLU L  82 "
            pdb=" OE1 GLU L  82 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   ALA A 301 "
            pdb=" OH  TYR A 321 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ALA B 301 "
            pdb=" OH  TYR B 321 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" NZ  LYS A 292 "
            pdb=" OG1 THR A 298 "
     model   vdw
     2.347 3.120
  ... (remaining 70071 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 7 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 68 or (resid 69 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 135 through 175 or \ 
 (resid 176 through 177 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 178 through 368))
  selection = (chain 'B' and (resid 7 through 203 or (resid 204 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 205 through 214 or (resid 215 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 216 through 336 or (resid 33 \ 
7 and (name N or name CA or name C or name O or name CB )) or resid 338 through  \ 
368))
}
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 5 through 50 or (resid 51 through 52 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 53 through 107))
  selection = chain 'M'
}
ncs_group {
  reference = chain 'U'
  selection = chain 'V'
}

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 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:             52.910
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.260
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   80.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
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      :  0.006   0.110   9351  Z= 0.289
  Angle     :  0.714  12.591  12741  Z= 0.331
  Chirality :  0.044   0.201   1450
  Planarity :  0.004   0.040   1622
  Dihedral  : 14.608  89.840   3379
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 12.13 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.25), residues: 1160
  helix:  0.07 (1.25), residues: 20
  sheet:  0.53 (0.23), residues: 534
  loop : -0.33 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP H  39 
 HIS   0.005   0.001   HIS A 353 
 PHE   0.013   0.002   PHE A 349 
 TYR   0.012   0.001   TYR M  92 
 ARG   0.008   0.001   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22026 (  345)
  hydrogen bonds       : angle       8.89481 ( 1035)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       0.36433 (    8)
  covalent geometry    : bond        0.00595 ( 9347)
  covalent geometry    : angle       0.71421 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.002 
Fit side-chains
REVERT: B  204 ASP cc_start: 0.7870 (m-30) cc_final: 0.7634 (m-30)
REVERT: L   43 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8207 (mmtp)
REVERT: M   43 LYS cc_start: 0.8434 (mmmm) cc_final: 0.8151 (mmtp)
  outliers start: 6
  outliers final: 4
  residues processed: 97
  average time/residue: 0.2678
  time to fit residues: 35.3614
Evaluate side-chains
  87 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 ASN
Chi-restraints excluded: chain B residue  135 ASP
Chi-restraints excluded: chain B residue  245 ASN
Chi-restraints excluded: chain I residue   21 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    0.2980
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 89 optimal weight:    0.3980
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    0.1980
   chunk 66 optimal weight:    0.6980
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
B  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.144234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.115050 restraints weight = 12829.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 2.57
r_work: 0.3199 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9351  Z= 0.115
  Angle     :  0.546   4.867  12741  Z= 0.287
  Chirality :  0.044   0.144   1450
  Planarity :  0.004   0.030   1622
  Dihedral  :  5.876  66.853   1320
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 10.79 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.25), residues: 1160
  helix: -0.01 (1.15), residues: 20
  sheet:  0.74 (0.23), residues: 534
  loop : -0.14 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP I  50 
 HIS   0.004   0.001   HIS A 353 
 PHE   0.012   0.002   PHE M  84 
 TYR   0.014   0.001   TYR A  21 
 ARG   0.004   0.000   ARG M  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  345)
  hydrogen bonds       : angle       5.41889 ( 1035)
  SS BOND              : bond        0.00347 (    4)
  SS BOND              : angle       0.25720 (    8)
  covalent geometry    : bond        0.00269 ( 9347)
  covalent geometry    : angle       0.54642 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 1.135 
Fit side-chains
REVERT: B  204 ASP cc_start: 0.8233 (m-30) cc_final: 0.7962 (m-30)
REVERT: H  120 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.7988 (p)
