Starting phenix.real_space_refine
on Thu Mar  5 00:14:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tgg_25881/03_2026/7tgg_25881.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tgg_25881/03_2026/7tgg_25881.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tgg_25881/03_2026/7tgg_25881.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tgg_25881/03_2026/7tgg_25881.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tgg_25881/03_2026/7tgg_25881.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tgg_25881/03_2026/7tgg_25881.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.003 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C   11445      2.51       5
     N    2985      2.21       5
     O    3810      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18255
  Number of models: 1
  Model: ""
    Number of chains: 30
    Chain: "A"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "a"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "C"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "E"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "F"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "G"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "I"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "J"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "K"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "L"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "M"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "N"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "O"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "P"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "Q"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "R"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "S"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "T"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "U"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "V"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "W"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "X"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "Y"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "Z"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "0"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
    Chain: "1"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 454
          Classifications: {'peptide': 60}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 56}
    Chain: "2"
      Number of atoms: 763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 763
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
  Time building chain proxies: 3.48, per 1000 atoms: 0.19
  Number of scatterers: 18255
  At special positions: 0
  Unit cell: (83.16, 83.16, 246.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O    3810      8.00
     N    2985      7.00
     C   11445      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: 1.63
  Conformation dependent library (CDL) restraints added in 784.7 milliseconds
  

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4530

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 15 sheets defined
      27.6% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A  11 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A  15 " --> pdb=" O   ALA A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA A  31 " --> pdb=" O   TYR A  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR A  45 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL B  10 " --> pdb=" O   LEU B   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE B  15 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 55
      removed outlier: 4.473A  pdb=" N   ALA B  31 " --> pdb=" O   TYR B  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR B  45 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL D  10 " --> pdb=" O   LEU D   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA D  11 " --> pdb=" O   LEU D   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE D  15 " --> pdb=" O   ALA D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 55
      removed outlier: 4.473A  pdb=" N   ALA D  31 " --> pdb=" O   TYR D  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR D  45 " --> pdb=" O   ARG D  41 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL F  10 " --> pdb=" O   LEU F   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA F  11 " --> pdb=" O   LEU F   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE F  15 " --> pdb=" O   ALA F  11 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA F  31 " --> pdb=" O   TYR F  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR F  45 " --> pdb=" O   ARG F  41 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL H  10 " --> pdb=" O   LEU H   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA H  11 " --> pdb=" O   LEU H   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE H  15 " --> pdb=" O   ALA H  11 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 55
      removed outlier: 4.473A  pdb=" N   ALA H  31 " --> pdb=" O   TYR H  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR H  45 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL J  10 " --> pdb=" O   LEU J   6 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA J  11 " --> pdb=" O   LEU J   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE J  15 " --> pdb=" O   ALA J  11 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA J  31 " --> pdb=" O   TYR J  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR J  45 " --> pdb=" O   ARG J  41 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL L  10 " --> pdb=" O   LEU L   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA L  11 " --> pdb=" O   LEU L   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE L  15 " --> pdb=" O   ALA L  11 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA L  31 " --> pdb=" O   TYR L  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR L  45 " --> pdb=" O   ARG L  41 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL N  10 " --> pdb=" O   LEU N   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA N  11 " --> pdb=" O   LEU N   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE N  15 " --> pdb=" O   ALA N  11 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 25 through 55
      removed outlier: 4.473A  pdb=" N   ALA N  31 " --> pdb=" O   TYR N  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR N  45 " --> pdb=" O   ARG N  41 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL P  10 " --> pdb=" O   LEU P   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA P  11 " --> pdb=" O   LEU P   7 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE P  15 " --> pdb=" O   ALA P  11 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA P  31 " --> pdb=" O   TYR P  27 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   THR P  45 " --> pdb=" O   ARG P  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL R  10 " --> pdb=" O   LEU R   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA R  11 " --> pdb=" O   LEU R   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE R  15 " --> pdb=" O   ALA R  11 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 25 through 55
      removed outlier: 4.473A  pdb=" N   ALA R  31 " --> pdb=" O   TYR R  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR R  45 " --> pdb=" O   ARG R  41 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL T  10 " --> pdb=" O   LEU T   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA T  11 " --> pdb=" O   LEU T   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE T  15 " --> pdb=" O   ALA T  11 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA T  31 " --> pdb=" O   TYR T  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR T  45 " --> pdb=" O   ARG T  41 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL V  10 " --> pdb=" O   LEU V   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA V  11 " --> pdb=" O   LEU V   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE V  15 " --> pdb=" O   ALA V  11 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA V  31 " --> pdb=" O   TYR V  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR V  45 " --> pdb=" O   ARG V  41 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL X  10 " --> pdb=" O   LEU X   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA X  11 " --> pdb=" O   LEU X   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE X  15 " --> pdb=" O   ALA X  11 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 25 through 55
      removed outlier: 4.473A  pdb=" N   ALA X  31 " --> pdb=" O   TYR X  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR X  45 " --> pdb=" O   ARG X  41 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL Z  10 " --> pdb=" O   LEU Z   6 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA Z  11 " --> pdb=" O   LEU Z   7 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ILE Z  15 " --> pdb=" O   ALA Z  11 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA Z  31 " --> pdb=" O   TYR Z  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR Z  45 " --> pdb=" O   ARG Z  41 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 4 through 17
      removed outlier: 4.005A  pdb=" N   VAL 1  10 " --> pdb=" O   LEU 1   6 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA 1  11 " --> pdb=" O   LEU 1   7 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE 1  15 " --> pdb=" O   ALA 1  11 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 25 through 55
      removed outlier: 4.472A  pdb=" N   ALA 1  31 " --> pdb=" O   TYR 1  27 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR 1  45 " --> pdb=" O   ARG 1  41 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'a' and resid 22 through 28
    Processing sheet with id=2, first strand: chain 'C' and resid 22 through 28
    Processing sheet with id=3, first strand: chain 'E' and resid 22 through 28
    Processing sheet with id=4, first strand: chain 'G' and resid 22 through 28
    Processing sheet with id=5, first strand: chain 'I' and resid 22 through 28
    Processing sheet with id=6, first strand: chain 'K' and resid 22 through 28
    Processing sheet with id=7, first strand: chain 'M' and resid 22 through 28
    Processing sheet with id=8, first strand: chain 'O' and resid 22 through 28
    Processing sheet with id=9, first strand: chain 'Q' and resid 22 through 28
    Processing sheet with id=10, first strand: chain 'S' and resid 22 through 28
    Processing sheet with id=11, first strand: chain 'U' and resid 22 through 28
    Processing sheet with id=12, first strand: chain 'W' and resid 22 through 28
    Processing sheet with id=13, first strand: chain 'Y' and resid 22 through 28
    Processing sheet with id=14, first strand: chain '0' and resid 22 through 28
    Processing sheet with id=15, first strand: chain '2' and resid 22 through 28

    660 hydrogen bonds defined for protein.
    1935 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.48

