Starting phenix.real_space_refine
on Thu Mar  6 04:01:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rt0_4994/03_2025/6rt0_4994.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rt0_4994/03_2025/6rt0_4994.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rt0_4994/03_2025/6rt0_4994.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rt0_4994/03_2025/6rt0_4994.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rt0_4994/03_2025/6rt0_4994.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rt0_4994/03_2025/6rt0_4994.cif"
  }
  resolution = 3.1
  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: 3
    Type Number    sf(0)   Gaussians
     C    3065      2.51       5
     N     865      2.21       5
     O     995      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4925
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 495
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 73}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 495
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 73}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 495
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 73}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 495
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 73}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 495
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 73}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 490
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 72}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 490
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 72}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 490
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 72}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 490
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 72}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "J"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 490
          Classifications: {'peptide': 73}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 72}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.75, per 1000 atoms: 0.76
  Number of scatterers: 4925
  At special positions: 0
  Unit cell: (80.688, 126.608, 42.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     995      8.00
     N     865      7.00
     C    3065      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: 1.21
  Conformation dependent library (CDL) restraints added in 676.5 milliseconds
  

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1230

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 17 sheets defined
      0.0% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 23
      removed outlier: 6.417A  pdb=" N   VAL A  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL D  15 " --> pdb=" O   VAL E  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 23
    Processing sheet with id=AA3, first strand: chain 'C' and resid 37 through 41
      removed outlier: 6.433A  pdb=" N   LEU A  38 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   GLY D  41 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   VAL A  40 " --> pdb=" O   GLY D  41 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   LEU D  38 " --> pdb=" O   TYR E  39 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   GLY E  41 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL D  40 " --> pdb=" O   GLY E  41 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 49
      removed outlier: 6.434A  pdb=" N   VAL B  48 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL A  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 8.263A  pdb=" N   GLY B  51 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 8.583A  pdb=" N   HIS A  50 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 66
      removed outlier: 6.609A  pdb=" N   GLU B  61 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   THR C  64 " --> pdb=" O   GLU B  61 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL B  63 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   VAL C  66 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ASN B  65 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   GLN A  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   ASN D  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   THR A  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   GLN D  62 " --> pdb=" O   VAL E  63 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   ASN E  65 " --> pdb=" O   GLN D  62 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR D  64 " --> pdb=" O   ASN E  65 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 71
      removed outlier: 6.268A  pdb=" N   VAL A  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   VAL D  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 75 through 79
      removed outlier: 6.350A  pdb=" N   ALA B  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   GLN C  79 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ALA B  78 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ALA A  76 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 8.058A  pdb=" N   GLN B  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ALA A  78 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 88 through 89
      removed outlier: 8.383A  pdb=" N   ALA C  89 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ILE B  88 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   SER A  87 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ALA D  90 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA A  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   THR D  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   THR A  92 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   THR B  92 " --> pdb=" O   GLY C  93 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 89
      removed outlier: 8.383A  pdb=" N   ALA C  89 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ILE B  88 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   SER A  87 " --> pdb=" O   ILE D  88 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   ALA D  90 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA A  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   THR D  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA D  89 " --> pdb=" O   ALA E  90 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 19 through 23
