Starting phenix.real_space_refine
on Fri Dec 27 19:07:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ovt_13089/12_2024/7ovt_13089.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ovt_13089/12_2024/7ovt_13089.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ovt_13089/12_2024/7ovt_13089.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ovt_13089/12_2024/7ovt_13089.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ovt_13089/12_2024/7ovt_13089.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ovt_13089/12_2024/7ovt_13089.cif"
  }
  resolution = 2.69
  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=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    4212      2.51       5
     N    1128      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 2.60, per 1000 atoms: 0.39
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (105.04, 127.92, 54.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1224      8.00
     N    1128      7.00
     C    4212      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.61
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1392

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 58.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 21
      removed outlier: 6.752A  pdb=" N   PHE A  10 " --> pdb=" O   ALA C   9 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN C  11 " --> pdb=" O   PHE A  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY A  12 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA C  13 " --> pdb=" O   GLY A  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET A  16 " --> pdb=" O   ASP C  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP C  17 " --> pdb=" O   MET A  16 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE C  10 " --> pdb=" O   ALA E   9 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN E  11 " --> pdb=" O   PHE C  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY C  12 " --> pdb=" O   GLN E  11 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ALA E  13 " --> pdb=" O   GLY C  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET C  16 " --> pdb=" O   ASP E  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP E  17 " --> pdb=" O   MET C  16 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE E  10 " --> pdb=" O   ALA G   9 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   GLN G  11 " --> pdb=" O   PHE E  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY E  12 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA G  13 " --> pdb=" O   GLY E  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET E  16 " --> pdb=" O   ASP G  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP G  17 " --> pdb=" O   MET E  16 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE G  10 " --> pdb=" O   ALA I   9 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN I  11 " --> pdb=" O   PHE G  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY G  12 " --> pdb=" O   GLN I  11 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ALA I  13 " --> pdb=" O   GLY G  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET G  16 " --> pdb=" O   ASP I  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP I  17 " --> pdb=" O   MET G  16 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE I  10 " --> pdb=" O   ALA K   9 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN K  11 " --> pdb=" O   PHE I  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY I  12 " --> pdb=" O   GLN K  11 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ALA K  13 " --> pdb=" O   GLY I  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET I  16 " --> pdb=" O   ASP K  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP K  17 " --> pdb=" O   MET I  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29
    Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 38
      removed outlier: 6.533A  pdb=" N   LYS A  33 " --> pdb=" O   TYR C  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS C  36 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   PHE A  35 " --> pdb=" O   HIS C  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG C  38 " --> pdb=" O   PHE A  35 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA A  37 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LYS C  33 " --> pdb=" O   TYR E  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS E  36 " --> pdb=" O   LYS C  33 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   PHE C  35 " --> pdb=" O   HIS E  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG E  38 " --> pdb=" O   PHE C  35 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA C  37 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LYS E  33 " --> pdb=" O   TYR G  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS G  36 " --> pdb=" O   LYS E  33 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   PHE E  35 " --> pdb=" O   HIS G  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG G  38 " --> pdb=" O   PHE E  35 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA E  37 " --> pdb=" O   ARG G  38 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LYS G  33 " --> pdb=" O   TYR I  34 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   HIS I  36 " --> pdb=" O   LYS G  33 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   PHE G  35 " --> pdb=" O   HIS I  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG I  38 " --> pdb=" O   PHE G  35 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ALA G  37 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LYS I  33 " --> pdb=" O   TYR K  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS K  36 " --> pdb=" O   LYS I  33 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   PHE I  35 " --> pdb=" O   HIS K  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG K  38 " --> pdb=" O   PHE I  35 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA I  37 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 46
      removed outlier: 6.879A  pdb=" N   ALA C  43 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA A  44 " --> pdb=" O   ALA C  43 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ALA E  43 " --> pdb=" O   ASP C  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA C  44 " --> pdb=" O   ALA E  43 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ALA G  43 " --> pdb=" O   ASP E  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA E  44 " --> pdb=" O   ALA G  43 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ALA I  43 " --> pdb=" O   ASP G  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA G  44 " --> pdb=" O   ALA I  43 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ALA K  43 " --> pdb=" O   ASP I  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA I  44 " --> pdb=" O   ALA K  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 58
      removed outlier: 6.214A  pdb=" N   VAL A  51 " --> pdb=" O   TRP C  52 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ALA C  54 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ALA A  53 " --> pdb=" O   ALA C  54 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS C  56 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   GLU A  55 " --> pdb=" O   LYS C  56 " (cutoff:3.500A)
      removed outlier: 9.966A  pdb=" N   SER C  58 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE A  57 " --> pdb=" O   SER C  58 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   VAL C  51 " --> pdb=" O   TRP E  52 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ALA E  54 " --> pdb=" O   VAL C  51 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ALA C  53 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS E  56 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   GLU C  55 " --> pdb=" O   LYS E  56 " (cutoff:3.500A)
      removed outlier: 9.965A  pdb=" N   SER E  58 " --> pdb=" O   GLU C  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE C  57 " --> pdb=" O   SER E  58 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL E  51 " --> pdb=" O   TRP G  52 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ALA G  54 " --> pdb=" O   VAL E  51 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ALA E  53 " --> pdb=" O   ALA G  54 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS G  56 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   GLU E  55 " --> pdb=" O   LYS G  56 " (cutoff:3.500A)
      removed outlier: 9.966A  pdb=" N   SER G  58 " --> pdb=" O   GLU E  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE E  57 " --> pdb=" O   SER G  58 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL G  51 " --> pdb=" O   TRP I  52 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ALA I  54 " --> pdb=" O   VAL G  51 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ALA G  53 " --> pdb=" O   ALA I  54 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LYS I  56 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   GLU G  55 " --> pdb=" O   LYS I  56 " (cutoff:3.500A)
      removed outlier: 9.966A  pdb=" N   SER I  58 " --> pdb=" O   GLU G  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE G  57 " --> pdb=" O   SER I  58 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL I  51 " --> pdb=" O   TRP K  52 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ALA K  54 " --> pdb=" O   VAL I  51 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ALA I  53 " --> pdb=" O   ALA K  54 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LYS K  56 " --> pdb=" O   ALA I  53 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   GLU I  55 " --> pdb=" O   LYS K  56 " (cutoff:3.500A)