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5880
        1.34 -     1.46: 3411
        1.46 -     1.57: 9264
        1.57 -     1.69: 0
        1.69 -     1.80: 30
  Bond restraints: 18585
  Sorted by residual:
  bond pdb=" CA  THR K  15 "
       pdb=" CB  THR K  15 "
    ideal  model  delta    sigma   weight residual
    1.529  1.551 -0.022 1.58e-02 4.01e+03 2.00e+00
  bond pdb=" CA  THR W  15 "
       pdb=" CB  THR W  15 "
    ideal  model  delta    sigma   weight residual
    1.529  1.551 -0.022 1.58e-02 4.01e+03 1.96e+00
  bond pdb=" CA  THR 2  15 "
       pdb=" CB  THR 2  15 "
    ideal  model  delta    sigma   weight residual
    1.529  1.551 -0.022 1.58e-02 4.01e+03 1.94e+00
  bond pdb=" CA  THR E  15 "
       pdb=" CB  THR E  15 "
    ideal  model  delta    sigma   weight residual
    1.529  1.551 -0.022 1.58e-02 4.01e+03 1.93e+00
  bond pdb=" CA  THR O  15 "
       pdb=" CB  THR O  15 "
    ideal  model  delta    sigma   weight residual
    1.529  1.551 -0.022 1.58e-02 4.01e+03 1.93e+00
  ... (remaining 18580 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 23739
        1.35 -     2.69: 1342
        2.69 -     4.04: 174
        4.04 -     5.39: 65
        5.39 -     6.73: 15
  Bond angle restraints: 25335
  Sorted by residual:
  angle pdb=" CA  ASP Q  71 "
        pdb=" CB  ASP Q  71 "
        pdb=" CG  ASP Q  71 "
      ideal   model   delta    sigma   weight residual
     112.60  115.10   -2.50 1.00e+00 1.00e+00 6.26e+00
  angle pdb=" CA  ASP I  71 "
        pdb=" CB  ASP I  71 "
        pdb=" CG  ASP I  71 "
      ideal   model   delta    sigma   weight residual
     112.60  115.10   -2.50 1.00e+00 1.00e+00 6.23e+00
  angle pdb=" CA  ASP O  71 "
        pdb=" CB  ASP O  71 "
        pdb=" CG  ASP O  71 "
      ideal   model   delta    sigma   weight residual
     112.60  115.09   -2.49 1.00e+00 1.00e+00 6.19e+00
  angle pdb=" CA  ASP a  71 "
        pdb=" CB  ASP a  71 "
        pdb=" CG  ASP a  71 "
      ideal   model   delta    sigma   weight residual
     112.60  115.07   -2.47 1.00e+00 1.00e+00 6.11e+00
  angle pdb=" CA  ASP C  71 "
        pdb=" CB  ASP C  71 "
        pdb=" CG  ASP C  71 "
      ideal   model   delta    sigma   weight residual
     112.60  115.07   -2.47 1.00e+00 1.00e+00 6.08e+00
  ... (remaining 25330 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.36: 10125
       15.36 -    30.72: 585
       30.72 -    46.09: 135
       46.09 -    61.45: 45
       61.45 -    76.81: 15
  Dihedral angle restraints: 10905
    sinusoidal: 3870
      harmonic: 7035
  Sorted by residual:
  dihedral pdb=" CA  PHE I  14 "
           pdb=" C   PHE I  14 "
           pdb=" N   THR I  15 "
           pdb=" CA  THR I  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  PHE C  14 "
           pdb=" C   PHE C  14 "
           pdb=" N   THR C  15 "
           pdb=" CA  THR C  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  PHE Y  14 "
           pdb=" C   PHE Y  14 "
           pdb=" N   THR Y  15 "
           pdb=" CA  THR Y  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 10902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 2028
       0.038 -    0.077: 800
       0.077 -    0.115: 127
       0.115 -    0.154: 15
       0.154 -    0.192: 45
  Chirality restraints: 3015
  Sorted by residual:
  chirality pdb=" CB  ILE X  19 "
            pdb=" CA  ILE X  19 "
            pdb=" CG1 ILE X  19 "
            pdb=" CG2 ILE X  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.22e-01
  chirality pdb=" CB  ILE R  19 "
            pdb=" CA  ILE R  19 "
            pdb=" CG1 ILE R  19 "
            pdb=" CG2 ILE R  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.21e-01
  chirality pdb=" CB  ILE J  19 "
            pdb=" CA  ILE J  19 "
            pdb=" CG1 ILE J  19 "
            pdb=" CG2 ILE J  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.20e-01
  ... (remaining 3012 not shown)

  Planarity restraints: 3225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP Q  73 "   -0.016 2.00e-02 2.50e+03   1.24e-02 3.83e+00
        pdb=" CG  TRP Q  73 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP Q  73 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP Q  73 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP Q  73 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP Q  73 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP Q  73 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP Q  73 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP Q  73 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP Q  73 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP G  73 "    0.016 2.00e-02 2.50e+03   1.24e-02 3.82e+00
        pdb=" CG  TRP G  73 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP G  73 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP G  73 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP G  73 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP G  73 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP G  73 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP G  73 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP G  73 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP G  73 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP M  73 "    0.016 2.00e-02 2.50e+03   1.23e-02 3.81e+00
        pdb=" CG  TRP M  73 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP M  73 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP M  73 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP M  73 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP M  73 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP M  73 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP M  73 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP M  73 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP M  73 "    0.005 2.00e-02 2.50e+03
  ... (remaining 3222 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 272
        2.64 -     3.20: 19500
        3.20 -     3.77: 28414
        3.77 -     4.33: 39128
        4.33 -     4.90: 62501
  Nonbonded interactions: 149815
  Sorted by model distance:
  nonbonded pdb=" OG1 THR O  15 "
            pdb=" NE2 GLN T  23 "
     model   vdw
     2.070 3.120
  nonbonded pdb=" OG1 THR G  15 "
            pdb=" NE2 GLN L  23 "
     model   vdw
     2.070 3.120
  nonbonded pdb=" OG1 THR K  15 "
            pdb=" NE2 GLN N  23 "
     model   vdw
     2.070 3.120
  nonbonded pdb=" OG1 THR U  15 "
            pdb=" NE2 GLN Z  23 "
     model   vdw
     2.070 3.120
  nonbonded pdb=" OG1 THR C  15 "
            pdb=" NE2 GLN H  23 "
     model   vdw
     2.070 3.120
  ... (remaining 149810 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
  selection = chain 'N'
  selection = chain 'P'
  selection = chain 'R'
  selection = chain 'T'
  selection = chain 'V'
  selection = chain 'X'
  selection = chain 'Z'
  selection = chain '1'
}
ncs_group {
  reference = chain 'a'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'M'
  selection = chain 'O'
  selection = chain 'Q'
  selection = chain 'S'
  selection = chain 'U'
  selection = chain 'W'
  selection = chain 'Y'
  selection = chain '0'
  selection = chain '2'
}