      removed outlier: 6.497A  pdb=" N   ALA F  17 " --> pdb=" O   ALA G  18 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   GLU G  20 " --> pdb=" O   ALA F  17 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ALA F  19 " --> pdb=" O   GLU G  20 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   THR G  22 " --> pdb=" O   ALA F  19 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   LYS F  21 " --> pdb=" O   THR G  22 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   VAL G  15 " --> pdb=" O   VAL I  16 " (cutoff:3.500A)
      removed outlier: 8.110A  pdb=" N   ALA I  18 " --> pdb=" O   VAL G  15 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ALA G  17 " --> pdb=" O   ALA I  18 " (cutoff:3.500A)
      removed outlier: 8.317A  pdb=" N   GLU I  20 " --> pdb=" O   ALA G  17 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ALA G  19 " --> pdb=" O   GLU I  20 " (cutoff:3.500A)
      removed outlier: 8.277A  pdb=" N   THR I  22 " --> pdb=" O   ALA G  19 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LYS G  21 " --> pdb=" O   THR I  22 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   VAL I  15 " --> pdb=" O   VAL J  16 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   ALA J  18 " --> pdb=" O   VAL I  15 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ALA I  17 " --> pdb=" O   ALA J  18 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   GLU J  20 " --> pdb=" O   ALA I  17 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   ALA I  19 " --> pdb=" O   GLU J  20 " (cutoff:3.500A)
      removed outlier: 8.259A  pdb=" N   THR J  22 " --> pdb=" O   ALA I  19 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   LYS I  21 " --> pdb=" O   THR J  22 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 37 through 41
      removed outlier: 6.502A  pdb=" N   LEU F  38 " --> pdb=" O   TYR G  39 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   GLY G  41 " --> pdb=" O   LEU F  38 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   VAL F  40 " --> pdb=" O   GLY G  41 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   LEU G  38 " --> pdb=" O   TYR I  39 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   GLY I  41 " --> pdb=" O   LEU G  38 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   VAL G  40 " --> pdb=" O   GLY I  41 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   LEU I  38 " --> pdb=" O   TYR J  39 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   GLY J  41 " --> pdb=" O   LEU I  38 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   VAL I  40 " --> pdb=" O   GLY J  41 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 47 through 49
    Processing sheet with id=AB4, first strand: chain 'H' and resid 61 through 66
      removed outlier: 6.394A  pdb=" N   GLN F  62 " --> pdb=" O   VAL G  63 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   ASN G  65 " --> pdb=" O   GLN F  62 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   THR F  64 " --> pdb=" O   ASN G  65 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   GLN G  62 " --> pdb=" O   VAL I  63 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ASN I  65 " --> pdb=" O   GLN G  62 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   THR G  64 " --> pdb=" O   ASN I  65 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   GLN I  62 " --> pdb=" O   VAL J  63 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   ASN J  65 " --> pdb=" O   GLN I  62 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   THR I  64 " --> pdb=" O   ASN J  65 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 69 through 71
      removed outlier: 6.793A  pdb=" N   ALA F  69 " --> pdb=" O   VAL H  70 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   VAL F  70 " --> pdb=" O   VAL G  71 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   VAL G  70 " --> pdb=" O   VAL I  71 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL I  70 " --> pdb=" O   VAL J  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'H' and resid 75 through 79
      removed outlier: 6.449A  pdb=" N   ALA F  76 " --> pdb=" O   VAL H  77 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   GLN H  79 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ALA F  78 " --> pdb=" O   GLN H  79 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   THR G  75 " --> pdb=" O   ALA I  76 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   ALA I  78 " --> pdb=" O   THR G  75 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   VAL G  77 " --> pdb=" O   ALA I  78 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   THR I  75 " --> pdb=" O   ALA J  76 " (cutoff:3.500A)
      removed outlier: 7.763A  pdb=" N   ALA J  78 " --> pdb=" O   THR I  75 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL I  77 " --> pdb=" O   ALA J  78 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 88 through 93
      removed outlier: 6.320A  pdb=" N   ILE F  88 " --> pdb=" O   ALA H  89 " (cutoff:3.500A)
      removed outlier: 8.491A  pdb=" N   ALA H  91 " --> pdb=" O   ILE F  88 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ALA F  90 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
      removed outlier: 8.483A  pdb=" N   GLY H  93 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   THR F  92 " --> pdb=" O   GLY H  93 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   SER G  87 " --> pdb=" O   ILE I  88 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   ALA I  90 " --> pdb=" O   SER G  87 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ALA G  89 " --> pdb=" O   ALA I  90 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   SER I  87 " --> pdb=" O   ILE J  88 " (cutoff:3.500A)
      removed outlier: 8.195A  pdb=" N   ALA J  90 " --> pdb=" O   SER I  87 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ALA I  89 " --> pdb=" O   ALA J  90 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 55
      removed outlier: 6.444A  pdb=" N   THR G  54 " --> pdb=" O   VAL I  55 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8

    96 hydrogen bonds defined for protein.