      removed outlier: 9.965A  pdb=" N   SER K  58 " --> pdb=" O   GLU I  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE I  57 " --> pdb=" O   SER K  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 65 through 67
    Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 21
      removed outlier: 6.752A  pdb=" N   PHE B  10 " --> pdb=" O   ALA D   9 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN D  11 " --> pdb=" O   PHE B  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY B  12 " --> pdb=" O   GLN D  11 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA D  13 " --> pdb=" O   GLY B  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET B  16 " --> pdb=" O   ASP D  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP D  17 " --> pdb=" O   MET B  16 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE D  10 " --> pdb=" O   ALA F   9 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN F  11 " --> pdb=" O   PHE D  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY D  12 " --> pdb=" O   GLN F  11 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ALA F  13 " --> pdb=" O   GLY D  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET D  16 " --> pdb=" O   ASP F  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP F  17 " --> pdb=" O   MET D  16 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE F  10 " --> pdb=" O   ALA H   9 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN H  11 " --> pdb=" O   PHE F  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY F  12 " --> pdb=" O   GLN H  11 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ALA H  13 " --> pdb=" O   GLY F  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET F  16 " --> pdb=" O   ASP H  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP H  17 " --> pdb=" O   MET F  16 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE H  10 " --> pdb=" O   ALA J   9 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   GLN J  11 " --> pdb=" O   PHE H  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY H  12 " --> pdb=" O   GLN J  11 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA J  13 " --> pdb=" O   GLY H  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET H  16 " --> pdb=" O   ASP J  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP J  17 " --> pdb=" O   MET H  16 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE J  10 " --> pdb=" O   ALA L   9 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   GLN L  11 " --> pdb=" O   PHE J  10 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   GLY J  12 " --> pdb=" O   GLN L  11 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   ALA L  13 " --> pdb=" O   GLY J  12 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   MET J  16 " --> pdb=" O   ASP L  15 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   TRP L  17 " --> pdb=" O   MET J  16 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29
    Processing sheet with id=AA9, first strand: chain 'B' and resid 33 through 38
      removed outlier: 6.534A  pdb=" N   LYS B  33 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS D  36 " --> pdb=" O   LYS B  33 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   PHE B  35 " --> pdb=" O   HIS D  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG D  38 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ALA B  37 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LYS D  33 " --> pdb=" O   TYR F  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS F  36 " --> pdb=" O   LYS D  33 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   PHE D  35 " --> pdb=" O   HIS F  36 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   ARG F  38 " --> pdb=" O   PHE D  35 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ALA D  37 " --> pdb=" O   ARG F  38 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LYS F  33 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS H  36 " --> pdb=" O   LYS F  33 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   PHE F  35 " --> pdb=" O   HIS H  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG H  38 " --> pdb=" O   PHE F  35 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA F  37 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LYS H  33 " --> pdb=" O   TYR J  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS J  36 " --> pdb=" O   LYS H  33 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   PHE H  35 " --> pdb=" O   HIS J  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG J  38 " --> pdb=" O   PHE H  35 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA H  37 " --> pdb=" O   ARG J  38 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   LYS J  33 " --> pdb=" O   TYR L  34 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   HIS L  36 " --> pdb=" O   LYS J  33 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   PHE J  35 " --> pdb=" O   HIS L  36 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ARG L  38 " --> pdb=" O   PHE J  35 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA J  37 " --> pdb=" O   ARG L  38 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 46
      removed outlier: 6.879A  pdb=" N   ALA D  43 " --> pdb=" O   ASP B  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA B  44 " --> pdb=" O   ALA D  43 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ALA F  43 " --> pdb=" O   ASP D  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA D  44 " --> pdb=" O   ALA F  43 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ALA H  43 " --> pdb=" O   ASP F  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA F  44 " --> pdb=" O   ALA H  43 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ALA J  43 " --> pdb=" O   ASP H  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA H  44 " --> pdb=" O   ALA J  43 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ALA L  43 " --> pdb=" O   ASP J  42 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA J  44 " --> pdb=" O   ALA L  43 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 51 through 58
      removed outlier: 6.214A  pdb=" N   VAL B  51 " --> pdb=" O   TRP D  52 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   ALA D  54 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ALA B  53 " --> pdb=" O   ALA D  54 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LYS D  56 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   GLU B  55 " --> pdb=" O   LYS D  56 " (cutoff:3.500A)
      removed outlier: 9.966A  pdb=" N   SER D  58 " --> pdb=" O   GLU B  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE B  57 " --> pdb=" O   SER D  58 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL D  51 " --> pdb=" O   TRP F  52 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ALA F  54 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ALA D  53 " --> pdb=" O   ALA F  54 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LYS F  56 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   GLU D  55 " --> pdb=" O   LYS F  56 " (cutoff:3.500A)
      removed outlier: 9.965A  pdb=" N   SER F  58 " --> pdb=" O   GLU D  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE D  57 " --> pdb=" O   SER F  58 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL F  51 " --> pdb=" O   TRP H  52 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   ALA H  54 " --> pdb=" O   VAL F  51 " (cutoff:3.500A)
      removed outlier: 5.760A  pdb=" N   ALA F  53 " --> pdb=" O   ALA H  54 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS H  56 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   GLU F  55 " --> pdb=" O   LYS H  56 " (cutoff:3.500A)
      removed outlier: 9.965A  pdb=" N   SER H  58 " --> pdb=" O   GLU F  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE F  57 " --> pdb=" O   SER H  58 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL H  51 " --> pdb=" O   TRP J  52 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ALA J  54 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ALA H  53 " --> pdb=" O   ALA J  54 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS J  56 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   GLU H  55 " --> pdb=" O   LYS J  56 " (cutoff:3.500A)
      removed outlier: 9.965A  pdb=" N   SER J  58 " --> pdb=" O   GLU H  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE H  57 " --> pdb=" O   SER J  58 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL J  51 " --> pdb=" O   TRP L  52 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   ALA L  54 " --> pdb=" O   VAL J  51 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ALA J  53 " --> pdb=" O   ALA L  54 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   LYS L  56 " --> pdb=" O   ALA J  53 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   GLU J  55 " --> pdb=" O   LYS L  56 " (cutoff:3.500A)
      removed outlier: 9.965A  pdb=" N   SER L  58 " --> pdb=" O   GLU J  55 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   ILE J  57 " --> pdb=" O   SER L  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 67

    200 hydrogen bonds defined for protein.