REVERT: I  120 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.7964 (p)
REVERT: L   43 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8438 (mmtp)
REVERT: L   82 GLU cc_start: 0.7377 (pm20) cc_final: 0.7027 (pm20)
REVERT: M    6 THR cc_start: 0.8579 (m) cc_final: 0.8378 (t)
REVERT: M   43 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8377 (mmtp)
  outliers start: 22
  outliers final: 14
  residues processed: 108
  average time/residue: 0.2342
  time to fit residues: 35.4457
Evaluate side-chains
  104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain I residue   21 LEU
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue  120 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   73 THR
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain U residue  335 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0000
   chunk 89 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.1390

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 GLN
A 111 HIS
B 111 HIS
B 189 GLN
I  85 GLN
L   7 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.138919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.109378 restraints weight = 12916.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.65
r_work: 0.3158 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   9351  Z= 0.182
  Angle     :  0.568   7.417  12741  Z= 0.295
  Chirality :  0.045   0.147   1450
  Planarity :  0.004   0.026   1622
  Dihedral  :  5.574  61.607   1314
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 11.31 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1160
  helix:  0.32 (1.05), residues: 24
  sheet:  0.74 (0.24), residues: 530
  loop : -0.14 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP I  50 
 HIS   0.007   0.001   HIS A 353 
 PHE   0.013   0.002   PHE L  99 
 TYR   0.018   0.002   TYR L  92 
 ARG   0.006   0.001   ARG V 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03493 (  345)
  hydrogen bonds       : angle       4.93349 ( 1035)
  SS BOND              : bond        0.00271 (    4)
  SS BOND              : angle       0.39112 (    8)
  covalent geometry    : bond        0.00443 ( 9347)
  covalent geometry    : angle       0.56817 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 1.123 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.5966 (OUTLIER) cc_final: 0.5644 (tp)
REVERT: B   29 ASP cc_start: 0.8258 (t0) cc_final: 0.8038 (t0)
REVERT: B  204 ASP cc_start: 0.8445 (m-30) cc_final: 0.8197 (m-30)
REVERT: B  206 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7949 (tp30)
REVERT: H  120 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8056 (p)
REVERT: I  120 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7966 (p)
REVERT: L   43 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8469 (mmtp)
REVERT: L   82 GLU cc_start: 0.7428 (pm20) cc_final: 0.7179 (pm20)
REVERT: V  335 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7693 (m-10)
  outliers start: 32
  outliers final: 19
  residues processed: 117
  average time/residue: 0.2296
  time to fit residues: 37.5256
Evaluate side-chains
  111 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  245 ASN
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain H residue   14 LEU
Chi-restraints excluded: chain H residue   21 LEU
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   61 THR
Chi-restraints excluded: chain I residue  120 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   55 LEU
Chi-restraints excluded: chain M residue   73 THR
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain V residue  335 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0770
   chunk 81 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.139859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.109835 restraints weight = 12717.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.90
r_work: 0.3177 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9351  Z= 0.125
  Angle     :  0.507   4.733  12741  Z= 0.263
  Chirality :  0.043   0.139   1450
  Planarity :  0.004   0.026   1622
  Dihedral  :  5.165  56.974   1312
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 13.67 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1160
  helix:  0.49 (1.05), residues: 24
  sheet:  0.79 (0.24), residues: 534
  loop : -0.10 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  50 
 HIS   0.004   0.001   HIS B 353 
 PHE   0.009   0.001   PHE A 349 
 TYR   0.014   0.001   TYR A 249 
 ARG   0.003   0.000   ARG M  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02848 (  345)
  hydrogen bonds       : angle       4.59256 ( 1035)
  SS BOND              : bond        0.00329 (    4)
  SS BOND              : angle       0.68247 (    8)
  covalent geometry    : bond        0.00301 ( 9347)
  covalent geometry    : angle       0.50687 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 1.401 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5685 (tp)