    285 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: 1.11

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 875
        1.29 -     1.36: 785
        1.36 -     1.43: 260
        1.43 -     1.51: 1036
        1.51 -     1.58: 1979
  Bond restraints: 4935
  Sorted by residual:
  bond pdb=" CA  LYS A  97 "
       pdb=" CB  LYS A  97 "
    ideal  model  delta    sigma   weight residual
    1.530  1.491  0.039 2.00e-02 2.50e+03 3.77e+00
  bond pdb=" CB  GLU C  46 "
       pdb=" CG  GLU C  46 "
    ideal  model  delta    sigma   weight residual
    1.520  1.577 -0.057 3.00e-02 1.11e+03 3.62e+00
  bond pdb=" CA  LYS D  97 "
       pdb=" CB  LYS D  97 "
    ideal  model  delta    sigma   weight residual
    1.530  1.499  0.031 2.00e-02 2.50e+03 2.41e+00
  bond pdb=" CA  GLY A  47 "
       pdb=" C   GLY A  47 "
    ideal  model  delta    sigma   weight residual
    1.519  1.529 -0.010 7.00e-03 2.04e+04 2.23e+00
  bond pdb=" CA  LYS B  97 "
       pdb=" CB  LYS B  97 "
    ideal  model  delta    sigma   weight residual
    1.530  1.502  0.028 2.00e-02 2.50e+03 1.97e+00
  ... (remaining 4930 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 6135
        1.63 -     3.27: 438
        3.27 -     4.90: 67
        4.90 -     6.53: 23
        6.53 -     8.16: 2
  Bond angle restraints: 6665
  Sorted by residual:
  angle pdb=" CA  GLU C  46 "
        pdb=" CB  GLU C  46 "
        pdb=" CG  GLU C  46 "
      ideal   model   delta    sigma   weight residual
     114.10  122.26   -8.16 2.00e+00 2.50e-01 1.67e+01
  angle pdb=" C   THR A  22 "
        pdb=" N   LYS A  23 "
        pdb=" CA  LYS A  23 "
      ideal   model   delta    sigma   weight residual
     121.94  115.84    6.10 1.76e+00 3.23e-01 1.20e+01
  angle pdb=" C   THR D  22 "
        pdb=" N   LYS D  23 "
        pdb=" CA  LYS D  23 "
      ideal   model   delta    sigma   weight residual
     122.33  116.64    5.69 1.68e+00 3.54e-01 1.15e+01
  angle pdb=" CB  GLU C  46 "
        pdb=" CG  GLU C  46 "
        pdb=" CD  GLU C  46 "
      ideal   model   delta    sigma   weight residual
     112.60  118.22   -5.62 1.70e+00 3.46e-01 1.09e+01
  angle pdb=" N   GLU G  83 "
        pdb=" CA  GLU G  83 "
        pdb=" C   GLU G  83 "
      ideal   model   delta    sigma   weight residual
     111.71  116.01   -4.30 1.34e+00 5.57e-01 1.03e+01
  ... (remaining 6660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 2559
       17.43 -    34.85: 250
       34.85 -    52.27: 37
       52.27 -    69.70: 7
       69.70 -    87.12: 2
  Dihedral angle restraints: 2855
    sinusoidal: 900
      harmonic: 1955
  Sorted by residual:
  dihedral pdb=" CA  GLY I  73 "
           pdb=" C   GLY I  73 "
           pdb=" N   VAL I  74 "
           pdb=" CA  VAL I  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.49   27.51     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  GLY E  84 "
           pdb=" C   GLY E  84 "
           pdb=" N   ALA E  85 "
           pdb=" CA  ALA E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.23   26.77     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  GLY G  73 "
           pdb=" C   GLY G  73 "
           pdb=" N   VAL G  74 "
           pdb=" CA  VAL G  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.64   26.36     0      5.00e+00 4.00e-02 2.78e+01
  ... (remaining 2852 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 336
       0.030 -    0.059: 237
       0.059 -    0.088: 132
       0.088 -    0.118: 120
       0.118 -    0.147: 50
  Chirality restraints: 875
  Sorted by residual:
  chirality pdb=" CA  ILE H  88 "
            pdb=" N   ILE H  88 "
            pdb=" C   ILE H  88 "
            pdb=" CB  ILE H  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.41e-01
  chirality pdb=" CA  VAL E  70 "
            pdb=" N   VAL E  70 "
            pdb=" C   VAL E  70 "
            pdb=" CB  VAL E  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.35e-01
  chirality pdb=" CA  LYS D  23 "
            pdb=" N   LYS D  23 "
            pdb=" C   LYS D  23 "
            pdb=" CB  LYS D  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.25e-01
  ... (remaining 872 not shown)

  Planarity restraints: 835
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR G  72 "    0.011 2.00e-02 2.50e+03   2.22e-02 4.92e+00
        pdb=" C   THR G  72 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   THR G  72 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY G  73 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  72 "    0.011 2.00e-02 2.50e+03   2.21e-02 4.87e+00
        pdb=" C   THR B  72 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   THR B  72 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY B  73 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR F  72 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.97e+00
        pdb=" C   THR F  72 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   THR F  72 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY F  73 "    0.012 2.00e-02 2.50e+03