    600 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: 1.94

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1140
        1.30 -     1.42: 2280
        1.42 -     1.54: 3324
        1.54 -     1.66: 12
        1.66 -     1.79: 48
  Bond restraints: 6804
  Sorted by residual:
  bond pdb=" C   ILE D   6 "
       pdb=" O   ILE D   6 "
    ideal  model  delta    sigma   weight residual
    1.236  1.180  0.056 1.04e-02 9.25e+03 2.91e+01
  bond pdb=" C   ILE L   6 "
       pdb=" O   ILE L   6 "
    ideal  model  delta    sigma   weight residual
    1.236  1.180  0.056 1.04e-02 9.25e+03 2.91e+01
  bond pdb=" C   ILE K   6 "
       pdb=" O   ILE K   6 "
    ideal  model  delta    sigma   weight residual
    1.236  1.180  0.056 1.04e-02 9.25e+03 2.91e+01
  bond pdb=" C   ILE H   6 "
       pdb=" O   ILE H   6 "
    ideal  model  delta    sigma   weight residual
    1.236  1.180  0.056 1.04e-02 9.25e+03 2.90e+01
  bond pdb=" C   ILE G   6 "
       pdb=" O   ILE G   6 "
    ideal  model  delta    sigma   weight residual
    1.236  1.180  0.056 1.04e-02 9.25e+03 2.90e+01
  ... (remaining 6799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 7353
        1.93 -     3.86: 1419
        3.86 -     5.79: 264
        5.79 -     7.72: 61
        7.72 -     9.66: 11
  Bond angle restraints: 9108
  Sorted by residual:
  angle pdb=" N   GLY H  49 "
        pdb=" CA  GLY H  49 "
        pdb=" C   GLY H  49 "
      ideal   model   delta    sigma   weight residual
     110.46  120.12   -9.66 1.43e+00 4.89e-01 4.56e+01
  angle pdb=" N   GLY B  49 "
        pdb=" CA  GLY B  49 "
        pdb=" C   GLY B  49 "
      ideal   model   delta    sigma   weight residual
     110.46  120.11   -9.65 1.43e+00 4.89e-01 4.55e+01
  angle pdb=" N   GLY A  49 "
        pdb=" CA  GLY A  49 "
        pdb=" C   GLY A  49 "
      ideal   model   delta    sigma   weight residual
     110.46  120.09   -9.63 1.43e+00 4.89e-01 4.54e+01
  angle pdb=" N   GLY G  49 "
        pdb=" CA  GLY G  49 "
        pdb=" C   GLY G  49 "
      ideal   model   delta    sigma   weight residual
     110.46  120.08   -9.62 1.43e+00 4.89e-01 4.52e+01
  angle pdb=" N   GLY C  49 "
        pdb=" CA  GLY C  49 "
        pdb=" C   GLY C  49 "
      ideal   model   delta    sigma   weight residual
     110.46  120.07   -9.61 1.43e+00 4.89e-01 4.52e+01
  ... (remaining 9103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.12: 3048
       11.12 -    22.25: 384
       22.25 -    33.37: 180
       33.37 -    44.49: 60
       44.49 -    55.62: 36
  Dihedral angle restraints: 3708
    sinusoidal: 1464
      harmonic: 2244
  Sorted by residual:
  dihedral pdb=" CA  SER K  58 "
           pdb=" C   SER K  58 "
           pdb=" N   ASP K  59 "
           pdb=" CA  ASP K  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.03   13.97     0      5.00e+00 4.00e-02 7.80e+00
  dihedral pdb=" CA  SER L  58 "
           pdb=" C   SER L  58 "
           pdb=" N   ASP L  59 "
           pdb=" CA  ASP L  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.07   13.93     0      5.00e+00 4.00e-02 7.77e+00
  dihedral pdb=" CA  SER A  58 "
           pdb=" C   SER A  58 "
           pdb=" N   ASP A  59 "
           pdb=" CA  ASP A  59 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  166.09   13.91     0      5.00e+00 4.00e-02 7.74e+00
  ... (remaining 3705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 349
       0.056 -    0.111: 191
       0.111 -    0.167: 108
       0.167 -    0.222: 84
       0.222 -    0.278: 12
  Chirality restraints: 744
  Sorted by residual:
  chirality pdb=" CA  ALA A   9 "
            pdb=" N   ALA A   9 "
            pdb=" C   ALA A   9 "
            pdb=" CB  ALA A   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.21    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  ALA E   9 "
            pdb=" N   ALA E   9 "
            pdb=" C   ALA E   9 "
            pdb=" CB  ALA E   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.21    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  ALA B   9 "
            pdb=" N   ALA B   9 "
            pdb=" C   ALA B   9 "
            pdb=" CB  ALA B   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.21    0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 741 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN K  45 "    0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   GLN K  45 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   GLN K  45 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ARG K  46 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B  45 "   -0.017 2.00e-02 2.50e+03   3.45e-02 1.19e+01
        pdb=" C   GLN B  45 "    0.060 2.00e-02 2.50e+03
        pdb=" O   GLN B  45 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ARG B  46 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN I  45 "    0.017 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   GLN I  45 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   GLN I  45 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ARG I  46 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 3855
        3.02 -     3.49: 5880
        3.49 -     3.96: 11333
        3.96 -     4.43: 13888
        4.43 -     4.90: 25547
  Nonbonded interactions: 60503
  Sorted by model distance:
  nonbonded pdb=" O   ASP L  22 "
            pdb=" OD1 ASP L  22 "
     model   vdw
     2.550 3.040
  nonbonded pdb=" O   ASP J  22 "
            pdb=" OD1 ASP J  22 "
     model   vdw
     2.550 3.040
  nonbonded pdb=" O   ASP H  22 "
            pdb=" OD1 ASP H  22 "
     model   vdw
     2.551 3.040
  nonbonded pdb=" O   ASP D  22 "
            pdb=" OD1 ASP D  22 "
     model   vdw
     2.551 3.040
  nonbonded pdb=" O   ASP F  22 "
            pdb=" OD1 ASP F  22 "
     model   vdw
     2.551 3.040
  ... (remaining 60498 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

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:             3.090
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     17.260