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 group one per residue
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:             2.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     15.220
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.080
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
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      :  0.004   0.029  18585  Z= 0.178
  Angle     :  0.714   6.733  25335  Z= 0.413
  Chirality :  0.045   0.192   3015
  Planarity :  0.007   0.060   3225
  Dihedral  : 11.742  76.809   6375
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.16), residues: 2385
  helix: -0.87 (0.19), residues: 675
  sheet:  0.48 (0.20), residues: 285
  loop : -2.31 (0.16), residues: 1425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG V  28 
 TYR   0.011   0.002   TYR P  27 
 PHE   0.029   0.004   PHE B  24 
 TRP   0.032   0.003   TRP Q  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 (18585)
  covalent geometry    : angle       0.71375 (25335)
  hydrogen bonds       : bond        0.15122 (  660)
  hydrogen bonds       : angle       6.85141 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  366 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 366
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8911 (tt) cc_final: 0.8202 (tt)
REVERT: a   13 ASP cc_start: 0.8724 (m-30) cc_final: 0.8478 (t0)
REVERT: a  101 TRP cc_start: 0.8632 (p-90) cc_final: 0.7702 (p-90)
REVERT: C  101 TRP cc_start: 0.8368 (p-90) cc_final: 0.7501 (p-90)
REVERT: D    3 LEU cc_start: 0.8893 (tt) cc_final: 0.8322 (tt)
REVERT: E   13 ASP cc_start: 0.8660 (m-30) cc_final: 0.8456 (t0)
REVERT: E   43 TYR cc_start: 0.9024 (p90) cc_final: 0.8707 (p90)
REVERT: E  101 TRP cc_start: 0.8468 (p-90) cc_final: 0.7470 (p-90)
REVERT: F    3 LEU cc_start: 0.8952 (tt) cc_final: 0.8243 (tp)
REVERT: G   13 ASP cc_start: 0.8637 (m-30) cc_final: 0.8429 (t0)
REVERT: G  101 TRP cc_start: 0.8547 (p-90) cc_final: 0.7353 (p-90)
REVERT: H    3 LEU cc_start: 0.8951 (tt) cc_final: 0.8427 (tp)
REVERT: I   43 TYR cc_start: 0.9062 (p90) cc_final: 0.8785 (p90)
REVERT: I  101 TRP cc_start: 0.8415 (p-90) cc_final: 0.8207 (p-90)
REVERT: K   13 ASP cc_start: 0.8723 (m-30) cc_final: 0.8516 (t0)
REVERT: K   40 ASN cc_start: 0.6570 (m-40) cc_final: 0.5786 (m-40)
REVERT: K   42 ASP cc_start: 0.8118 (m-30) cc_final: 0.7829 (t70)
REVERT: K  101 TRP cc_start: 0.8476 (p-90) cc_final: 0.7831 (p-90)
REVERT: L    3 LEU cc_start: 0.8908 (tt) cc_final: 0.8678 (tt)
REVERT: M  101 TRP cc_start: 0.8383 (p-90) cc_final: 0.7434 (p-90)
REVERT: N    3 LEU cc_start: 0.8901 (tt) cc_final: 0.8119 (tt)
REVERT: P    3 LEU cc_start: 0.8863 (tt) cc_final: 0.8207 (tt)
REVERT: Q   13 ASP cc_start: 0.8585 (m-30) cc_final: 0.8330 (t0)
REVERT: Q  101 TRP cc_start: 0.8452 (p-90) cc_final: 0.8038 (p90)
REVERT: R    3 LEU cc_start: 0.8886 (tt) cc_final: 0.8344 (tt)
REVERT: R    5 GLU cc_start: 0.8757 (tt0) cc_final: 0.8491 (tp30)
REVERT: S  101 TRP cc_start: 0.8474 (p-90) cc_final: 0.7631 (p-90)
REVERT: T    3 LEU cc_start: 0.8803 (tt) cc_final: 0.8013 (tt)
REVERT: T    5 GLU cc_start: 0.8888 (tt0) cc_final: 0.8677 (tp30)
REVERT: U   13 ASP cc_start: 0.8684 (m-30) cc_final: 0.8347 (t0)
REVERT: U   43 TYR cc_start: 0.9084 (p90) cc_final: 0.8577 (p90)
REVERT: U  101 TRP cc_start: 0.8525 (p-90) cc_final: 0.7597 (p-90)
REVERT: V    3 LEU cc_start: 0.8859 (tt) cc_final: 0.8231 (tt)
REVERT: W  101 TRP cc_start: 0.8525 (p-90) cc_final: 0.7549 (p-90)
REVERT: X    3 LEU cc_start: 0.8798 (tt) cc_final: 0.7867 (tp)
REVERT: Y   40 ASN cc_start: 0.6363 (m-40) cc_final: 0.5660 (m-40)
REVERT: Y  101 TRP cc_start: 0.8481 (p-90) cc_final: 0.8054 (p-90)
REVERT: Z    3 LEU cc_start: 0.8788 (tt) cc_final: 0.8523 (tp)
REVERT: 0  101 TRP cc_start: 0.8560 (p-90) cc_final: 0.8091 (p-90)
REVERT: 1    3 LEU cc_start: 0.8835 (tt) cc_final: 0.8336 (tp)
REVERT: 1    5 GLU cc_start: 0.8701 (tt0) cc_final: 0.8332 (tp30)
REVERT: 2  101 TRP cc_start: 0.8492 (p-90) cc_final: 0.7616 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 366
  average time/residue: 0.1219
  time to fit residues: 70.3170
Evaluate side-chains
  222 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 216 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 194 optimal weight:    2.9990
   chunk 227 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    8.9990
   chunk 235 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 ASN
** J  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** V  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.047737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.040208 restraints weight = 99318.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.041897 restraints weight = 54417.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.043114 restraints weight = 34648.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.043994 restraints weight = 24014.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.044644 restraints weight = 17494.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  18585  Z= 0.184
  Angle     :  0.606   4.837  25335  Z= 0.341
  Chirality :  0.044   0.150   3015
  Planarity :  0.004   0.045   3225
  Dihedral  :  7.056  66.810   2565
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.18), residues: 2385
  helix:  0.36 (0.21), residues: 675
  sheet: -0.30 (0.23), residues: 375
  loop : -1.74 (0.18), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG X  28 
 TYR   0.012   0.002   TYR K  43 
 PHE   0.015   0.002   PHE F  24 
 TRP   0.019   0.002   TRP G  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (18585)
  covalent geometry    : angle       0.60644 (25335)
  hydrogen bonds       : bond        0.05193 (  660)
  hydrogen bonds       : angle       4.82696 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   43 TYR cc_start: 0.9290 (p90) cc_final: 0.9020 (p90)
REVERT: C  101 TRP cc_start: 0.8434 (p-90) cc_final: 0.7485 (p-90)
REVERT: D    3 LEU cc_start: 0.8717 (tt) cc_final: 0.8513 (tt)
REVERT: D    6 LEU cc_start: 0.9570 (mm) cc_final: 0.9369 (mm)
REVERT: E  101 TRP cc_start: 0.8435 (p-90) cc_final: 0.7530 (p-90)
REVERT: G  101 TRP cc_start: 0.8601 (p-90) cc_final: 0.7578 (p-90)
REVERT: I  101 TRP cc_start: 0.8397 (p-90) cc_final: 0.8088 (p-90)
REVERT: K  101 TRP cc_start: 0.8495 (p-90) cc_final: 0.7748 (p-90)
REVERT: L    5 GLU cc_start: 0.9304 (mm-30) cc_final: 0.9084 (tp30)
REVERT: M   43 TYR cc_start: 0.9212 (p90) cc_final: 0.8551 (p90)
REVERT: N    6 LEU cc_start: 0.9595 (mm) cc_final: 0.9354 (mm)
REVERT: O   40 ASN cc_start: 0.7166 (m-40) cc_final: 0.6424 (m-40)
REVERT: Q   43 TYR cc_start: 0.9292 (p90) cc_final: 0.9043 (p90)
REVERT: Q  101 TRP cc_start: 0.8520 (p-90) cc_final: 0.8048 (p-90)
REVERT: S  101 TRP cc_start: 0.8495 (p-90) cc_final: 0.7517 (p-90)
REVERT: T    3 LEU cc_start: 0.8704 (tt) cc_final: 0.8386 (tt)
REVERT: U  101 TRP cc_start: 0.8611 (p-90) cc_final: 0.7756 (p-90)
REVERT: V    5 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8920 (tp30)
REVERT: V    6 LEU cc_start: 0.9642 (mm) cc_final: 0.9433 (mm)
REVERT: V   30 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8673 (tmtt)
REVERT: V   48 GLU cc_start: 0.9492 (tp30) cc_final: 0.9228 (mm-30)
REVERT: W   43 TYR cc_start: 0.9213 (p90) cc_final: 0.8900 (p90)
REVERT: W  101 TRP cc_start: 0.8572 (p-90) cc_final: 0.7723 (p-90)
REVERT: Y   43 TYR cc_start: 0.9346 (p90) cc_final: 0.9124 (p90)
REVERT: Y  101 TRP cc_start: 0.8620 (p-90) cc_final: 0.8222 (p-90)
REVERT: Z    3 LEU cc_start: 0.8825 (tt) cc_final: 0.8583 (tp)
REVERT: Z   30 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8633 (tmtt)
REVERT: 0   40 ASN cc_start: 0.7209 (m-40) cc_final: 0.6381 (m-40)
REVERT: 0  101 TRP cc_start: 0.8530 (p-90) cc_final: 0.7918 (p-90)
REVERT: 1    5 GLU cc_start: 0.8849 (tt0) cc_final: 0.8358 (tp30)
REVERT: 1   30 LYS cc_start: 0.9290 (mmtt) cc_final: 0.8574 (tmtt)
REVERT: 2  101 TRP cc_start: 0.8518 (p-90) cc_final: 0.7566 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 317
  average time/residue: 0.1289
  time to fit residues: 64.3946
Evaluate side-chains
  198 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 138 optimal weight:    0.8980
   chunk 177 optimal weight:    0.5980
   chunk 139 optimal weight:    6.9990
   chunk 190 optimal weight:    9.9990
   chunk 205 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 124 optimal weight:    5.9990
   chunk 130 optimal weight:    0.0050
   chunk 25 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 84 optimal weight:    0.9990
   overall best weight:    1.2998