  ... (remaining 832 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.91: 1913
        2.91 -     3.41: 3889
        3.41 -     3.91: 7720
        3.91 -     4.40: 7881
        4.40 -     4.90: 16278
  Nonbonded interactions: 37681
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS G  45 "
            pdb=" OE2 GLU G  46 "
     model   vdw
     2.415 3.120
  nonbonded pdb=" O   THR C  75 "
            pdb=" OG1 THR C  75 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" N   VAL G  74 "
            pdb=" O   VAL I  74 "
     model   vdw
     2.428 3.120
  nonbonded pdb=" OE1 GLN A  24 "
            pdb=" NE2 GLN B  24 "
     model   vdw
     2.439 3.120
  nonbonded pdb=" NE2 GLN F  62 "
            pdb=" OE1 GLN H  62 "
     model   vdw
     2.445 3.120
  ... (remaining 37676 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 14 through 96)
  selection = (chain 'B' and resid 14 through 96)
  selection = (chain 'C' and resid 14 through 96)
  selection = (chain 'D' and resid 14 through 96)
  selection = (chain 'E' and resid 14 through 96)
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.180
  Find NCS groups from input model:        0.230
  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:3.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   4935  Z= 0.448
  Angle     :  0.974   8.165   6665  Z= 0.585
  Chirality :  0.062   0.147    875
  Planarity :  0.004   0.022    835
  Dihedral  : 14.226  87.119   1625
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.51 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.15 %
    Favored  : 89.79 %
  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: -3.76 (0.27), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.86 (0.21), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  50 
 PHE   0.016   0.002   PHE C  94 
 TYR   0.021   0.005   TYR F  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.488 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7183 (tp30)
REVERT: B   58 LYS cc_start: 0.7357 (ttmt) cc_final: 0.6543 (tptt)
REVERT: B   80 LYS cc_start: 0.8228 (mttp) cc_final: 0.7670 (mtpp)
REVERT: D   80 LYS cc_start: 0.8353 (mttp) cc_final: 0.8058 (mttt)
REVERT: F   58 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7207 (tptm)
REVERT: G   24 GLN cc_start: 0.7398 (mp10) cc_final: 0.7057 (tm-30)
  outliers start: 5
  outliers final: 0
  residues processed: 83
  average time/residue: 0.2944
  time to fit residues: 28.4655
Evaluate side-chains
  71 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
B  50 HIS
G  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.121240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.101129 restraints weight = 6322.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 2.25
r_work: 0.3604 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4935  Z= 0.303
  Angle     :  0.710   7.597   6665  Z= 0.407
  Chirality :  0.054   0.137    875
  Planarity :  0.002   0.014    835
  Dihedral  :  7.333  26.949    725
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.50 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 13.83 %
    Favored  : 85.53 %
  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: -3.80 (0.26), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  50 
 PHE   0.004   0.001   PHE I  94 
 TYR   0.015   0.003   TYR F  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.509 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7400 (tp30)
REVERT: B   58 LYS cc_start: 0.7301 (ttmt) cc_final: 0.6260 (tptt)
REVERT: B   80 LYS cc_start: 0.8224 (mttp) cc_final: 0.7774 (mtpp)
REVERT: C   24 GLN cc_start: 0.7561 (mp10) cc_final: 0.7035 (tm-30)
REVERT: E   58 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7062 (tptm)
REVERT: F   58 LYS cc_start: 0.7840 (ttmt) cc_final: 0.6939 (tptm)
REVERT: G   24 GLN cc_start: 0.7496 (mp10) cc_final: 0.6838 (tm-30)
REVERT: I   20 GLU cc_start: 0.8222 (mp0) cc_final: 0.7982 (mp0)
REVERT: I   43 LYS cc_start: 0.7652 (tttt) cc_final: 0.7307 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 82
  average time/residue: 0.2712
  time to fit residues: 26.2180
Evaluate side-chains
  79 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   54 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 62 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   overall best weight:    3.3586

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

Flipped N/Q/H residues before XYZ refinement:
F  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.117315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.097454 restraints weight = 6419.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.24
r_work: 0.3535 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.032   4935  Z= 0.448
  Angle     :  0.774   7.243   6665  Z= 0.447
  Chirality :  0.057   0.147    875
  Planarity :  0.003   0.010    835
  Dihedral  :  7.577  26.760    725