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  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:13.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
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      :  0.017   0.060   6804  Z= 1.115
  Angle     :  1.671   9.655   9108  Z= 1.121
  Chirality :  0.100   0.278    744
  Planarity :  0.008   0.040   1236
  Dihedral  : 13.711  55.616   2316
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.46 (0.17), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.13), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP L  17 
 HIS   0.001   0.001   HIS I  36 
 PHE   0.028   0.002   PHE F   2 
 TYR   0.043   0.007   TYR D  20 
 ARG   0.003   0.001   ARG C  46 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A   65 GLN cc_start: 0.9123 (mt0) cc_final: 0.8892 (mt0)
REVERT: B   38 ARG cc_start: 0.7783 (ttt180) cc_final: 0.7416 (tpp80)
REVERT: B   45 GLN cc_start: 0.8993 (mt0) cc_final: 0.8778 (mt0)
REVERT: B   56 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8274 (mttt)
REVERT: B   65 GLN cc_start: 0.9030 (mt0) cc_final: 0.8773 (mt0)
REVERT: C   22 ASP cc_start: 0.7977 (t0) cc_final: 0.7696 (t0)
REVERT: C   38 ARG cc_start: 0.7552 (ttt180) cc_final: 0.7254 (tpp-160)
REVERT: C   65 GLN cc_start: 0.9045 (mt0) cc_final: 0.8822 (mt0)
REVERT: D   25 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7811 (mp0)
REVERT: D   38 ARG cc_start: 0.7511 (ttt180) cc_final: 0.7252 (ttt90)
REVERT: D   45 GLN cc_start: 0.9012 (mt0) cc_final: 0.8776 (mt0)
REVERT: E   38 ARG cc_start: 0.7575 (ttt180) cc_final: 0.7168 (tpp80)
REVERT: F   16 MET cc_start: 0.9173 (mtt) cc_final: 0.8970 (mtt)
REVERT: F   25 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7942 (mt-10)
REVERT: F   38 ARG cc_start: 0.7597 (ttt180) cc_final: 0.7028 (tpp80)
REVERT: F   66 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8593 (mt-10)
REVERT: G   22 ASP cc_start: 0.7943 (t0) cc_final: 0.7161 (t0)
REVERT: G   25 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8123 (mp0)
REVERT: G   38 ARG cc_start: 0.7549 (ttt180) cc_final: 0.7081 (tpp80)
REVERT: H   25 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7740 (mp0)
REVERT: H   38 ARG cc_start: 0.7526 (ttt180) cc_final: 0.7097 (tpp80)
REVERT: I   22 ASP cc_start: 0.7958 (t0) cc_final: 0.7738 (t0)
REVERT: I   25 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7840 (mt-10)
REVERT: I   38 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7457 (tpp-160)
REVERT: I   56 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8115 (mttp)
REVERT: I   66 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8536 (mt-10)
REVERT: J   16 MET cc_start: 0.9156 (mtt) cc_final: 0.8941 (mtt)
REVERT: J   22 ASP cc_start: 0.7976 (t0) cc_final: 0.7461 (t0)
REVERT: J   23 MET cc_start: 0.8768 (mtt) cc_final: 0.8469 (mtt)
REVERT: J   25 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7463 (mt-10)
REVERT: J   38 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7262 (ttt90)
REVERT: J   65 GLN cc_start: 0.9189 (mt0) cc_final: 0.8983 (mt0)
REVERT: K   63 SER cc_start: 0.8847 (m) cc_final: 0.8526 (p)
REVERT: K   66 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8585 (mt-10)
REVERT: L   25 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8157 (mp0)
REVERT: L   29 LYS cc_start: 0.8468 (tttp) cc_final: 0.8173 (tttp)
REVERT: L   38 ARG cc_start: 0.7834 (ttt180) cc_final: 0.7620 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 1.7184
  time to fit residues: 376.4999
Evaluate side-chains
  201 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** D  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6804  Z= 0.211
  Angle     :  0.539   4.574   9108  Z= 0.338
  Chirality :  0.043   0.123    744
  Planarity :  0.004   0.039   1236
  Dihedral  :  4.413  16.122    900
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.49 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.73 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J  28 
 HIS   0.001   0.000   HIS F  36 
 PHE   0.014   0.001   PHE E   2 
 TYR   0.007   0.001   TYR G  20 
 ARG   0.003   0.000   ARG L  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7788 (mt-10)
REVERT: B   45 GLN cc_start: 0.8858 (mt0) cc_final: 0.8649 (mt0)
REVERT: B   56 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8215 (mttt)
REVERT: C   38 ARG cc_start: 0.7488 (ttt180) cc_final: 0.7276 (tpp-160)
REVERT: C   65 GLN cc_start: 0.8886 (mt0) cc_final: 0.8606 (mt0)
REVERT: D   38 ARG cc_start: 0.7478 (ttt180) cc_final: 0.7207 (ttt90)
REVERT: E   25 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8069 (mp0)
REVERT: E   29 LYS cc_start: 0.8455 (tttt) cc_final: 0.7748 (tptt)
REVERT: E   38 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7156 (tpp80)
REVERT: F   38 ARG cc_start: 0.7497 (ttt180) cc_final: 0.7026 (tpp80)
REVERT: G   38 ARG cc_start: 0.7481 (ttt180) cc_final: 0.7066 (tpp80)
REVERT: H   25 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8043 (mt-10)
REVERT: H   38 ARG cc_start: 0.7500 (ttt180) cc_final: 0.6842 (tpp80)
REVERT: H   46 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8252 (tmt170)
REVERT: I   22 ASP cc_start: 0.7912 (t0) cc_final: 0.7706 (t0)
REVERT: I   25 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8140 (mt-10)
REVERT: I   38 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7539 (tpp-160)
REVERT: I   56 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8024 (mttp)
REVERT: I   62 GLU cc_start: 0.7496 (tp30) cc_final: 0.7154 (tp30)
REVERT: J   25 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7703 (mt-10)
REVERT: J   38 ARG cc_start: 0.7587 (ttt180) cc_final: 0.7251 (tpp-160)
REVERT: J   65 GLN cc_start: 0.9015 (mt0) cc_final: 0.8651 (mt0)
REVERT: K   25 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8034 (mt-10)
REVERT: K   38 ARG cc_start: 0.7833 (ttt180) cc_final: 0.7176 (tpp80)
REVERT: K   63 SER cc_start: 0.8971 (m) cc_final: 0.8673 (p)
  outliers start: 15
  outliers final: 3
  residues processed: 162
  average time/residue: 1.9676
  time to fit residues: 328.8686
Evaluate side-chains