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 ASN
J  42 ASN
L  42 ASN
** N  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  42 ASN
R  42 ASN
T  42 ASN
V  42 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.046602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.039715 restraints weight = 99904.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.041328 restraints weight = 53438.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.042463 restraints weight = 33454.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.043274 restraints weight = 22832.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.043869 restraints weight = 16470.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18585  Z= 0.123
  Angle     :  0.550   7.095  25335  Z= 0.299
  Chirality :  0.043   0.198   3015
  Planarity :  0.004   0.034   3225
  Dihedral  :  6.564  61.299   2565
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.18), residues: 2385
  helix:  0.96 (0.22), residues: 675
  sheet: -0.32 (0.25), residues: 375
  loop : -1.48 (0.18), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG X  28 
 TYR   0.016   0.001   TYR C  43 
 PHE   0.011   0.001   PHE H  24 
 TRP   0.018   0.001   TRP Y  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (18585)
  covalent geometry    : angle       0.54988 (25335)
  hydrogen bonds       : bond        0.04567 (  660)
  hydrogen bonds       : angle       4.59270 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 296
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.9206 (tp30) cc_final: 0.8871 (tp30)
REVERT: a   13 ASP cc_start: 0.8418 (p0) cc_final: 0.8067 (p0)
REVERT: C  101 TRP cc_start: 0.8331 (p-90) cc_final: 0.7396 (p-90)
REVERT: D    6 LEU cc_start: 0.9562 (mm) cc_final: 0.9354 (mm)
REVERT: E   13 ASP cc_start: 0.8499 (p0) cc_final: 0.8152 (p0)
REVERT: E  101 TRP cc_start: 0.8395 (p-90) cc_final: 0.7563 (p-90)
REVERT: G   13 ASP cc_start: 0.8425 (p0) cc_final: 0.7986 (p0)
REVERT: G  101 TRP cc_start: 0.8518 (p-90) cc_final: 0.7495 (p-90)
REVERT: I  101 TRP cc_start: 0.8367 (p-90) cc_final: 0.8084 (p-90)
REVERT: K   13 ASP cc_start: 0.8655 (p0) cc_final: 0.8290 (p0)
REVERT: K  101 TRP cc_start: 0.8393 (p-90) cc_final: 0.7624 (p-90)
REVERT: M   43 TYR cc_start: 0.9228 (p90) cc_final: 0.9018 (p90)
REVERT: N    5 GLU cc_start: 0.9269 (tp30) cc_final: 0.8975 (tp30)
REVERT: N    6 LEU cc_start: 0.9582 (mm) cc_final: 0.9296 (mm)
REVERT: P    5 GLU cc_start: 0.9309 (tp30) cc_final: 0.9047 (tp30)
REVERT: Q   13 ASP cc_start: 0.8614 (p0) cc_final: 0.8197 (p0)
REVERT: Q   48 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8558 (ttmm)
REVERT: Q  101 TRP cc_start: 0.8398 (p-90) cc_final: 0.7980 (p-90)
REVERT: R    6 LEU cc_start: 0.9655 (mm) cc_final: 0.9439 (mm)
REVERT: S  101 TRP cc_start: 0.8438 (p-90) cc_final: 0.7514 (p-90)
REVERT: T    3 LEU cc_start: 0.8833 (tt) cc_final: 0.8590 (tt)
REVERT: U   13 ASP cc_start: 0.8540 (p0) cc_final: 0.8191 (p0)
REVERT: V   30 LYS cc_start: 0.9247 (mmtt) cc_final: 0.8660 (tmtt)
REVERT: V   48 GLU cc_start: 0.9546 (tp30) cc_final: 0.9319 (mm-30)
REVERT: W   48 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8632 (ttmm)
REVERT: W  101 TRP cc_start: 0.8428 (p-90) cc_final: 0.7633 (p-90)
REVERT: X    3 LEU cc_start: 0.8614 (tt) cc_final: 0.8408 (tt)
REVERT: X    6 LEU cc_start: 0.9642 (mm) cc_final: 0.9439 (mm)
REVERT: X   30 LYS cc_start: 0.9240 (mmtt) cc_final: 0.8436 (tmtt)
REVERT: Y  101 TRP cc_start: 0.8501 (p-90) cc_final: 0.8126 (p-90)
REVERT: Z    5 GLU cc_start: 0.9143 (tp30) cc_final: 0.8861 (tp30)
REVERT: Z   30 LYS cc_start: 0.9258 (mmtt) cc_final: 0.8669 (tmtt)
REVERT: 0   40 ASN cc_start: 0.7197 (m-40) cc_final: 0.6430 (m-40)
REVERT: 0  101 TRP cc_start: 0.8463 (p-90) cc_final: 0.7990 (p-90)
REVERT: 1    5 GLU cc_start: 0.8805 (tt0) cc_final: 0.8308 (tp30)
REVERT: 1   30 LYS cc_start: 0.9307 (mmtt) cc_final: 0.8500 (tmtt)
REVERT: 2   43 TYR cc_start: 0.9235 (p90) cc_final: 0.8676 (p90)
REVERT: 2  101 TRP cc_start: 0.8513 (p-90) cc_final: 0.7622 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 296
  average time/residue: 0.1381
  time to fit residues: 62.4921
Evaluate side-chains
  197 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 212 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9990
   chunk 220 optimal weight:    0.4980
   chunk 163 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   chunk 170 optimal weight:    6.9990
   chunk 200 optimal weight:    9.9990
   chunk 192 optimal weight:    0.0010
   chunk 105 optimal weight:   10.0000
   chunk 213 optimal weight:    0.9990
   overall best weight:    1.0992

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 ASN
J  42 ASN
L  42 ASN
N  42 ASN
P  42 ASN
R  42 ASN
T  42 ASN
V  42 ASN
** Y  60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
0  64 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.046382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.039356 restraints weight = 100015.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.040982 restraints weight = 52998.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.042099 restraints weight = 33046.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.042917 restraints weight = 22657.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.043514 restraints weight = 16371.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  18585  Z= 0.117
  Angle     :  0.536   6.961  25335  Z= 0.290
  Chirality :  0.042   0.180   3015
  Planarity :  0.003   0.035   3225
  Dihedral  :  6.036  55.408   2565
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.18), residues: 2385
  helix:  1.39 (0.22), residues: 675
  sheet: -0.35 (0.26), residues: 375
  loop : -1.40 (0.18), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O  54 
 TYR   0.018   0.001   TYR Q  43 
 PHE   0.009   0.001   PHE A  51 
 TRP   0.017   0.001   TRP S  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (18585)
  covalent geometry    : angle       0.53614 (25335)
  hydrogen bonds       : bond        0.04164 (  660)
  hydrogen bonds       : angle       4.40873 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.9224 (tp30) cc_final: 0.8951 (tp30)
REVERT: a   13 ASP cc_start: 0.8526 (p0) cc_final: 0.8212 (p0)
REVERT: C  101 TRP cc_start: 0.8335 (p-90) cc_final: 0.7385 (p-90)
REVERT: D    6 LEU cc_start: 0.9574 (mm) cc_final: 0.9366 (mm)
REVERT: E   13 ASP cc_start: 0.8588 (p0) cc_final: 0.8274 (p0)
REVERT: E  101 TRP cc_start: 0.8266 (p-90) cc_final: 0.7399 (p-90)
REVERT: G   13 ASP cc_start: 0.8563 (p0) cc_final: 0.8122 (p0)
REVERT: G  101 TRP cc_start: 0.8476 (p-90) cc_final: 0.7474 (p-90)
REVERT: I  101 TRP cc_start: 0.8334 (p-90) cc_final: 0.8070 (p-90)
REVERT: K   13 ASP cc_start: 0.8790 (p0) cc_final: 0.8469 (p0)
REVERT: K   43 TYR cc_start: 0.9316 (p90) cc_final: 0.8584 (p90)
REVERT: K  101 TRP cc_start: 0.8297 (p-90) cc_final: 0.7523 (p-90)
REVERT: L    5 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9078 (tp30)
REVERT: N    6 LEU cc_start: 0.9601 (mm) cc_final: 0.9280 (mm)
REVERT: P    5 GLU cc_start: 0.9333 (tp30) cc_final: 0.8973 (tp30)
REVERT: Q   13 ASP cc_start: 0.8769 (p0) cc_final: 0.8318 (p0)
REVERT: Q   43 TYR cc_start: 0.9370 (p90) cc_final: 0.9135 (p90)
REVERT: Q   48 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8612 (ttmm)
REVERT: Q  101 TRP cc_start: 0.8414 (p-90) cc_final: 0.7982 (p-90)
REVERT: S  101 TRP cc_start: 0.8413 (p-90) cc_final: 0.7399 (p-90)
REVERT: T    3 LEU cc_start: 0.8866 (tt) cc_final: 0.8466 (tt)
REVERT: U   13 ASP cc_start: 0.8722 (p0) cc_final: 0.8358 (p0)
REVERT: V    5 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8945 (tp30)
REVERT: V   30 LYS cc_start: 0.9220 (mmtt) cc_final: 0.8674 (tmtt)
REVERT: W   48 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8638 (ttmm)
REVERT: W  101 TRP cc_start: 0.8373 (p-90) cc_final: 0.7586 (p-90)
REVERT: X    6 LEU cc_start: 0.9644 (mm) cc_final: 0.9421 (mm)
REVERT: X   30 LYS cc_start: 0.9244 (mmtt) cc_final: 0.8472 (tmtt)
REVERT: Y  101 TRP cc_start: 0.8464 (p-90) cc_final: 0.8103 (p-90)
REVERT: Z    5 GLU cc_start: 0.9203 (tp30) cc_final: 0.8963 (tp30)
REVERT: Z   30 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8663 (tmtt)
REVERT: 0  101 TRP cc_start: 0.8487 (p-90) cc_final: 0.7972 (p-90)
REVERT: 1    5 GLU cc_start: 0.8788 (tt0) cc_final: 0.8282 (tp30)
REVERT: 1    6 LEU cc_start: 0.9677 (mm) cc_final: 0.9470 (mm)
REVERT: 1   30 LYS cc_start: 0.9300 (mmtt) cc_final: 0.8582 (tmtt)
REVERT: 2   43 TYR cc_start: 0.9241 (p90) cc_final: 0.8685 (p90)
REVERT: 2  101 TRP cc_start: 0.8489 (p-90) cc_final: 0.7619 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.1161
  time to fit residues: 50.3338
Evaluate side-chains
  195 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 190 optimal weight:    0.0670
   chunk 66 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 145 optimal weight:    7.9990
   chunk 188 optimal weight:    6.9990
   chunk 238 optimal weight:    5.9990
   overall best weight:    1.5522