REVERT: A  189 GLN cc_start: 0.7016 (tp-100) cc_final: 0.6747 (tp40)
REVERT: B   44 ASP cc_start: 0.7308 (t0) cc_final: 0.7009 (t0)
REVERT: B  204 ASP cc_start: 0.8478 (m-30) cc_final: 0.8211 (m-30)
REVERT: B  248 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8345 (tp40)
REVERT: L   43 LYS cc_start: 0.8824 (mmmm) cc_final: 0.8590 (mmtp)
REVERT: L   79 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7431 (tp)
REVERT: L   82 GLU cc_start: 0.7407 (pm20) cc_final: 0.7154 (pm20)
REVERT: M   83 ASP cc_start: 0.8069 (m-30) cc_final: 0.7860 (m-30)
REVERT: V  335 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7667 (m-10)
  outliers start: 29
  outliers final: 18
  residues processed: 111
  average time/residue: 0.2502
  time to fit residues: 39.5769
Evaluate side-chains
  106 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  245 ASN
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  248 GLN
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain I residue   14 LEU
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   61 THR
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain V residue  335 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 108 optimal weight:    0.0030
   chunk 4 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0170
   chunk 110 optimal weight:    4.9990
   overall best weight:    0.7230

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.140779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.112516 restraints weight = 12825.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.49
r_work: 0.3161 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9351  Z= 0.129
  Angle     :  0.515   6.019  12741  Z= 0.265
  Chirality :  0.043   0.140   1450
  Planarity :  0.004   0.026   1622
  Dihedral  :  5.057  59.382   1312
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.59 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1160
  helix:  0.57 (1.05), residues: 24
  sheet:  0.87 (0.23), residues: 532
  loop : -0.10 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  50 
 HIS   0.004   0.001   HIS A 353 
 PHE   0.009   0.001   PHE L  99 
 TYR   0.013   0.001   TYR B 249 
 ARG   0.005   0.000   ARG H  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02741 (  345)
  hydrogen bonds       : angle       4.45846 ( 1035)
  SS BOND              : bond        0.00281 (    4)
  SS BOND              : angle       0.79781 (    8)
  covalent geometry    : bond        0.00313 ( 9347)
  covalent geometry    : angle       0.51449 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 88
  time to evaluate  : 1.131 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6163 (OUTLIER) cc_final: 0.5881 (tp)
REVERT: A  189 GLN cc_start: 0.7110 (tp-100) cc_final: 0.6836 (tp40)
REVERT: B   44 ASP cc_start: 0.7324 (t0) cc_final: 0.7021 (t0)
REVERT: B   75 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6201 (p90)
REVERT: B  206 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7947 (tp30)
REVERT: B  248 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8342 (tp40)
REVERT: I  120 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8023 (p)
REVERT: L   43 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8534 (mmtp)
REVERT: L   79 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7413 (tp)
REVERT: L   82 GLU cc_start: 0.7371 (pm20) cc_final: 0.7159 (pm20)
REVERT: M   83 ASP cc_start: 0.7708 (m-30) cc_final: 0.7391 (m-30)
REVERT: V  335 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7650 (m-10)
  outliers start: 35
  outliers final: 22
  residues processed: 114
  average time/residue: 0.2141
  time to fit residues: 34.3520
Evaluate side-chains
  114 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  245 ASN
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  248 GLN
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain I residue   14 LEU
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue  120 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   55 LEU
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain V residue  335 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0870
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    1.0962

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.138119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.108364 restraints weight = 12741.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.64
r_work: 0.3152 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9351  Z= 0.176
  Angle     :  0.547   8.403  12741  Z= 0.280
  Chirality :  0.044   0.143   1450
  Planarity :  0.004   0.030   1622
  Dihedral  :  5.104  58.832   1312
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 15.01 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.25), residues: 1160
  helix:  0.43 (1.03), residues: 24
  sheet:  0.76 (0.24), residues: 528
  loop : -0.14 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP I  50 
