Starting phenix.real_space_refine
on Tue Feb 13 09:32:11 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rt0_4994/02_2024/6rt0_4994.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rt0_4994/02_2024/6rt0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rt0_4994/02_2024/6rt0_4994.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rt0_4994/02_2024/6rt0_4994.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rt0_4994/02_2024/6rt0_4994.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rt0_4994/02_2024/6rt0_4994.pdb"
  }
  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
    Residue "C GLU   46": "OE1" <-> "OE2"
    Residue "C GLU   57": "OE1" <-> "OE2"
    Residue "C PHE   94": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 2.84, per 1000 atoms: 0.58
  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  - 3.50
        Amino acid           : False - 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: 1.70
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.72
  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: 1.19

  Time building geometry restraints manager: 1.87 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:
      105.17 -   110.43: 1375
      110.43 -   115.69: 1998
      115.69 -   120.94: 1602
      120.94 -   126.20: 1678
      126.20 -   131.46: 12
  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 2.520
  nonbonded pdb=" O   THR C  75 "
            pdb=" OG1 THR C  75 "
     model   vdw
     2.417 2.440
  nonbonded pdb=" N   VAL G  74 "
            pdb=" O   VAL I  74 "
     model   vdw
     2.428 2.520
  nonbonded pdb=" OE1 GLN A  24 "
            pdb=" NE2 GLN B  24 "
     model   vdw
     2.439 2.520
  nonbonded pdb=" NE2 GLN F  62 "
            pdb=" OE1 GLN H  62 "
     model   vdw
     2.445 2.520
  ... (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
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:             1.580
  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:          4.540
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     16.960
  Find NCS groups from input model:        0.380
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.400
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.554 
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: 0.2961
  time to fit residues: 28.7797
Evaluate side-chains
  71 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 29 optimal weight:    0.2980
   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:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   overall best weight:    2.0386

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1324

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= 0.281
  Angle     :  0.682   7.642   6665  Z= 0.391
  Chirality :  0.053   0.137    875
  Planarity :  0.002   0.017    835
  Dihedral  :  7.147  27.021    725
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.79 %
    Favored  : 89.21 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 15.96 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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   0.003   0.001   PHE I  94 
 TYR   0.014   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
  82 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.482 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7341 (ttmt) cc_final: 0.6483 (tptt)
REVERT: B   80 LYS cc_start: 0.8101 (mttp) cc_final: 0.7684 (mtpp)
REVERT: C   24 GLN cc_start: 0.7154 (mp10) cc_final: 0.6937 (tm-30)
REVERT: E   58 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7020 (tptm)
REVERT: F   58 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7165 (tptm)
REVERT: G   24 GLN cc_start: 0.7448 (mp10) cc_final: 0.6978 (tm-30)
REVERT: I   20 GLU cc_start: 0.7668 (mp0) cc_final: 0.7452 (mp0)
REVERT: I   43 LYS cc_start: 0.7531 (tttt) cc_final: 0.7238 (tttm)
  outliers start: 3
  outliers final: 1
  residues processed: 80
  average time/residue: 0.2781
  time to fit residues: 26.1716
Evaluate side-chains
  78 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
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 35 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0470
   chunk 63 optimal weight:    6.9990
   chunk 68 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 21 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0040
   chunk 62 optimal weight:    5.9990
   overall best weight:    3.2096