  155 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 150
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain L residue   59 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:    0.1980
   chunk 58 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A  45 GLN
C  45 GLN
D  65 GLN
E  45 GLN
L  65 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   6804  Z= 0.397
  Angle     :  0.565   5.092   9108  Z= 0.346
  Chirality :  0.044   0.127    744
  Planarity :  0.003   0.027   1236
  Dihedral  :  4.765  19.603    900
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.40 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.78 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.13), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP J  28 
 HIS   0.001   0.000   HIS B  36 
 PHE   0.014   0.002   PHE I   2 
 TYR   0.009   0.001   TYR A  20 
 ARG   0.007   0.001   ARG B  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7461 (tt0)
REVERT: B   45 GLN cc_start: 0.8966 (mt0) cc_final: 0.8734 (mt0)
REVERT: B   56 LYS cc_start: 0.8283 (mtmt) cc_final: 0.8028 (mttt)
REVERT: B   65 GLN cc_start: 0.8846 (mt0) cc_final: 0.8594 (mt0)
REVERT: C   65 GLN cc_start: 0.8900 (mt0) cc_final: 0.8680 (mt0)
REVERT: D   25 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7679 (mp0)
REVERT: D   38 ARG cc_start: 0.7527 (ttt180) cc_final: 0.7193 (ttt90)
REVERT: E   25 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8104 (mp0)
REVERT: E   29 LYS cc_start: 0.8419 (tttt) cc_final: 0.7673 (tptt)
REVERT: E   38 ARG cc_start: 0.7466 (ttt180) cc_final: 0.7124 (tpp80)
REVERT: F   38 ARG cc_start: 0.7508 (ttt180) cc_final: 0.7245 (tpp80)
REVERT: G    8 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7625 (mt-10)
REVERT: G   38 ARG cc_start: 0.7495 (ttt180) cc_final: 0.7065 (tpp80)
REVERT: G   62 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7646 (tp30)
REVERT: H   25 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8003 (mt-10)
REVERT: H   38 ARG cc_start: 0.7450 (ttt180) cc_final: 0.6774 (tpp80)
REVERT: H   46 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8466 (tmt170)
REVERT: I   25 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8024 (mt-10)
REVERT: I   38 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7607 (tpp-160)
REVERT: I   56 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8045 (mttp)
REVERT: J   25 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7713 (mt-10)
REVERT: J   38 ARG cc_start: 0.7563 (ttt180) cc_final: 0.7360 (tpp-160)
REVERT: J   65 GLN cc_start: 0.9021 (mt0) cc_final: 0.8658 (mt0)
REVERT: K   25 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8016 (mt-10)
REVERT: L   29 LYS cc_start: 0.8104 (tttp) cc_final: 0.7862 (tttp)
  outliers start: 24
  outliers final: 4
  residues processed: 161
  average time/residue: 1.9463
  time to fit residues: 323.4657
Evaluate side-chains
  158 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue   62 GLU
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   56 LYS
Chi-restraints excluded: chain J residue   46 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
L  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6804  Z= 0.278
  Angle     :  0.517   4.746   9108  Z= 0.317
  Chirality :  0.043   0.127    744
  Planarity :  0.003   0.031   1236
  Dihedral  :  4.686  19.069    900
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 17.01 %
    Favored  : 78.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  28 
 HIS   0.001   0.000   HIS F  36 
 PHE   0.012   0.001   PHE I   2 
 TYR   0.008   0.001   TYR L  34 
 ARG   0.005   0.000   ARG B  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7447 (tt0)
REVERT: A   32 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7954 (m-30)
REVERT: B   45 GLN cc_start: 0.8939 (mt0) cc_final: 0.8711 (mt0)
REVERT: B   56 LYS cc_start: 0.8280 (mtmt) cc_final: 0.8033 (mttt)
REVERT: B   65 GLN cc_start: 0.8859 (mt0) cc_final: 0.8599 (mt0)
REVERT: D   25 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7708 (mp0)
REVERT: D   38 ARG cc_start: 0.7510 (ttt180) cc_final: 0.6963 (ttm-80)
REVERT: E   25 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8134 (mp0)
REVERT: E   29 LYS cc_start: 0.8436 (tttt) cc_final: 0.7685 (tptt)
REVERT: E   38 ARG cc_start: 0.7421 (ttt180) cc_final: 0.7121 (tpp80)
REVERT: G    8 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7590 (mt-10)
REVERT: G   25 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7727 (mp0)
REVERT: G   38 ARG cc_start: 0.7489 (ttt180) cc_final: 0.7054 (tpp80)
REVERT: G   46 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.6624 (tmt170)
REVERT: G   66 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8281 (mt-10)
REVERT: H   38 ARG cc_start: 0.7472 (ttt180) cc_final: 0.6802 (tpp80)
REVERT: H   46 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8194 (tmt170)
REVERT: I    8 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7621 (mt-10)
REVERT: I   25 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8101 (mt-10)
REVERT: I   38 ARG cc_start: 0.7845 (ttt180) cc_final: 0.7607 (tpp-160)
REVERT: I   62 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7420 (tp30)
REVERT: J   38 ARG cc_start: 0.7587 (ttt180) cc_final: 0.7370 (tpp-160)
REVERT: J   65 GLN cc_start: 0.9003 (mt0) cc_final: 0.8683 (mt0)
REVERT: K   25 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8041 (mt-10)
  outliers start: 27
  outliers final: 6
  residues processed: 159
  average time/residue: 1.8665
  time to fit residues: 306.5637
Evaluate side-chains
  167 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 153
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue   46 ARG
Chi-restraints excluded: chain G residue   66 GLU
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   62 GLU
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain J residue   29 LYS
Chi-restraints excluded: chain J residue   46 ARG
Chi-restraints excluded: chain L residue   63 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  45 GLN
L  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.051   6804  Z= 0.580