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 ASN
J  42 ASN
L  42 ASN
N  42 ASN
P  42 ASN
R  42 ASN
T  42 ASN
V  42 ASN
Y  64 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.045416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.038617 restraints weight = 100199.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.040199 restraints weight = 53654.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.041296 restraints weight = 33426.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.042075 restraints weight = 22946.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.042658 restraints weight = 16716.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18585  Z= 0.123
  Angle     :  0.531   6.653  25335  Z= 0.286
  Chirality :  0.042   0.181   3015
  Planarity :  0.003   0.036   3225
  Dihedral  :  5.710  50.889   2565
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.18), residues: 2385
  helix:  1.89 (0.22), residues: 675
  sheet: -0.35 (0.26), residues: 375
  loop : -1.49 (0.18), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG P  41 
 TYR   0.016   0.001   TYR S  43 
 PHE   0.010   0.001   PHE H  51 
 TRP   0.016   0.001   TRP Y  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (18585)
  covalent geometry    : angle       0.53131 (25335)
  hydrogen bonds       : bond        0.04031 (  660)
  hydrogen bonds       : angle       4.39761 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.9263 (tp30) cc_final: 0.8962 (tp30)
REVERT: A    6 LEU cc_start: 0.9572 (mm) cc_final: 0.9371 (mm)
REVERT: a   13 ASP cc_start: 0.8635 (p0) cc_final: 0.8340 (p0)
REVERT: C  101 TRP cc_start: 0.8355 (p-90) cc_final: 0.7420 (p-90)
REVERT: D    6 LEU cc_start: 0.9597 (mm) cc_final: 0.9374 (mm)
REVERT: E   13 ASP cc_start: 0.8663 (p0) cc_final: 0.8346 (p0)
REVERT: E  101 TRP cc_start: 0.8340 (p-90) cc_final: 0.7463 (p-90)
REVERT: G   13 ASP cc_start: 0.8632 (p0) cc_final: 0.8205 (p0)
REVERT: G  101 TRP cc_start: 0.8399 (p-90) cc_final: 0.7373 (p-90)
REVERT: I  101 TRP cc_start: 0.8370 (p-90) cc_final: 0.8078 (p-90)
REVERT: J    6 LEU cc_start: 0.9621 (mm) cc_final: 0.9418 (mm)
REVERT: K   13 ASP cc_start: 0.8827 (p0) cc_final: 0.8478 (p0)
REVERT: K   43 TYR cc_start: 0.9362 (p90) cc_final: 0.8745 (p90)
REVERT: K  101 TRP cc_start: 0.8311 (p-90) cc_final: 0.7496 (p-90)
REVERT: L    5 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8974 (tp30)
REVERT: N    5 GLU cc_start: 0.9286 (tp30) cc_final: 0.9067 (tp30)
REVERT: N    6 LEU cc_start: 0.9598 (mm) cc_final: 0.9272 (mm)
REVERT: P    5 GLU cc_start: 0.9359 (tp30) cc_final: 0.9113 (tp30)
REVERT: Q   13 ASP cc_start: 0.8846 (p0) cc_final: 0.8422 (p0)
REVERT: Q   43 TYR cc_start: 0.9407 (p90) cc_final: 0.9041 (p90)
REVERT: Q   48 LYS cc_start: 0.8884 (ttpp) cc_final: 0.8655 (ttmm)
REVERT: Q  101 TRP cc_start: 0.8390 (p-90) cc_final: 0.7912 (p-90)
REVERT: R    6 LEU cc_start: 0.9741 (mm) cc_final: 0.9466 (mm)
REVERT: S  101 TRP cc_start: 0.8415 (p-90) cc_final: 0.7365 (p-90)
REVERT: U   13 ASP cc_start: 0.8802 (p0) cc_final: 0.8443 (p0)
REVERT: V   30 LYS cc_start: 0.9245 (mmtt) cc_final: 0.8707 (tmtt)
REVERT: W   48 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8658 (ttmm)
REVERT: W  101 TRP cc_start: 0.8328 (p-90) cc_final: 0.7533 (p-90)
REVERT: X   30 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8521 (tmtt)
REVERT: Y  101 TRP cc_start: 0.8475 (p-90) cc_final: 0.8123 (p-90)
REVERT: Z    5 GLU cc_start: 0.9236 (tp30) cc_final: 0.9008 (tp30)
REVERT: Z   30 LYS cc_start: 0.9299 (mmtt) cc_final: 0.8743 (tmtt)
REVERT: 0   43 TYR cc_start: 0.9186 (p90) cc_final: 0.8977 (p90)
REVERT: 0  101 TRP cc_start: 0.8452 (p-90) cc_final: 0.7921 (p-90)
REVERT: 1    5 GLU cc_start: 0.8739 (tt0) cc_final: 0.8278 (tp30)
REVERT: 1    6 LEU cc_start: 0.9637 (mm) cc_final: 0.9428 (mm)
REVERT: 1   30 LYS cc_start: 0.9314 (mmtt) cc_final: 0.8588 (tmtt)
REVERT: 2   43 TYR cc_start: 0.9218 (p90) cc_final: 0.8635 (p90)
REVERT: 2  101 TRP cc_start: 0.8499 (p-90) cc_final: 0.7576 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1125
  time to fit residues: 43.6678
Evaluate side-chains
  183 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 222 optimal weight:    0.0970
   chunk 66 optimal weight:    6.9990
   chunk 154 optimal weight:    8.9990
   chunk 158 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 132 optimal weight:    0.8980
   chunk 238 optimal weight:    2.9990
   chunk 155 optimal weight:    4.9990
   chunk 192 optimal weight:    2.9990
   chunk 202 optimal weight:    3.9990
   chunk 218 optimal weight:    5.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 ASN
J  42 ASN
L  42 ASN
N  42 ASN
P  42 ASN
R  42 ASN
T  42 ASN
V  42 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.045279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.038242 restraints weight = 101434.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.039806 restraints weight = 54066.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.040911 restraints weight = 33953.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.041703 restraints weight = 23279.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.042285 restraints weight = 16931.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  18585  Z= 0.114
  Angle     :  0.532   8.308  25335  Z= 0.286
  Chirality :  0.042   0.177   3015
  Planarity :  0.003   0.025   3225
  Dihedral  :  5.378  45.691   2565
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.19), residues: 2385
  helix:  2.11 (0.22), residues: 675
  sheet: -0.31 (0.27), residues: 375
  loop : -1.58 (0.18), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P  41 
 TYR   0.014   0.001   TYR K  43 
 PHE   0.009   0.001   PHE F  51 
 TRP   0.016   0.001   TRP Q  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (18585)
  covalent geometry    : angle       0.53164 (25335)
  hydrogen bonds       : bond        0.03823 (  660)
  hydrogen bonds       : angle       4.32077 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8842 (tt) cc_final: 0.8528 (tt)
REVERT: A    5 GLU cc_start: 0.9251 (tp30) cc_final: 0.8931 (tp30)
REVERT: A    6 LEU cc_start: 0.9568 (mm) cc_final: 0.9342 (mm)
REVERT: a   13 ASP cc_start: 0.8692 (p0) cc_final: 0.8396 (p0)
REVERT: a  101 TRP cc_start: 0.8497 (p-90) cc_final: 0.7494 (p-90)
REVERT: C  101 TRP cc_start: 0.8428 (p-90) cc_final: 0.7463 (p-90)
REVERT: D    6 LEU cc_start: 0.9597 (mm) cc_final: 0.9369 (mm)
REVERT: E   13 ASP cc_start: 0.8704 (p0) cc_final: 0.8398 (p0)
REVERT: E  101 TRP cc_start: 0.8317 (p-90) cc_final: 0.7492 (p-90)
REVERT: G   13 ASP cc_start: 0.8686 (p0) cc_final: 0.8255 (p0)
REVERT: G  101 TRP cc_start: 0.8378 (p-90) cc_final: 0.7303 (p-90)
REVERT: H    6 LEU cc_start: 0.9584 (mm) cc_final: 0.9375 (mm)
REVERT: I  101 TRP cc_start: 0.8440 (p-90) cc_final: 0.8134 (p-90)
REVERT: K   13 ASP cc_start: 0.8821 (p0) cc_final: 0.8467 (p0)
REVERT: K   43 TYR cc_start: 0.9242 (p90) cc_final: 0.8711 (p90)
REVERT: K  101 TRP cc_start: 0.8317 (p-90) cc_final: 0.7446 (p-90)
REVERT: L    5 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8943 (tp30)
REVERT: N    5 GLU cc_start: 0.9273 (tp30) cc_final: 0.9012 (tp30)
REVERT: N    6 LEU cc_start: 0.9555 (mm) cc_final: 0.9174 (mm)
REVERT: P    5 GLU cc_start: 0.9345 (tp30) cc_final: 0.9068 (tp30)
REVERT: Q   13 ASP cc_start: 0.8840 (p0) cc_final: 0.8450 (p0)
REVERT: Q   43 TYR cc_start: 0.9397 (p90) cc_final: 0.8890 (p90)
REVERT: Q  101 TRP cc_start: 0.8388 (p-90) cc_final: 0.7884 (p-90)
REVERT: R    6 LEU cc_start: 0.9742 (mm) cc_final: 0.9487 (mm)
REVERT: S  101 TRP cc_start: 0.8380 (p-90) cc_final: 0.7307 (p-90)
REVERT: U   13 ASP cc_start: 0.8826 (p0) cc_final: 0.8467 (p0)
REVERT: V    5 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8999 (tp30)
REVERT: V   30 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8725 (tmtt)
REVERT: W  101 TRP cc_start: 0.8321 (p-90) cc_final: 0.7551 (p-90)
REVERT: X    5 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8853 (pt0)
REVERT: X   30 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8550 (tmtt)
REVERT: Y  101 TRP cc_start: 0.8457 (p-90) cc_final: 0.8086 (p-90)
REVERT: Z   30 LYS cc_start: 0.9293 (mmtt) cc_final: 0.8753 (tmtt)
REVERT: 0   43 TYR cc_start: 0.9204 (p90) cc_final: 0.8927 (p90)
REVERT: 0  101 TRP cc_start: 0.8426 (p-90) cc_final: 0.7898 (p-90)
REVERT: 1    5 GLU cc_start: 0.8701 (tt0) cc_final: 0.8193 (tp30)
REVERT: 1    6 LEU cc_start: 0.9634 (mm) cc_final: 0.9432 (mm)
REVERT: 1   30 LYS cc_start: 0.9289 (mmtt) cc_final: 0.8679 (tmtt)
REVERT: 2   43 TYR cc_start: 0.9229 (p90) cc_final: 0.8786 (p90)
REVERT: 2  101 TRP cc_start: 0.8462 (p-90) cc_final: 0.7549 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1082
  time to fit residues: 41.1285
Evaluate side-chains
  179 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 168 optimal weight:    9.9990
   chunk 213 optimal weight:    0.0020
   chunk 66 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 214 optimal weight:    7.9990
   chunk 174 optimal weight:    4.9990
   chunk 205 optimal weight:    0.3980
   chunk 93 optimal weight:    0.0670
   chunk 234 optimal weight:    3.9990
   chunk 151 optimal weight:    5.9990
   overall best weight:    1.0928