 HIS   0.006   0.001   HIS A 353 
 PHE   0.011   0.002   PHE M  99 
 TYR   0.014   0.001   TYR L  92 
 ARG   0.006   0.001   ARG I  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02871 (  345)
  hydrogen bonds       : angle       4.56629 ( 1035)
  SS BOND              : bond        0.00274 (    4)
  SS BOND              : angle       0.92364 (    8)
  covalent geometry    : bond        0.00428 ( 9347)
  covalent geometry    : angle       0.54654 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5772 (tp)
REVERT: B   44 ASP cc_start: 0.7322 (t0) cc_final: 0.7032 (t0)
REVERT: B   75 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6208 (p90)
REVERT: B  206 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8140 (tp30)
REVERT: B  248 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8352 (tp40)
REVERT: I  120 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8092 (p)
REVERT: L   43 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8630 (mmtp)
REVERT: L   79 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7523 (tp)
REVERT: M   83 ASP cc_start: 0.7498 (m-30) cc_final: 0.7263 (m-30)
REVERT: V  335 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7549 (m-10)
  outliers start: 38
  outliers final: 27
  residues processed: 110
  average time/residue: 0.2111
  time to fit residues: 32.8798
Evaluate side-chains
  115 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 81
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  242 CYS
Chi-restraints excluded: chain A residue  245 ASN
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue   18 LEU
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  206 GLU
Chi-restraints excluded: chain B residue  248 GLN
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain I residue   14 LEU
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain I residue  120 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain M residue   12 LEU
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   55 LEU
Chi-restraints excluded: chain M residue   73 THR
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain M residue  107 ILE
Chi-restraints excluded: chain V residue  335 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 76 optimal weight:    0.2980
   chunk 62 optimal weight:    3.9990
   chunk 99 optimal weight:    0.5980
   chunk 102 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0000
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.141567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.111049 restraints weight = 12834.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.81
r_work: 0.3187 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9351  Z= 0.101
  Angle     :  0.501   7.001  12741  Z= 0.256
  Chirality :  0.043   0.140   1450
  Planarity :  0.003   0.027   1622
  Dihedral  :  4.857  55.617   1312
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.55 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.25), residues: 1160
  helix:  0.75 (1.06), residues: 24
  sheet:  0.82 (0.23), residues: 534
  loop : -0.07 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  50 
 HIS   0.004   0.001   HIS I  38 
 PHE   0.008   0.001   PHE A 349 
 TYR   0.013   0.001   TYR B 249 
 ARG   0.006   0.000   ARG M  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02488 (  345)
  hydrogen bonds       : angle       4.34858 ( 1035)
  SS BOND              : bond        0.00310 (    4)
  SS BOND              : angle       0.71138 (    8)
  covalent geometry    : bond        0.00240 ( 9347)
  covalent geometry    : angle       0.50103 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 1.179 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5814 (tp)
REVERT: B   44 ASP cc_start: 0.7297 (t0) cc_final: 0.7011 (t0)
REVERT: B   75 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6101 (p90)
REVERT: B  248 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8376 (tp40)
REVERT: H   90 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7281 (ttm110)
REVERT: H   92 GLU cc_start: 0.8047 (mm-30) cc_final: 0.6726 (pm20)
REVERT: I   90 ARG cc_start: 0.7365 (ttm110) cc_final: 0.7118 (ttm110)
REVERT: I   92 GLU cc_start: 0.8054 (mm-30) cc_final: 0.6741 (pm20)
REVERT: L   43 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8476 (mmtp)
REVERT: L   79 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7410 (tp)
REVERT: M    2 ASP cc_start: 0.7382 (p0) cc_final: 0.7110 (p0)
REVERT: V  335 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7480 (m-10)
  outliers start: 28
  outliers final: 20
  residues processed: 109
  average time/residue: 0.2319
  time to fit residues: 35.4129
Evaluate side-chains
  110 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  297 ASP
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  248 GLN
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue   14 LEU
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   79 LEU