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.24 %
    Favored  : 86.76 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 18.72 %
    Favored  : 79.57 %
  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: -4.07 (0.25), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.19), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  50 
 PHE   0.005   0.001   PHE B  94 
 TYR   0.019   0.004   TYR J  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.541 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7517 (tp30)
REVERT: B   58 LYS cc_start: 0.7344 (ttmt) cc_final: 0.6319 (tptt)
REVERT: C   24 GLN cc_start: 0.7584 (mp10) cc_final: 0.7020 (tm-30)
REVERT: E   58 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7196 (tptm)
REVERT: F   58 LYS cc_start: 0.7769 (ttmt) cc_final: 0.6828 (tptm)
REVERT: G   24 GLN cc_start: 0.7534 (mp10) cc_final: 0.6873 (tm-30)
REVERT: I   20 GLU cc_start: 0.8300 (mp0) cc_final: 0.8042 (mp0)
REVERT: I   43 LYS cc_start: 0.7678 (tttt) cc_final: 0.7351 (tttm)
REVERT: I   83 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8619 (mt-10)
  outliers start: 8
  outliers final: 7
  residues processed: 86
  average time/residue: 0.2627
  time to fit residues: 26.8267
Evaluate side-chains
  88 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain E residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain J residue   54 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0370
   chunk 25 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.1864

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.122751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.102784 restraints weight = 6448.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.27
r_work: 0.3624 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4935  Z= 0.186
  Angle     :  0.625   7.412   6665  Z= 0.355
  Chirality :  0.053   0.137    875
  Planarity :  0.002   0.009    835
  Dihedral  :  6.543  25.685    725
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 20.21 %
    Favored  : 78.72 %
  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: -3.79 (0.26), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A  50 
 PHE   0.002   0.000   PHE I  94 
 TYR   0.011   0.002   TYR F  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.477 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.7611 (mp0) cc_final: 0.7344 (mm-30)
REVERT: B   46 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7337 (tp30)
REVERT: B   58 LYS cc_start: 0.7354 (ttmt) cc_final: 0.6346 (tptt)
REVERT: C   24 GLN cc_start: 0.7542 (mp10) cc_final: 0.6935 (tm-30)
REVERT: E   58 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7056 (tptm)
REVERT: F   58 LYS cc_start: 0.7742 (ttmt) cc_final: 0.6874 (tptm)
REVERT: I   20 GLU cc_start: 0.8197 (mp0) cc_final: 0.7918 (mp0)
REVERT: I   43 LYS cc_start: 0.7592 (tttt) cc_final: 0.7247 (tttm)
REVERT: I   83 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8395 (mt-10)
  outliers start: 5
  outliers final: 3
  residues processed: 81
  average time/residue: 0.2783
  time to fit residues: 26.4943
Evaluate side-chains
  78 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain D residue   54 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 56 optimal weight:    8.9990
   chunk 57 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS
B  24 GLN
J  50 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.112585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.093136 restraints weight = 6788.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.22
r_work: 0.3468 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.061   4935  Z= 0.820
  Angle     :  0.960   7.501   6665  Z= 0.565
  Chirality :  0.064   0.181    875
  Planarity :  0.004   0.012    835
  Dihedral  :  8.208  26.467    725
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.86 %
    Favored  : 80.14 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.00 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.42 (0.24), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.19), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  50 
 PHE   0.010   0.002   PHE B  94 
 TYR   0.028   0.006   TYR J  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A   46 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7454 (tp30)
REVERT: B   46 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7656 (tp30)
REVERT: B   58 LYS cc_start: 0.7371 (ttmt) cc_final: 0.6337 (tptt)
REVERT: D   46 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7583 (tp30)
REVERT: E   58 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7284 (tptm)
REVERT: F   58 LYS cc_start: 0.7744 (ttmt) cc_final: 0.6809 (tptm)
REVERT: I   43 LYS cc_start: 0.7728 (tttt) cc_final: 0.7441 (tttm)
  outliers start: 15
  outliers final: 10
  residues processed: 100
  average time/residue: 0.2448
  time to fit residues: 29.1020
Evaluate side-chains