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 ASN
J  42 ASN
L  42 ASN
N  42 ASN
P  42 ASN
R  42 ASN
T  42 ASN
V  42 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.044732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 20)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.038018 restraints weight = 100227.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.039566 restraints weight = 52968.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.040654 restraints weight = 33175.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.041456 restraints weight = 22763.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.042042 restraints weight = 16476.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  18585  Z= 0.118
  Angle     :  0.537   6.199  25335  Z= 0.289
  Chirality :  0.043   0.189   3015
  Planarity :  0.003   0.027   3225
  Dihedral  :  5.210  42.827   2565
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.19), residues: 2385
  helix:  2.18 (0.22), residues: 675
  sheet: -0.32 (0.27), residues: 375
  loop : -1.65 (0.18), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P  41 
 TYR   0.013   0.001   TYR 2  26 
 PHE   0.009   0.001   PHE F  24 
 TRP   0.012   0.001   TRP W  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (18585)
  covalent geometry    : angle       0.53673 (25335)
  hydrogen bonds       : bond        0.03716 (  660)
  hydrogen bonds       : angle       4.30280 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8867 (tt) cc_final: 0.8635 (tt)
REVERT: A    5 GLU cc_start: 0.9270 (tp30) cc_final: 0.8953 (tp30)
REVERT: A    6 LEU cc_start: 0.9559 (mm) cc_final: 0.9316 (mm)
REVERT: a   13 ASP cc_start: 0.8709 (p0) cc_final: 0.8422 (p0)
REVERT: a  101 TRP cc_start: 0.8460 (p-90) cc_final: 0.7454 (p-90)
REVERT: C   13 ASP cc_start: 0.8388 (p0) cc_final: 0.8077 (p0)
REVERT: C  101 TRP cc_start: 0.8407 (p-90) cc_final: 0.7408 (p-90)
REVERT: D    6 LEU cc_start: 0.9590 (mm) cc_final: 0.9342 (mm)
REVERT: E   13 ASP cc_start: 0.8709 (p0) cc_final: 0.8399 (p0)
REVERT: G   13 ASP cc_start: 0.8599 (p0) cc_final: 0.8183 (p0)
REVERT: G  101 TRP cc_start: 0.8289 (p-90) cc_final: 0.7237 (p-90)
REVERT: H    6 LEU cc_start: 0.9579 (mm) cc_final: 0.9374 (mm)
REVERT: I  101 TRP cc_start: 0.8276 (p-90) cc_final: 0.8001 (p-90)
REVERT: J    6 LEU cc_start: 0.9625 (mm) cc_final: 0.9423 (mm)
REVERT: K   13 ASP cc_start: 0.8779 (p0) cc_final: 0.8448 (p0)
REVERT: K   43 TYR cc_start: 0.9243 (p90) cc_final: 0.8710 (p90)
REVERT: K  101 TRP cc_start: 0.8251 (p-90) cc_final: 0.7352 (p-90)
REVERT: L    5 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9108 (tp30)
REVERT: M   13 ASP cc_start: 0.8491 (p0) cc_final: 0.8218 (p0)
REVERT: N    5 GLU cc_start: 0.9294 (tp30) cc_final: 0.9016 (tp30)
REVERT: N    6 LEU cc_start: 0.9567 (mm) cc_final: 0.9256 (mm)
REVERT: P    5 GLU cc_start: 0.9348 (tp30) cc_final: 0.9069 (tp30)
REVERT: Q   13 ASP cc_start: 0.8851 (p0) cc_final: 0.8457 (p0)
REVERT: Q   43 TYR cc_start: 0.9407 (p90) cc_final: 0.8890 (p90)
REVERT: Q  101 TRP cc_start: 0.8315 (p-90) cc_final: 0.7836 (p-90)
REVERT: R    6 LEU cc_start: 0.9692 (mm) cc_final: 0.9416 (mm)
REVERT: S   43 TYR cc_start: 0.9225 (p90) cc_final: 0.8817 (p90)
REVERT: S  101 TRP cc_start: 0.8367 (p-90) cc_final: 0.7346 (p-90)
REVERT: U   13 ASP cc_start: 0.8766 (p0) cc_final: 0.8411 (p0)
REVERT: V    5 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8954 (tp30)
REVERT: V   30 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8752 (tmtt)
REVERT: W  101 TRP cc_start: 0.8346 (p-90) cc_final: 0.7604 (p-90)
REVERT: X    5 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8844 (pt0)
REVERT: X   30 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8554 (tmtt)
REVERT: Y  101 TRP cc_start: 0.8375 (p-90) cc_final: 0.8073 (p-90)
REVERT: Z    5 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8747 (tp30)
REVERT: Z   30 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8735 (tmtt)
REVERT: 0   43 TYR cc_start: 0.9256 (p90) cc_final: 0.8969 (p90)
REVERT: 0  101 TRP cc_start: 0.8371 (p-90) cc_final: 0.7840 (p-90)
REVERT: 1    5 GLU cc_start: 0.8704 (tt0) cc_final: 0.8223 (tp30)
REVERT: 1    6 LEU cc_start: 0.9625 (mm) cc_final: 0.9423 (mm)
REVERT: 1   30 LYS cc_start: 0.9312 (mmtt) cc_final: 0.8709 (tmtt)
REVERT: 2   43 TYR cc_start: 0.9100 (p90) cc_final: 0.8798 (p90)
REVERT: 2  101 TRP cc_start: 0.8321 (p-90) cc_final: 0.7457 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1138
  time to fit residues: 41.5931
Evaluate side-chains
  178 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 135 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 185 optimal weight:    9.9990
   chunk 237 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 175 optimal weight:    7.9990
   chunk 199 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 144 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 129 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
a  64 ASN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 ASN
J  42 ASN
L  42 ASN
** N  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  42 ASN
R  42 ASN
S  64 ASN
T  42 ASN
V  42 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.045420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.038363 restraints weight = 100982.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.039952 restraints weight = 53794.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.041066 restraints weight = 33770.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.041832 restraints weight = 23203.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.042446 restraints weight = 17115.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8527
moved from start:          0.4123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  18585  Z= 0.113
  Angle     :  0.558   6.760  25335  Z= 0.293
  Chirality :  0.044   0.199   3015
  Planarity :  0.003   0.028   3225
  Dihedral  :  5.038  40.644   2565
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.19), residues: 2385
  helix:  2.18 (0.22), residues: 675
  sheet: -0.32 (0.27), residues: 375
  loop : -1.68 (0.18), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P  41 
 TYR   0.014   0.001   TYR 2  26 
 PHE   0.007   0.001   PHE F  24 
 TRP   0.011   0.001   TRP W  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (18585)
  covalent geometry    : angle       0.55788 (25335)
  hydrogen bonds       : bond        0.03592 (  660)
  hydrogen bonds       : angle       4.27728 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8887 (tt) cc_final: 0.8480 (tt)
REVERT: A    5 GLU cc_start: 0.9277 (tp30) cc_final: 0.8886 (tp30)
REVERT: A    6 LEU cc_start: 0.9550 (mm) cc_final: 0.9334 (mm)
REVERT: a   13 ASP cc_start: 0.8722 (p0) cc_final: 0.8438 (p0)
REVERT: a  101 TRP cc_start: 0.8359 (p-90) cc_final: 0.7382 (p-90)
REVERT: C   13 ASP cc_start: 0.8589 (p0) cc_final: 0.8315 (p0)
REVERT: C  101 TRP cc_start: 0.8266 (p-90) cc_final: 0.7270 (p-90)
REVERT: D    6 LEU cc_start: 0.9572 (mm) cc_final: 0.9324 (mm)
REVERT: E   13 ASP cc_start: 0.8699 (p0) cc_final: 0.8389 (p0)
REVERT: G   13 ASP cc_start: 0.8601 (p0) cc_final: 0.8196 (p0)
REVERT: G  101 TRP cc_start: 0.8288 (p-90) cc_final: 0.7265 (p-90)
REVERT: I  101 TRP cc_start: 0.8272 (p-90) cc_final: 0.7976 (p-90)
REVERT: K   13 ASP cc_start: 0.8780 (p0) cc_final: 0.8454 (p0)
REVERT: K  101 TRP cc_start: 0.8210 (p-90) cc_final: 0.7324 (p-90)
REVERT: L    5 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8874 (tp30)
REVERT: M   13 ASP cc_start: 0.8600 (p0) cc_final: 0.8301 (p0)
REVERT: M  101 TRP cc_start: 0.8203 (p-90) cc_final: 0.7159 (p-90)
REVERT: N    5 GLU cc_start: 0.9289 (tp30) cc_final: 0.8998 (tp30)
REVERT: N    6 LEU cc_start: 0.9543 (mm) cc_final: 0.9172 (mm)
REVERT: P    5 GLU cc_start: 0.9332 (tp30) cc_final: 0.9044 (tp30)
REVERT: Q   13 ASP cc_start: 0.8828 (p0) cc_final: 0.8449 (p0)
REVERT: Q  101 TRP cc_start: 0.8282 (p-90) cc_final: 0.7807 (p-90)
REVERT: R    6 LEU cc_start: 0.9698 (mm) cc_final: 0.9442 (mm)
REVERT: S   43 TYR cc_start: 0.9186 (p90) cc_final: 0.8869 (p90)
REVERT: S  101 TRP cc_start: 0.8333 (p-90) cc_final: 0.7238 (p-90)
REVERT: U   13 ASP cc_start: 0.8791 (p0) cc_final: 0.8452 (p0)
REVERT: V    5 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8969 (tp30)
REVERT: V   30 LYS cc_start: 0.9270 (mmtt) cc_final: 0.8773 (tmtt)
REVERT: W   13 ASP cc_start: 0.8575 (p0) cc_final: 0.8342 (p0)
REVERT: W  101 TRP cc_start: 0.8215 (p-90) cc_final: 0.7494 (p-90)
REVERT: X    5 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8794 (pt0)
REVERT: X   30 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8592 (tmtt)
REVERT: Y  101 TRP cc_start: 0.8263 (p-90) cc_final: 0.7972 (p-90)
REVERT: Z    5 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8829 (tp30)
REVERT: Z   30 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8721 (tmtt)
REVERT: 0  101 TRP cc_start: 0.8374 (p-90) cc_final: 0.7842 (p-90)
REVERT: 1    5 GLU cc_start: 0.8727 (tt0) cc_final: 0.8208 (tp30)
REVERT: 1    6 LEU cc_start: 0.9590 (mm) cc_final: 0.9352 (mm)
REVERT: 1   30 LYS cc_start: 0.9319 (mmtt) cc_final: 0.8727 (tmtt)
REVERT: 2   26 TYR cc_start: 0.9332 (t80) cc_final: 0.9121 (t80)
REVERT: 2   43 TYR cc_start: 0.9121 (p90) cc_final: 0.8756 (p90)
REVERT: 2  101 TRP cc_start: 0.8282 (p-90) cc_final: 0.7395 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1194
  time to fit residues: 42.0123
Evaluate side-chains
  177 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 72 optimal weight:    9.9990
   chunk 103 optimal weight:    0.3980
   chunk 178 optimal weight:    9.9990
   chunk 82 optimal weight:    3.9990
   chunk 217 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 234 optimal weight:    9.9990
   chunk 197 optimal weight:    5.9990
   chunk 239 optimal weight:    0.5980
   overall best weight:    2.1784