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   55 LEU
Chi-restraints excluded: chain M residue   73 THR
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain V residue  335 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 85 optimal weight:    0.3980
   chunk 92 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 79 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.141427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.111791 restraints weight = 13272.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.56
r_work: 0.3144 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9351  Z= 0.156
  Angle     :  0.530   6.093  12741  Z= 0.273
  Chirality :  0.043   0.142   1450
  Planarity :  0.004   0.028   1622
  Dihedral  :  4.889  54.472   1312
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 16.34 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.25), residues: 1160
  helix:  0.57 (1.02), residues: 24
  sheet:  0.78 (0.23), residues: 530
  loop : -0.11 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  50 
 HIS   0.005   0.001   HIS A 353 
 PHE   0.011   0.002   PHE M  99 
 TYR   0.013   0.001   TYR L  92 
 ARG   0.004   0.000   ARG M  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02707 (  345)
  hydrogen bonds       : angle       4.42160 ( 1035)
  SS BOND              : bond        0.00422 (    4)
  SS BOND              : angle       0.96622 (    8)
  covalent geometry    : bond        0.00380 ( 9347)
  covalent geometry    : angle       0.53008 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 86
  time to evaluate  : 1.109 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5922 (tp)
REVERT: B   44 ASP cc_start: 0.7310 (t0) cc_final: 0.7039 (t0)
REVERT: B   75 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6124 (p90)
REVERT: B  248 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8369 (tp40)
REVERT: H   92 GLU cc_start: 0.8116 (mm-30) cc_final: 0.6805 (pm20)
REVERT: I   90 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7358 (ttm110)
REVERT: I   92 GLU cc_start: 0.8113 (mm-30) cc_final: 0.6818 (pm20)
REVERT: L   43 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8521 (mmtp)
REVERT: M    2 ASP cc_start: 0.7404 (p0) cc_final: 0.7127 (p0)
REVERT: V  335 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7520 (m-10)
  outliers start: 34
  outliers final: 24
  residues processed: 110
  average time/residue: 0.2351
  time to fit residues: 36.4957
Evaluate side-chains
  108 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  248 GLN
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain H residue  111 ASP
Chi-restraints excluded: chain I residue   14 LEU
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   55 LEU
Chi-restraints excluded: chain M residue   73 THR
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain V residue  335 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0470
   chunk 38 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  83 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.139148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.109243 restraints weight = 12748.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.59
r_work: 0.3197 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9351  Z= 0.126
  Angle     :  0.508   5.892  12741  Z= 0.261
  Chirality :  0.043   0.140   1450
  Planarity :  0.004   0.028   1622
  Dihedral  :  4.782  51.864   1312
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 16.55 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1160
  helix:  0.67 (1.02), residues: 24
  sheet:  0.83 (0.23), residues: 534
  loop : -0.08 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  50 
 HIS   0.004   0.001   HIS A 353 
 PHE   0.009   0.001   PHE M  99 
 TYR   0.021   0.001   TYR B 238 
 ARG   0.003   0.000   ARG M  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02571 (  345)
  hydrogen bonds       : angle       4.35166 ( 1035)
  SS BOND              : bond        0.00352 (    4)
  SS BOND              : angle       0.93172 (    8)
  covalent geometry    : bond        0.00305 ( 9347)
  covalent geometry    : angle       0.50765 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 87
  time to evaluate  : 1.207 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5795 (tp)
REVERT: B   44 ASP cc_start: 0.7359 (t0) cc_final: 0.7109 (t0)
REVERT: B   75 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6093 (p90)
REVERT: H   90 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7223 (ttm110)
REVERT: H   92 GLU cc_start: 0.8123 (mm-30) cc_final: 0.6781 (pm20)
REVERT: I   90 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7203 (ttm110)
REVERT: I   92 GLU cc_start: 0.8100 (mm-30) cc_final: 0.6768 (pm20)
REVERT: M    2 ASP cc_start: 0.7450 (p0) cc_final: 0.7226 (p0)
REVERT: V  335 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7479 (m-10)
  outliers start: 30