  Angle     :  0.617   5.468   9108  Z= 0.373
  Chirality :  0.045   0.134    744
  Planarity :  0.003   0.037   1236
  Dihedral  :  5.104  20.566    900
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 17.36 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.87 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP K  17 
 HIS   0.002   0.001   HIS B  36 
 PHE   0.015   0.002   PHE A   5 
 TYR   0.012   0.002   TYR A  20 
 ARG   0.008   0.001   ARG B  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 156
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7480 (tt0)
REVERT: A   32 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8043 (m-30)
REVERT: A   46 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8143 (tmt170)
REVERT: B   45 GLN cc_start: 0.9018 (mt0) cc_final: 0.8791 (mt0)
REVERT: B   65 GLN cc_start: 0.8851 (mt0) cc_final: 0.8599 (mt0)
REVERT: D   25 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7660 (mp0)
REVERT: D   38 ARG cc_start: 0.7367 (ttt180) cc_final: 0.6875 (ttt90)
REVERT: E   29 LYS cc_start: 0.8425 (tttt) cc_final: 0.7608 (tptt)
REVERT: E   38 ARG cc_start: 0.7517 (ttt180) cc_final: 0.7153 (tpp80)
REVERT: F   56 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8104 (mttp)
REVERT: G    8 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7548 (mp0)
REVERT: G   38 ARG cc_start: 0.7539 (ttt180) cc_final: 0.7158 (tpp80)
REVERT: G   46 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.6607 (tmt170)
REVERT: G   66 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8319 (mt-10)
REVERT: H    8 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8054 (mt-10)
REVERT: H   46 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8420 (tmt170)
REVERT: I    8 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7743 (mt-10)
REVERT: I   25 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8139 (mt-10)
REVERT: I   38 ARG cc_start: 0.7846 (ttt180) cc_final: 0.7597 (tpp-160)
REVERT: J   25 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7862 (mt-10)
REVERT: J   38 ARG cc_start: 0.7601 (ttt180) cc_final: 0.7397 (tpp-160)
REVERT: J   65 GLN cc_start: 0.9028 (mt0) cc_final: 0.8815 (mt0)
REVERT: K   25 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8013 (mt-10)
REVERT: L   29 LYS cc_start: 0.8225 (tttp) cc_final: 0.7967 (tttp)
  outliers start: 32
  outliers final: 13
  residues processed: 162
  average time/residue: 1.9930
  time to fit residues: 334.8545
Evaluate side-chains
  180 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain F residue   56 LYS
Chi-restraints excluded: chain F residue   59 ASP
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue   32 ASP
Chi-restraints excluded: chain G residue   46 ARG
Chi-restraints excluded: chain G residue   66 GLU
Chi-restraints excluded: chain H residue    8 GLU
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain J residue   25 GLU
Chi-restraints excluded: chain J residue   32 ASP
Chi-restraints excluded: chain J residue   46 ARG
Chi-restraints excluded: chain J residue   63 SER
Chi-restraints excluded: chain K residue   63 SER
Chi-restraints excluded: chain L residue   32 ASP
Chi-restraints excluded: chain L residue   63 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 13 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
L  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   6804  Z= 0.190
  Angle     :  0.493   4.554   9108  Z= 0.302
  Chirality :  0.042   0.124    744
  Planarity :  0.002   0.030   1236
  Dihedral  :  4.578  18.038    900
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.10 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G  28 
 HIS   0.000   0.000   HIS F  36 
 PHE   0.012   0.001   PHE F   2 
 TYR   0.009   0.001   TYR J  34 
 ARG   0.003   0.000   ARG B  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7507 (tt0)
REVERT: A   32 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7927 (m-30)
REVERT: B   45 GLN cc_start: 0.8900 (mt0) cc_final: 0.8651 (mt0)
REVERT: B   65 GLN cc_start: 0.8812 (mt0) cc_final: 0.8557 (mt0)
REVERT: D   25 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7696 (mp0)
REVERT: D   38 ARG cc_start: 0.7472 (ttt180) cc_final: 0.6937 (ttt90)
REVERT: E   25 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8106 (mp0)
REVERT: E   29 LYS cc_start: 0.8390 (tttt) cc_final: 0.7613 (tptt)
REVERT: E   38 ARG cc_start: 0.7551 (ttt180) cc_final: 0.7256 (tpp80)
REVERT: G    8 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7594 (mt-10)
REVERT: G   25 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7784 (mp0)
REVERT: G   38 ARG cc_start: 0.7461 (ttt180) cc_final: 0.7020 (tpp80)
REVERT: H   38 ARG cc_start: 0.7497 (ttt180) cc_final: 0.7088 (tpp80)
REVERT: H   46 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8129 (tmt170)
REVERT: I   25 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8086 (mt-10)
REVERT: I   38 ARG cc_start: 0.7833 (ttt180) cc_final: 0.7606 (tpp-160)
REVERT: J   18 ARG cc_start: 0.8523 (ptp-170) cc_final: 0.8131 (pmm-80)
REVERT: J   38 ARG cc_start: 0.7565 (ttt180) cc_final: 0.7350 (tpp-160)
REVERT: J   65 GLN cc_start: 0.8988 (mt0) cc_final: 0.8694 (mt0)
REVERT: K   25 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8085 (mt-10)
  outliers start: 21
  outliers final: 4
  residues processed: 161
  average time/residue: 1.9014
  time to fit residues: 316.6731
Evaluate side-chains
  160 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain L residue   63 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  45 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   6804  Z= 0.408
  Angle     :  0.553   5.022   9108  Z= 0.335
  Chirality :  0.044   0.129    744
  Planarity :  0.003   0.079   1236
  Dihedral  :  4.883  20.046    900
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.27 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.89 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP G  28 
 HIS   0.001   0.000   HIS B  36 
 PHE   0.012   0.002   PHE A   5 
 TYR   0.009   0.001   TYR J  34 