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
** B  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  42 ASN
J  42 ASN
L  42 ASN
** N  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  42 ASN
R  42 ASN
T  42 ASN
V  42 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.043730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.037014 restraints weight = 101290.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.038529 restraints weight = 54981.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.039601 restraints weight = 34898.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.040392 restraints weight = 24177.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.040976 restraints weight = 17641.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  18585  Z= 0.142
  Angle     :  0.573   8.038  25335  Z= 0.305
  Chirality :  0.044   0.195   3015
  Planarity :  0.003   0.031   3225
  Dihedral  :  5.156  43.397   2565
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.35 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.19), residues: 2385
  helix:  2.29 (0.22), residues: 675
  sheet: -0.44 (0.26), residues: 375
  loop : -1.77 (0.18), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG W  54 
 TYR   0.013   0.001   TYR 2  26 
 PHE   0.012   0.001   PHE K  14 
 TRP   0.013   0.001   TRP W  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (18585)
  covalent geometry    : angle       0.57273 (25335)
  hydrogen bonds       : bond        0.03753 (  660)
  hydrogen bonds       : angle       4.33766 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.9292 (tp30) cc_final: 0.9003 (tp30)
REVERT: a   13 ASP cc_start: 0.8748 (p0) cc_final: 0.8463 (p0)
REVERT: a  101 TRP cc_start: 0.8464 (p-90) cc_final: 0.7527 (p-90)
REVERT: C   13 ASP cc_start: 0.8620 (p0) cc_final: 0.8344 (p0)
REVERT: C  101 TRP cc_start: 0.8368 (p-90) cc_final: 0.7406 (p-90)
REVERT: D    6 LEU cc_start: 0.9607 (mm) cc_final: 0.9394 (mm)
REVERT: E   13 ASP cc_start: 0.8735 (p0) cc_final: 0.8419 (p0)
REVERT: G   13 ASP cc_start: 0.8620 (p0) cc_final: 0.8230 (p0)
REVERT: G  101 TRP cc_start: 0.8260 (p-90) cc_final: 0.7213 (p-90)
REVERT: I  101 TRP cc_start: 0.8304 (p-90) cc_final: 0.7944 (p-90)
REVERT: J    6 LEU cc_start: 0.9644 (mm) cc_final: 0.9421 (mm)
REVERT: K   13 ASP cc_start: 0.8829 (p0) cc_final: 0.8540 (p0)
REVERT: K   43 TYR cc_start: 0.9253 (p90) cc_final: 0.8969 (p90)
REVERT: K  101 TRP cc_start: 0.8053 (p-90) cc_final: 0.7226 (p-90)
REVERT: M   13 ASP cc_start: 0.8701 (p0) cc_final: 0.8404 (p0)
REVERT: M  101 TRP cc_start: 0.8328 (p-90) cc_final: 0.7329 (p-90)
REVERT: N    5 GLU cc_start: 0.9356 (tp30) cc_final: 0.9067 (tp30)
REVERT: N    6 LEU cc_start: 0.9545 (mm) cc_final: 0.8972 (tp)
REVERT: P    5 GLU cc_start: 0.9356 (tp30) cc_final: 0.9092 (tp30)
REVERT: Q   13 ASP cc_start: 0.8816 (p0) cc_final: 0.8446 (p0)
REVERT: Q  101 TRP cc_start: 0.8309 (p-90) cc_final: 0.7755 (p-90)
REVERT: R    6 LEU cc_start: 0.9715 (mm) cc_final: 0.9459 (mm)
REVERT: S  101 TRP cc_start: 0.8292 (p-90) cc_final: 0.7248 (p-90)
REVERT: U   13 ASP cc_start: 0.8809 (p0) cc_final: 0.8474 (p0)
REVERT: U  101 TRP cc_start: 0.8401 (p-90) cc_final: 0.8141 (p-90)
REVERT: V   30 LYS cc_start: 0.9325 (mmtt) cc_final: 0.8889 (tmtt)
REVERT: W   13 ASP cc_start: 0.8679 (p0) cc_final: 0.8428 (p0)
REVERT: W  101 TRP cc_start: 0.8253 (p-90) cc_final: 0.7560 (p-90)
REVERT: X    6 LEU cc_start: 0.9645 (mm) cc_final: 0.9381 (mm)
REVERT: X   30 LYS cc_start: 0.9252 (mmtt) cc_final: 0.8627 (tmtt)
REVERT: Y  101 TRP cc_start: 0.8359 (p-90) cc_final: 0.8076 (p-90)
REVERT: Z   30 LYS cc_start: 0.9308 (mmtt) cc_final: 0.8842 (tmtt)
REVERT: 0  101 TRP cc_start: 0.8343 (p-90) cc_final: 0.7858 (p-90)
REVERT: 1    5 GLU cc_start: 0.8683 (tt0) cc_final: 0.8214 (tp30)
REVERT: 1    6 LEU cc_start: 0.9608 (mm) cc_final: 0.9405 (mm)
REVERT: 1   30 LYS cc_start: 0.9358 (mmtt) cc_final: 0.8740 (tmtt)
REVERT: 2   43 TYR cc_start: 0.9183 (p90) cc_final: 0.8912 (p90)
REVERT: 2  101 TRP cc_start: 0.8412 (p-90) cc_final: 0.7518 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.1162
  time to fit residues: 39.7129
Evaluate side-chains
  165 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 58 optimal weight:    8.9990
   chunk 235 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0770
   chunk 99 optimal weight:    5.9990
   chunk 204 optimal weight:    3.9990
   chunk 185 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 232 optimal weight:    6.9990
   chunk 218 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   overall best weight:    4.2146