  outliers final: 23
  residues processed: 107
  average time/residue: 0.2331
  time to fit residues: 35.8486
Evaluate side-chains
  109 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 1.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue   14 LEU
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   55 LEU
Chi-restraints excluded: chain M residue   73 THR
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain V residue  335 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0770
   chunk 108 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.142182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.110903 restraints weight = 13119.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.88
r_work: 0.3139 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9351  Z= 0.118
  Angle     :  0.500   5.580  12741  Z= 0.257
  Chirality :  0.043   0.141   1450
  Planarity :  0.003   0.027   1622
  Dihedral  :  4.661  49.080   1312
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 16.44 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1160
  helix:  0.68 (1.02), residues: 24
  sheet:  0.86 (0.23), residues: 534
  loop : -0.07 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  50 
 HIS   0.004   0.001   HIS A 353 
 PHE   0.009   0.001   PHE M  84 
 TYR   0.013   0.001   TYR A 249 
 ARG   0.003   0.000   ARG I  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02545 (  345)
  hydrogen bonds       : angle       4.28452 ( 1035)
  SS BOND              : bond        0.00348 (    4)
  SS BOND              : angle       0.78104 (    8)
  covalent geometry    : bond        0.00285 ( 9347)
  covalent geometry    : angle       0.50001 (12733)

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

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

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2320 Ramachandran restraints generated.
    1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 1.087 
Fit side-chains
REVERT: A   48 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5875 (tp)
REVERT: B   44 ASP cc_start: 0.7419 (t0) cc_final: 0.7164 (t0)
REVERT: B   75 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.6038 (p90)
REVERT: H   90 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7310 (ttm110)
REVERT: H   92 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7036 (pm20)
REVERT: I   90 ARG cc_start: 0.7563 (ttm110) cc_final: 0.7287 (ttm110)
REVERT: I   92 GLU cc_start: 0.8117 (mm-30) cc_final: 0.6974 (pm20)
REVERT: M    2 ASP cc_start: 0.7590 (p0) cc_final: 0.7353 (p0)
REVERT: V  335 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7543 (m-10)
  outliers start: 27
  outliers final: 22
  residues processed: 103
  average time/residue: 0.2236
  time to fit residues: 32.2127
Evaluate side-chains
  110 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  160 LYS
Chi-restraints excluded: chain B residue  328 VAL
Chi-restraints excluded: chain H residue   31 ASN
Chi-restraints excluded: chain H residue   77 THR
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain I residue   14 LEU
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   94 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain M residue   21 THR
Chi-restraints excluded: chain M residue   55 LEU
Chi-restraints excluded: chain M residue   73 THR
Chi-restraints excluded: chain M residue   75 THR
Chi-restraints excluded: chain V residue  335 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0470
   chunk 41 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0870
   chunk 94 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.4456

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   7 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.113218 restraints weight = 12773.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.47
r_work: 0.3190 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9351  Z= 0.099
  Angle     :  0.493   5.381  12741  Z= 0.252
  Chirality :  0.042   0.140   1450
  Planarity :  0.003   0.026   1622
  Dihedral  :  4.525  46.315   1312
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.75 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1160
  helix:  0.84 (1.05), residues: 24
  sheet:  0.92 (0.24), residues: 528
  loop : -0.09 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP I  50 
 HIS   0.004   0.001   HIS I  38 
 PHE   0.009   0.001   PHE B 115 
 TYR   0.010   0.001   TYR M  92 
 ARG   0.003   0.000   ARG I  90 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02442 (  345)
  hydrogen bonds       : angle       4.20036 ( 1035)
  SS BOND              : bond        0.00324 (    4)
  SS BOND              : angle       0.71649 (    8)
  covalent geometry    : bond        0.00234 ( 9347)
  covalent geometry    : angle       0.49246 (12733)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4908.18 seconds
wall clock time: 86 minutes 56.50 seconds (5216.50 seconds total)