 ARG   0.006   0.001   ARG B  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7510 (tt0)
REVERT: A   32 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8002 (m-30)
REVERT: A   46 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8009 (tmt170)
REVERT: B   45 GLN cc_start: 0.8958 (mt0) cc_final: 0.8724 (mt0)
REVERT: B   65 GLN cc_start: 0.8853 (mt0) cc_final: 0.8594 (mt0)
REVERT: D   25 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7685 (mp0)
REVERT: D   38 ARG cc_start: 0.7449 (ttt180) cc_final: 0.6910 (ttt90)
REVERT: E   29 LYS cc_start: 0.8430 (tttt) cc_final: 0.7629 (tptt)
REVERT: E   38 ARG cc_start: 0.7537 (ttt180) cc_final: 0.7173 (tpp80)
REVERT: G    8 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7486 (mt-10)
REVERT: G   38 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7127 (tpp80)
REVERT: G   46 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.6587 (tmt170)
REVERT: G   66 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8276 (mt-10)
REVERT: H   46 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8419 (tmt170)
REVERT: I    8 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7729 (mt-10)
REVERT: I   25 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8091 (mt-10)
REVERT: I   38 ARG cc_start: 0.7829 (ttt180) cc_final: 0.7588 (tpp-160)
REVERT: J   25 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7764 (mp0)
REVERT: J   65 GLN cc_start: 0.9034 (mt0) cc_final: 0.8788 (mt0)
REVERT: K   25 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8026 (mt-10)
REVERT: L   25 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7626 (mt-10)
  outliers start: 24
  outliers final: 8
  residues processed: 159
  average time/residue: 1.8410
  time to fit residues: 302.6977
Evaluate side-chains
  169 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue   32 ASP
Chi-restraints excluded: chain G residue   46 ARG
Chi-restraints excluded: chain G residue   66 GLU
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain J residue   25 GLU
Chi-restraints excluded: chain J residue   32 ASP
Chi-restraints excluded: chain L residue   63 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   6804  Z= 0.267
  Angle     :  0.511   4.706   9108  Z= 0.311
  Chirality :  0.043   0.126    744
  Planarity :  0.003   0.075   1236
  Dihedral  :  4.669  19.326    900
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 21.18 %
    Favored  : 75.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.89 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G  28 
 HIS   0.001   0.000   HIS F  36 
 PHE   0.012   0.001   PHE E   2 
 TYR   0.010   0.001   TYR J  34 
 ARG   0.004   0.000   ARG B  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7523 (tt0)
REVERT: A   29 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8553 (tttp)
REVERT: A   32 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7992 (m-30)
REVERT: A   46 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.7969 (tmt170)
REVERT: B   45 GLN cc_start: 0.8938 (mt0) cc_final: 0.8730 (mt0)
REVERT: B   65 GLN cc_start: 0.8828 (mt0) cc_final: 0.8575 (mt0)
REVERT: D   25 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7725 (mp0)
REVERT: D   38 ARG cc_start: 0.7484 (ttt180) cc_final: 0.6949 (ttt90)
REVERT: E   38 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7204 (tpp80)
REVERT: G    8 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7570 (mt-10)
REVERT: G   25 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7885 (mp0)
REVERT: G   38 ARG cc_start: 0.7470 (ttt180) cc_final: 0.7108 (tpp80)
REVERT: G   46 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.6652 (tmt170)
REVERT: G   66 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8246 (mt-10)
REVERT: H   38 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7177 (tpp80)
REVERT: H   46 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8130 (tmt170)
REVERT: H   62 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7517 (tp30)
REVERT: I   25 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8114 (mt-10)
REVERT: I   38 ARG cc_start: 0.7839 (ttt180) cc_final: 0.7601 (tpp-160)
REVERT: J   18 ARG cc_start: 0.8610 (ptp-170) cc_final: 0.8267 (pmm-80)
REVERT: J   25 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7769 (mp0)
REVERT: J   65 GLN cc_start: 0.8999 (mt0) cc_final: 0.8750 (mt0)
REVERT: K   25 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8091 (mt-10)
  outliers start: 18
  outliers final: 7
  residues processed: 159
  average time/residue: 1.8307
  time to fit residues: 300.8399
Evaluate side-chains
  169 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue   46 ARG
Chi-restraints excluded: chain G residue   66 GLU
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain H residue   62 GLU
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain J residue   25 GLU
Chi-restraints excluded: chain J residue   32 ASP
Chi-restraints excluded: chain L residue   63 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   6804  Z= 0.239
  Angle     :  0.502   4.542   9108  Z= 0.305
  Chirality :  0.042   0.125    744
  Planarity :  0.003   0.076   1236
  Dihedral  :  4.583  18.987    900
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 21.35 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.89 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G  28 
 HIS   0.001   0.000   HIS F  36 
 PHE   0.011   0.001   PHE E   2 
 TYR   0.011   0.001   TYR J  34 
 ARG   0.004   0.000   ARG B  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7526 (tt0)
REVERT: A   29 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8549 (tttp)
REVERT: A   32 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7953 (m-30)
REVERT: A   46 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8090 (tmt170)
REVERT: B   45 GLN cc_start: 0.8942 (mt0) cc_final: 0.8736 (mt0)
REVERT: B   65 GLN cc_start: 0.8819 (mt0) cc_final: 0.8562 (mt0)
REVERT: D   25 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7722 (mp0)
REVERT: D   38 ARG cc_start: 0.7528 (ttt180) cc_final: 0.6994 (ttt90)
REVERT: E   25 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8104 (mp0)