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

Flipped N/Q/H residues before XYZ refinement:
B  24 GLN
C  24 GLN
F  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   4935  Z= 0.426
  Angle     :  0.755   7.222   6665  Z= 0.435
  Chirality :  0.056   0.147    875
  Planarity :  0.003   0.013    835
  Dihedral  :  7.437  26.568    725
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.24 %
    Favored  : 85.76 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.36 %
    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: -4.08 (0.25), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (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 fitting.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7380 (ttmt) cc_final: 0.6530 (tptt)
REVERT: E   58 LYS cc_start: 0.7774 (ttmt) cc_final: 0.7072 (tptm)
REVERT: F   58 LYS cc_start: 0.7833 (ttmt) cc_final: 0.7074 (tptm)
REVERT: G   24 GLN cc_start: 0.7578 (mp10) cc_final: 0.7030 (tm-30)
REVERT: I   20 GLU cc_start: 0.7760 (mp0) cc_final: 0.7556 (mp0)
REVERT: I   43 LYS cc_start: 0.7517 (tttt) cc_final: 0.7224 (tttm)
  outliers start: 9
  outliers final: 5
  residues processed: 84
  average time/residue: 0.2565
  time to fit residues: 25.6622
Evaluate side-chains
  83 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 63 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   4935  Z= 0.349
  Angle     :  0.714   7.213   6665  Z= 0.411
  Chirality :  0.055   0.146    875
  Planarity :  0.002   0.022    835
  Dihedral  :  7.071  26.499    725
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.65 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.64 %
    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: -4.08 (0.25), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.19), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  50 
 PHE   0.003   0.001   PHE B  94 
 TYR   0.015   0.003   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
  90 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.546 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7355 (ttmt) cc_final: 0.6524 (tptt)
REVERT: E   58 LYS cc_start: 0.7773 (ttmt) cc_final: 0.7085 (tptm)
REVERT: F   58 LYS cc_start: 0.7835 (ttmt) cc_final: 0.7088 (tptm)
REVERT: I   20 GLU cc_start: 0.7782 (mp0) cc_final: 0.7549 (mp0)
REVERT: I   43 LYS cc_start: 0.7509 (tttt) cc_final: 0.7211 (tttm)
  outliers start: 12
  outliers final: 9
  residues processed: 85
  average time/residue: 0.2613
  time to fit residues: 26.3390
Evaluate side-chains
  86 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
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   54 THR
Chi-restraints excluded: chain E residue   60 LYS
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain J residue   54 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 17 optimal weight:    0.2980
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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: 0.8038
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4935  Z= 0.193
  Angle     :  0.620   7.177   6665  Z= 0.352
  Chirality :  0.053   0.139    875
  Planarity :  0.002   0.015    835
  Dihedral  :  6.312  24.859    725
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.85 %
    Favored  : 76.60 %
  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 : -2.93 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS G  50 
 PHE   0.002   0.000   PHE D  94 
 TYR   0.011   0.002   TYR F  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
  85 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.538 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7343 (ttmt) cc_final: 0.6557 (tptt)
REVERT: E   58 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7063 (tptm)
REVERT: F   58 LYS cc_start: 0.7782 (ttmt) cc_final: 0.7067 (tptm)
REVERT: I   20 GLU cc_start: 0.7720 (mp0) cc_final: 0.7487 (mp0)
REVERT: I   43 LYS cc_start: 0.7465 (tttt) cc_final: 0.7164 (tttm)
  outliers start: 12
  outliers final: 6
  residues processed: 80
  average time/residue: 0.2601
  time to fit residues: 24.6515
Evaluate side-chains
  76 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0170
   chunk 56 optimal weight:    7.9990
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 35 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.7224

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

Flipped N/Q/H residues before XYZ refinement:
B  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4935  Z= 0.244
  Angle     :  0.636   7.164   6665  Z= 0.363
  Chirality :  0.053   0.141    875
  Planarity :  0.002   0.010    835
  Dihedral  :  6.457  24.727    725
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.07 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 22.13 %
    Favored  : 75.53 %
  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: -3.81 (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   0.001   0.001   HIS F  50 
 PHE   0.003   0.001   PHE B  94 
 TYR   0.012   0.003   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
  82 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.621 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7354 (ttmt) cc_final: 0.6566 (tptt)
REVERT: E   58 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7084 (tptm)
REVERT: F   58 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7070 (tptm)
REVERT: I   20 GLU cc_start: 0.7770 (mp0) cc_final: 0.7529 (mp0)
REVERT: I   43 LYS cc_start: 0.7449 (tttt) cc_final: 0.7146 (tttm)
  outliers start: 11
  outliers final: 8
  residues processed: 79
  average time/residue: 0.2563
  time to fit residues: 24.2147
Evaluate side-chains
  79 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
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   22 THR
Chi-restraints excluded: chain B residue   75 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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: 0.8108
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   4935  Z= 0.374
  Angle     :  0.710   7.229   6665  Z= 0.410
  Chirality :  0.055   0.147    875
  Planarity :  0.002   0.010    835
  Dihedral  :  6.989  25.154    725
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.09 %
    Favored  : 86.91 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 22.34 %
    Favored  : 75.32 %
  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 (0.25), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.19), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 PHE   0.004   0.001   PHE B  94 
 TYR   0.016   0.003   TYR J  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
  85 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.509 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7386 (ttmt) cc_final: 0.6571 (tptt)
REVERT: B   80 LYS cc_start: 0.8114 (mttp) cc_final: 0.7673 (mtpp)
REVERT: E   58 LYS cc_start: 0.7790 (ttmt) cc_final: 0.7173 (tptm)
REVERT: F   58 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7083 (tptm)
REVERT: I   43 LYS cc_start: 0.7488 (tttt) cc_final: 0.7230 (tttm)
  outliers start: 11
  outliers final: 9
  residues processed: 80
  average time/residue: 0.2618
  time to fit residues: 24.8899
Evaluate side-chains
  83 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
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   22 THR
Chi-restraints excluded: chain B residue   75 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 J residue   54 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 42 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 58 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4935  Z= 0.139
  Angle     :  0.581   7.210   6665  Z= 0.328
  Chirality :  0.052   0.137    875
  Planarity :  0.001   0.011    835
  Dihedral  :  5.921  24.191    725
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 22.77 %
    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: -3.71 (0.26), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.82 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS J  50 
 PHE   0.002   0.000   PHE E  94 
 TYR   0.009   0.002   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
  84 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.528 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7380 (ttmt) cc_final: 0.6615 (tptt)
REVERT: C   20 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7462 (tp30)
REVERT: E   58 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7001 (tptm)
REVERT: F   43 LYS cc_start: 0.7396 (tttt) cc_final: 0.7105 (mtpt)
REVERT: F   58 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7035 (tptm)
REVERT: I   20 GLU cc_start: 0.7695 (mp0) cc_final: 0.7459 (mp0)
REVERT: I   43 LYS cc_start: 0.7440 (tttt) cc_final: 0.7222 (ttmt)
  outliers start: 11
  outliers final: 8
  residues processed: 80
  average time/residue: 0.2648
  time to fit residues: 24.9800
Evaluate side-chains
  78 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   75 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   75 THR
Chi-restraints excluded: chain F residue   92 THR
Chi-restraints excluded: chain I residue   65 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 56 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    3.6988