  100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   22 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain E residue   22 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   58 LYS
Chi-restraints excluded: chain J residue   54 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0980
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:    0.2980
   chunk 60 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.123335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.103555 restraints weight = 6411.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.24
r_work: 0.3636 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4935  Z= 0.165
  Angle     :  0.628   7.622   6665  Z= 0.356
  Chirality :  0.054   0.140    875
  Planarity :  0.002   0.010    835
  Dihedral  :  6.455  25.747    725
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 23.62 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.00 (0.25), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.19), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS D  50 
 PHE   0.004   0.001   PHE J  94 
 TYR   0.009   0.002   TYR F  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.7569 (mp0) cc_final: 0.7296 (mm-30)
REVERT: B   24 GLN cc_start: 0.7571 (mt0) cc_final: 0.6938 (pp30)
REVERT: B   46 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7363 (tp30)
REVERT: B   58 LYS cc_start: 0.7372 (ttmt) cc_final: 0.6382 (tptt)
REVERT: E   58 LYS cc_start: 0.7841 (ttmt) cc_final: 0.7071 (tptm)
REVERT: F   58 LYS cc_start: 0.7748 (ttmt) cc_final: 0.6876 (tptm)
REVERT: I   43 LYS cc_start: 0.7557 (tttt) cc_final: 0.7291 (tttm)
REVERT: J   83 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8602 (mt-10)
  outliers start: 6
  outliers final: 3
  residues processed: 75
  average time/residue: 0.2733
  time to fit residues: 24.1442
Evaluate side-chains
  73 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   75 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.7988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.125882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.105504 restraints weight = 6169.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.13
r_work: 0.3623 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3469 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4935  Z= 0.255
  Angle     :  0.645   7.153   6665  Z= 0.370
  Chirality :  0.054   0.145    875
  Planarity :  0.002   0.010    835
  Dihedral  :  6.551  23.972    725
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 23.62 %
    Favored  : 74.89 %
  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: -3.95 (0.26), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 PHE   0.003   0.001   PHE I  94 
 TYR   0.012   0.003   TYR F  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.527 
Fit side-chains
REVERT: B   24 GLN cc_start: 0.7582 (mt0) cc_final: 0.6849 (pp30)
REVERT: B   46 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7497 (tp30)
REVERT: B   58 LYS cc_start: 0.7451 (ttmt) cc_final: 0.6457 (tptt)
REVERT: E   58 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7164 (tptm)
REVERT: F   58 LYS cc_start: 0.7766 (ttmt) cc_final: 0.6866 (tptm)
REVERT: I   43 LYS cc_start: 0.7644 (tttt) cc_final: 0.7389 (tttm)
REVERT: I   83 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8608 (mt-10)
  outliers start: 7
  outliers final: 5
  residues processed: 78
  average time/residue: 0.2521
  time to fit residues: 23.3775
Evaluate side-chains
  78 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain H residue   22 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 23 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   overall best weight:    1.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.126110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.105558 restraints weight = 6278.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 2.14
r_work: 0.3623 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4935  Z= 0.257
  Angle     :  0.656   7.180   6665  Z= 0.377
  Chirality :  0.054   0.146    875
  Planarity :  0.002   0.010    835
  Dihedral  :  6.638  25.833    725
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 23.83 %
    Favored  : 74.47 %
  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: -3.91 (0.26), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 PHE   0.004   0.001   PHE I  94 
 TYR   0.012   0.003   TYR F  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.478 
Fit side-chains
REVERT: B   24 GLN cc_start: 0.7625 (mt0) cc_final: 0.6804 (pp30)
REVERT: B   46 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7467 (tp30)
REVERT: B   58 LYS cc_start: 0.7473 (ttmt) cc_final: 0.6517 (tptt)
REVERT: E   58 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7167 (tptm)
REVERT: F   58 LYS cc_start: 0.7761 (ttmt) cc_final: 0.6877 (tptm)
REVERT: I   43 LYS cc_start: 0.7649 (tttt) cc_final: 0.7400 (tttm)
  outliers start: 8
  outliers final: 8
  residues processed: 77
  average time/residue: 0.2536
  time to fit residues: 23.1464