REVERT: E   29 LYS cc_start: 0.8421 (tttt) cc_final: 0.7594 (tptt)
REVERT: E   38 ARG cc_start: 0.7563 (ttt180) cc_final: 0.7244 (tpp80)
REVERT: G    8 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7545 (mt-10)
REVERT: G   25 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7909 (mp0)
REVERT: G   38 ARG cc_start: 0.7460 (ttt180) cc_final: 0.7005 (tpp80)
REVERT: G   46 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6646 (tmt170)
REVERT: G   66 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8247 (mt-10)
REVERT: H   38 ARG cc_start: 0.7496 (ttt180) cc_final: 0.7127 (tpp80)
REVERT: H   46 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8123 (tmt170)
REVERT: H   62 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7517 (tp30)
REVERT: I   25 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8104 (mt-10)
REVERT: I   38 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7596 (tpp-160)
REVERT: I   62 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7401 (tp30)
REVERT: J   18 ARG cc_start: 0.8584 (ptp-170) cc_final: 0.8230 (pmm-80)
REVERT: J   25 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7906 (mt-10)
REVERT: J   65 GLN cc_start: 0.8997 (mt0) cc_final: 0.8743 (mt0)
REVERT: K   25 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8116 (mt-10)
  outliers start: 22
  outliers final: 8
  residues processed: 158
  average time/residue: 1.8476
  time to fit residues: 301.5721
Evaluate side-chains
  169 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   32 ASP
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue   32 ASP
Chi-restraints excluded: chain G residue   46 ARG
Chi-restraints excluded: chain G residue   66 GLU
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain H residue   62 GLU
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   62 GLU
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain J residue   25 GLU
Chi-restraints excluded: chain J residue   32 ASP
Chi-restraints excluded: chain L residue   63 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    0.1980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C  65 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6804  Z= 0.197
  Angle     :  0.491   4.457   9108  Z= 0.298
  Chirality :  0.042   0.125    744
  Planarity :  0.003   0.074   1236
  Dihedral  :  4.476  18.526    900
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 22.57 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.86 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP I  28 
 HIS   0.001   0.000   HIS F  36 
 PHE   0.011   0.001   PHE E   2 
 TYR   0.011   0.001   TYR J  34 
 ARG   0.004   0.000   ARG B  18 

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7528 (tt0)
REVERT: A   29 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8522 (tttp)
REVERT: A   46 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8101 (tmt170)
REVERT: B   45 GLN cc_start: 0.8930 (mt0) cc_final: 0.8729 (mt0)
REVERT: B   65 GLN cc_start: 0.8811 (mt0) cc_final: 0.8557 (mt0)
REVERT: D   25 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7723 (mp0)
REVERT: D   38 ARG cc_start: 0.7523 (ttt180) cc_final: 0.6984 (ttt90)
REVERT: E   25 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8135 (mp0)
REVERT: E   29 LYS cc_start: 0.8412 (tttt) cc_final: 0.7588 (tptt)
REVERT: E   38 ARG cc_start: 0.7561 (ttt180) cc_final: 0.7244 (tpp80)
REVERT: G    8 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7514 (mt-10)
REVERT: G   25 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7921 (mp0)
REVERT: G   38 ARG cc_start: 0.7450 (ttt180) cc_final: 0.6999 (tpp80)
REVERT: G   46 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6652 (tmt170)
REVERT: G   66 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8235 (mt-10)
REVERT: H   38 ARG cc_start: 0.7494 (ttt180) cc_final: 0.7125 (tpp80)
REVERT: H   46 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8225 (tmt170)
REVERT: H   62 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7495 (tp30)
REVERT: I   25 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8115 (mt-10)
REVERT: I   38 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7603 (tpp-160)
REVERT: I   62 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7362 (tp30)
REVERT: J   18 ARG cc_start: 0.8571 (ptp-170) cc_final: 0.8236 (pmm-80)
REVERT: J   65 GLN cc_start: 0.8994 (mt0) cc_final: 0.8689 (mt0)
REVERT: K   25 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8136 (mt-10)
  outliers start: 19
  outliers final: 6
  residues processed: 160
  average time/residue: 1.8721
  time to fit residues: 309.3512
Evaluate side-chains
  163 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   46 ARG
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain G residue    8 GLU
Chi-restraints excluded: chain G residue   46 ARG
Chi-restraints excluded: chain G residue   66 GLU
Chi-restraints excluded: chain H residue   46 ARG
Chi-restraints excluded: chain H residue   62 GLU
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   62 GLU
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain L residue   63 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  45 GLN
L  65 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.116235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.093552 restraints weight = 7824.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.52
r_work: 0.3379 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.056   6804  Z= 0.624
  Angle     :  0.627   5.442   9108  Z= 0.377
  Chirality :  0.046   0.134    744
  Planarity :  0.004   0.099   1236
  Dihedral  :  5.102  20.760    900
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.96 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.96 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP I  28 
 HIS   0.002   0.001   HIS F  36 
 PHE   0.016   0.002   PHE A   5 
 TYR   0.016   0.002   TYR J  34 
 ARG   0.007   0.001   ARG F  18 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4633.97 seconds
wall clock time: 82 minutes 58.82 seconds (4978.82 seconds total)