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
a  64 ASN
H  42 ASN
** J  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  42 ASN
R  42 ASN
S  64 ASN
T  42 ASN
V  42 ASN
W  64 ASN
Y  64 ASN
0  64 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.040804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.033954 restraints weight = 106561.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035397 restraints weight = 58646.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.036438 restraints weight = 37743.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.037239 restraints weight = 26363.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.037801 restraints weight = 19401.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.5007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  18585  Z= 0.223
  Angle     :  0.655   7.927  25335  Z= 0.351
  Chirality :  0.046   0.204   3015
  Planarity :  0.004   0.031   3225
  Dihedral  :  5.696  45.607   2565
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  9.81 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.18), residues: 2385
  helix:  2.24 (0.22), residues: 675
  sheet: -0.81 (0.26), residues: 375
  loop : -1.97 (0.17), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG W  54 
 TYR   0.016   0.002   TYR 0  43 
 PHE   0.012   0.002   PHE Y  27 
 TRP   0.016   0.002   TRP W  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (18585)
  covalent geometry    : angle       0.65459 (25335)
  hydrogen bonds       : bond        0.04441 (  660)
  hydrogen bonds       : angle       4.57947 ( 1935)

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

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

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4770 Ramachandran restraints generated.
    2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 GLU cc_start: 0.9298 (tp30) cc_final: 0.9050 (tp30)
REVERT: a   13 ASP cc_start: 0.8780 (p0) cc_final: 0.8534 (p0)
REVERT: a  101 TRP cc_start: 0.8526 (p-90) cc_final: 0.7657 (p-90)
REVERT: B    5 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8976 (mm-30)
REVERT: C   13 ASP cc_start: 0.8721 (p0) cc_final: 0.8497 (p0)
REVERT: C  101 TRP cc_start: 0.8597 (p-90) cc_final: 0.7637 (p-90)
REVERT: E   13 ASP cc_start: 0.8772 (p0) cc_final: 0.8450 (p0)
REVERT: E  101 TRP cc_start: 0.8515 (p-90) cc_final: 0.7457 (p-90)
REVERT: G   13 ASP cc_start: 0.8703 (p0) cc_final: 0.8310 (p0)
REVERT: G  101 TRP cc_start: 0.8598 (p-90) cc_final: 0.7604 (p-90)
REVERT: I  101 TRP cc_start: 0.8537 (p-90) cc_final: 0.8060 (p-90)
REVERT: K   13 ASP cc_start: 0.8866 (p0) cc_final: 0.8548 (p0)
REVERT: K  101 TRP cc_start: 0.8469 (p-90) cc_final: 0.7538 (p-90)
REVERT: M   13 ASP cc_start: 0.8762 (p0) cc_final: 0.8474 (p0)
REVERT: M  101 TRP cc_start: 0.8514 (p-90) cc_final: 0.7517 (p-90)
REVERT: N    5 GLU cc_start: 0.9419 (tp30) cc_final: 0.9183 (tp30)
REVERT: N    6 LEU cc_start: 0.9583 (mm) cc_final: 0.9258 (mm)
REVERT: Q   13 ASP cc_start: 0.8876 (p0) cc_final: 0.8505 (p0)
REVERT: Q  101 TRP cc_start: 0.8529 (p-90) cc_final: 0.7879 (p-90)
REVERT: R    6 LEU cc_start: 0.9726 (mm) cc_final: 0.9505 (mm)
REVERT: S  101 TRP cc_start: 0.8486 (p-90) cc_final: 0.7364 (p-90)
REVERT: U   13 ASP cc_start: 0.8845 (p0) cc_final: 0.8509 (p0)
REVERT: U  101 TRP cc_start: 0.8585 (p-90) cc_final: 0.7502 (p-90)
REVERT: V   30 LYS cc_start: 0.9473 (mmtt) cc_final: 0.8933 (tmtt)
REVERT: W   13 ASP cc_start: 0.8797 (p0) cc_final: 0.8521 (p0)
REVERT: W  101 TRP cc_start: 0.8542 (p-90) cc_final: 0.7799 (p-90)
REVERT: X    6 LEU cc_start: 0.9654 (mm) cc_final: 0.9398 (mm)
REVERT: X   30 LYS cc_start: 0.9341 (mmtt) cc_final: 0.8766 (tmtt)
REVERT: Y  101 TRP cc_start: 0.8571 (p-90) cc_final: 0.8133 (p-90)
REVERT: Z   30 LYS cc_start: 0.9432 (mmtt) cc_final: 0.8933 (tmtt)
REVERT: 0  101 TRP cc_start: 0.8636 (p-90) cc_final: 0.7965 (p-90)
REVERT: 1   30 LYS cc_start: 0.9437 (mmtt) cc_final: 0.8822 (tmtt)
REVERT: 2  101 TRP cc_start: 0.8512 (p-90) cc_final: 0.7565 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.1197
  time to fit residues: 40.7554
Evaluate side-chains
  159 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 240
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 170 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 222 optimal weight:    0.0170
   chunk 155 optimal weight:    9.9990
   chunk 238 optimal weight:    5.9990
   chunk 171 optimal weight:    3.9990
   chunk 178 optimal weight:    4.9990
   chunk 145 optimal weight:    9.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.1824

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
H  42 ASN
J  42 ASN
L  42 ASN
** N  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  42 ASN
R  42 ASN
T  42 ASN
V  42 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.041348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.034365 restraints weight = 105590.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.035841 restraints weight = 57456.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.036906 restraints weight = 36695.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.037685 restraints weight = 25511.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.038263 restraints weight = 18826.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.5146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019  18585  Z= 0.137
  Angle     :  0.578   8.494  25335  Z= 0.310
  Chirality :  0.045   0.183   3015
  Planarity :  0.003   0.028   3225
  Dihedral  :  5.266  41.930   2565
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.18), residues: 2385
  helix:  2.40 (0.22), residues: 675
  sheet: -0.81 (0.26), residues: 375
  loop : -1.91 (0.17), residues: 1335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG X  41 
 TYR   0.019   0.001   TYR S  26 
 PHE   0.008   0.001   PHE S  27 
 TRP   0.018   0.002   TRP Q  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (18585)
  covalent geometry    : angle       0.57771 (25335)
  hydrogen bonds       : bond        0.04140 (  660)
  hydrogen bonds       : angle       4.36589 ( 1935)

===============================================================================
Job complete
usr+sys time: 2229.31 seconds
wall clock time: 40 minutes 24.27 seconds (2424.27 seconds total)