Evaluate side-chains
  81 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain G residue   58 LYS
Chi-restraints excluded: chain H residue   22 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 68 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 29 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   overall best weight:    3.3188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.122404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.102107 restraints weight = 6322.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.13
r_work: 0.3567 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3413 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   4935  Z= 0.440
  Angle     :  0.749   7.130   6665  Z= 0.436
  Chirality :  0.056   0.153    875
  Planarity :  0.003   0.010    835
  Dihedral  :  7.194  24.807    725
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.39 %
    Favored  : 85.61 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 23.40 %
    Favored  : 74.47 %
  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: -4.10 (0.25), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.19), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 PHE   0.005   0.001   PHE I  94 
 TYR   0.018   0.004   TYR J  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 1.112 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7479 (ttmt) cc_final: 0.6480 (tptt)
REVERT: E   58 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7263 (tptm)
REVERT: F   58 LYS cc_start: 0.7741 (ttmt) cc_final: 0.6818 (tptm)
REVERT: I   43 LYS cc_start: 0.7675 (tttt) cc_final: 0.7428 (tttm)
  outliers start: 10
  outliers final: 8
  residues processed: 82
  average time/residue: 0.3173
  time to fit residues: 31.0645
Evaluate side-chains
  84 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   58 LYS
Chi-restraints excluded: chain H residue   22 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.9984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.128700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.108043 restraints weight = 6188.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.16
r_work: 0.3665 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4935  Z= 0.175
  Angle     :  0.611   7.286   6665  Z= 0.348
  Chirality :  0.053   0.140    875
  Planarity :  0.002   0.010    835
  Dihedral  :  6.304  25.694    725
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 24.26 %
    Favored  : 74.26 %
  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 (0.26), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS D  50 
 PHE   0.003   0.001   PHE I  94 
 TYR   0.010   0.002   TYR F  39 

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

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

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1390 Ramachandran restraints generated.
    695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 1.059 
Fit side-chains
REVERT: B   24 GLN cc_start: 0.7604 (mt0) cc_final: 0.6580 (pp30)
REVERT: B   46 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7466 (tp30)
REVERT: B   58 LYS cc_start: 0.7426 (ttmt) cc_final: 0.6453 (tptt)
REVERT: E   58 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7052 (tptm)
REVERT: F   43 LYS cc_start: 0.7440 (tttt) cc_final: 0.7169 (mtpt)
REVERT: F   58 LYS cc_start: 0.7751 (ttmt) cc_final: 0.6875 (tptm)
REVERT: I   20 GLU cc_start: 0.8190 (mp0) cc_final: 0.7872 (mp0)
REVERT: I   43 LYS cc_start: 0.7606 (tttt) cc_final: 0.7346 (tttm)
  outliers start: 7
  outliers final: 6
  residues processed: 75
  average time/residue: 0.2653
  time to fit residues: 24.4099
Evaluate side-chains
  75 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   54 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain G residue   58 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0670
   chunk 61 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   overall best weight:    2.2124

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.124727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.104229 restraints weight = 6295.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 2.14
r_work: 0.3608 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3456 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4935  Z= 0.305
  Angle     :  0.670   6.998   6665  Z= 0.386
  Chirality :  0.054   0.147    875
  Planarity :  0.002   0.009    835
  Dihedral  :  6.652  24.305    725
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.52 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 23.83 %
    Favored  : 74.68 %
  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: -3.91 (0.26), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.97 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 PHE   0.004   0.001   PHE I  94 
 TYR   0.013   0.003   TYR F  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3104.09 seconds
wall clock time: 55 minutes 23.39 seconds (3323.39 seconds total)