-------------------------------------------------------------------------------
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: 0.8135
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.035   4935  Z= 0.477
  Angle     :  0.758   7.332   6665  Z= 0.440
  Chirality :  0.056   0.151    875
  Planarity :  0.003   0.009    835
  Dihedral  :  7.186  24.639    725
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.83 %
    Favored  : 84.17 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 22.13 %
    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: -4.02 (0.25), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (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 B  94 
 TYR   0.019   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
  92 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.497 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7409 (ttmt) cc_final: 0.6566 (tptt)
REVERT: D   80 LYS cc_start: 0.8339 (mttp) cc_final: 0.8083 (mttt)
REVERT: E   58 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7164 (tptm)
REVERT: F   58 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7079 (tptm)
  outliers start: 13
  outliers final: 10
  residues processed: 87
  average time/residue: 0.2523
  time to fit residues: 26.0269
Evaluate side-chains
  89 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 79
  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   22 THR
Chi-restraints excluded: chain B residue   75 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   75 THR
Chi-restraints excluded: chain F residue   92 THR
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 69 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0870
   chunk 34 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.9362

-------------------------------------------------------------------------------
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: 0.8033
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4935  Z= 0.166
  Angle     :  0.611   7.354   6665  Z= 0.346
  Chirality :  0.053   0.139    875
  Planarity :  0.002   0.016    835
  Dihedral  :  6.200  25.581    725
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 22.98 %
    Favored  : 75.32 %
  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: -3.83 (0.26), residues: 695
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.20), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  50 
 PHE   0.001   0.000   PHE E  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
  77 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.546 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.7367 (ttmt) cc_final: 0.6597 (tptt)
REVERT: C   20 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7474 (tp30)
REVERT: E   58 LYS cc_start: 0.7739 (ttmt) cc_final: 0.7057 (tptm)
REVERT: F   43 LYS cc_start: 0.7383 (tttt) cc_final: 0.7055 (mtpt)
REVERT: F   58 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7063 (tptm)
REVERT: I   20 GLU cc_start: 0.7709 (mp0) cc_final: 0.7452 (mp0)
  outliers start: 8
  outliers final: 7
  residues processed: 74
  average time/residue: 0.2870
  time to fit residues: 25.2098
Evaluate side-chains
  76 residues out of total 495 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   75 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 I residue   65 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 55 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0370
   chunk 7 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 63 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   overall best weight:    1.5062

-------------------------------------------------------------------------------
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 = 0.4058 r_free = 0.4058 target = 0.125548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.106094 restraints weight = 6171.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 2.03
r_work: 0.3642 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3491 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2253

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= 0.219
  Angle     :  0.616   7.083   6665  Z= 0.351
  Chirality :  0.053   0.142    875
  Planarity :  0.002   0.015    835
  Dihedral  :  6.220  24.118    725
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 22.98 %
    Favored  : 75.32 %
  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 F  50 
 PHE   0.002   0.001   PHE D  94 
 TYR   0.011   0.002   TYR F  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1468.69 seconds
wall clock time: 27 minutes 12.21 seconds (1632.21 seconds total)