Starting phenix.real_space_refine
on Tue Feb  3 20:06:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r4z_53573/02_2026/9r4z_53573_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r4z_53573/02_2026/9r4z_53573.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r4z_53573/02_2026/9r4z_53573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r4z_53573/02_2026/9r4z_53573.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r4z_53573/02_2026/9r4z_53573_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r4z_53573/02_2026/9r4z_53573_neut.cif"
  }
  resolution = 3.5
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    4212      2.51       5
     N    1128      2.21       5
     O    1224      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6588
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 549
          Classifications: {'peptide': 69}
          Link IDs: {'PTRANS': 1, 'TRANS': 67}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, L, M, N
  Time building chain proxies: 0.71, per 1000 atoms: 0.11
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (113.36, 88.4, 50.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1224      8.00
     N    1128      7.00
     C    4212      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 343.3 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 36.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8
      removed outlier: 6.726A  pdb=" N   PHE A   3 " --> pdb=" O   SER C   4 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE C   6 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE A   5 " --> pdb=" O   ILE C   6 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   GLU C   8 " --> pdb=" O   PHE A   5 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY A   7 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE C   3 " --> pdb=" O   SER E   4 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE E   6 " --> pdb=" O   PHE C   3 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE C   5 " --> pdb=" O   ILE E   6 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   GLU E   8 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY C   7 " --> pdb=" O   GLU E   8 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE E   3 " --> pdb=" O   SER G   4 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE G   6 " --> pdb=" O   PHE E   3 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE E   5 " --> pdb=" O   ILE G   6 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   GLU G   8 " --> pdb=" O   PHE E   5 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY E   7 " --> pdb=" O   GLU G   8 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   PHE G   3 " --> pdb=" O   SER I   4 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE I   6 " --> pdb=" O   PHE G   3 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE G   5 " --> pdb=" O   ILE I   6 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   GLU I   8 " --> pdb=" O   PHE G   5 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY G   7 " --> pdb=" O   GLU I   8 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE I   3 " --> pdb=" O   SER M   4 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   ILE M   6 " --> pdb=" O   PHE I   3 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   PHE I   5 " --> pdb=" O   ILE M   6 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   GLU M   8 " --> pdb=" O   PHE I   5 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLY I   7 " --> pdb=" O   GLU M   8 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20
      removed outlier: 6.068A  pdb=" N   ALA A  19 " --> pdb=" O   TYR C  20 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ALA C  19 " --> pdb=" O   TYR E  20 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ALA E  19 " --> pdb=" O   TYR G  20 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ALA G  19 " --> pdb=" O   TYR I  20 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ALA I  19 " --> pdb=" O   TYR M  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 29
      removed outlier: 8.303A  pdb=" N   LYS A  24 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY C  27 " --> pdb=" O   LYS A  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA A  26 " --> pdb=" O   GLY C  27 " (cutoff:3.500A)
      removed outlier: 10.812A  pdb=" N   LYS C  29 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP A  28 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   LYS C  24 " --> pdb=" O   GLU E  25 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY E  27 " --> pdb=" O   LYS C  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA C  26 " --> pdb=" O   GLY E  27 " (cutoff:3.500A)
      removed outlier: 10.811A  pdb=" N   LYS E  29 " --> pdb=" O   ALA C  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP C  28 " --> pdb=" O   LYS E  29 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   LYS E  24 " --> pdb=" O   GLU G  25 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   GLY G  27 " --> pdb=" O   LYS E  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA E  26 " --> pdb=" O   GLY G  27 " (cutoff:3.500A)
      removed outlier: 10.812A  pdb=" N   LYS G  29 " --> pdb=" O   ALA E  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP E  28 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   LYS G  24 " --> pdb=" O   GLU I  25 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY I  27 " --> pdb=" O   LYS G  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA G  26 " --> pdb=" O   GLY I  27 " (cutoff:3.500A)
      removed outlier: 10.811A  pdb=" N   LYS I  29 " --> pdb=" O   ALA G  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP G  28 " --> pdb=" O   LYS I  29 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   LYS I  24 " --> pdb=" O   GLU M  25 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY M  27 " --> pdb=" O   LYS I  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA I  26 " --> pdb=" O   GLY M  27 " (cutoff:3.500A)
      removed outlier: 10.811A  pdb=" N   LYS M  29 " --> pdb=" O   ALA I  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP I  28 " --> pdb=" O   LYS M  29 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 38
    Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 46
      removed outlier: 6.689A  pdb=" N   GLN A  45 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN C  45 " --> pdb=" O   ARG E  46 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN E  45 " --> pdb=" O   ARG G  46 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN G  45 " --> pdb=" O   ARG I  46 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN I  45 " --> pdb=" O   ARG M  46 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 53
      removed outlier: 6.513A  pdb=" N   TRP A  52 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TRP C  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TRP E  52 " --> pdb=" O   ALA G  53 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   TRP G  52 " --> pdb=" O   ALA I  53 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TRP I  52 " --> pdb=" O   ALA M  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 57 through 58
      removed outlier: 6.726A  pdb=" N   ILE A  57 " --> pdb=" O   SER C  58 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE C  57 " --> pdb=" O   SER E  58 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE E  57 " --> pdb=" O   SER G  58 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE G  57 " --> pdb=" O   SER I  58 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE I  57 " --> pdb=" O   SER M  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 65 through 68
      removed outlier: 6.645A  pdb=" N   GLU A  66 " --> pdb=" O   PHE C  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU C  66 " --> pdb=" O   PHE E  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU E  66 " --> pdb=" O   PHE G  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU G  66 " --> pdb=" O   PHE I  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU I  66 " --> pdb=" O   PHE M  67 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 8
      removed outlier: 6.726A  pdb=" N   PHE B   3 " --> pdb=" O   SER D   4 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE D   6 " --> pdb=" O   PHE B   3 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE B   5 " --> pdb=" O   ILE D   6 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   GLU D   8 " --> pdb=" O   PHE B   5 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY B   7 " --> pdb=" O   GLU D   8 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE D   3 " --> pdb=" O   SER F   4 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE F   6 " --> pdb=" O   PHE D   3 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE D   5 " --> pdb=" O   ILE F   6 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   GLU F   8 " --> pdb=" O   PHE D   5 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY D   7 " --> pdb=" O   GLU F   8 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE F   3 " --> pdb=" O   SER H   4 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE H   6 " --> pdb=" O   PHE F   3 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE F   5 " --> pdb=" O   ILE H   6 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   GLU H   8 " --> pdb=" O   PHE F   5 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY F   7 " --> pdb=" O   GLU H   8 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   PHE H   3 " --> pdb=" O   SER L   4 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   ILE L   6 " --> pdb=" O   PHE H   3 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   PHE H   5 " --> pdb=" O   ILE L   6 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   GLU L   8 " --> pdb=" O   PHE H   5 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLY H   7 " --> pdb=" O   GLU L   8 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   PHE L   3 " --> pdb=" O   SER N   4 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   ILE N   6 " --> pdb=" O   PHE L   3 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   PHE L   5 " --> pdb=" O   ILE N   6 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   GLU N   8 " --> pdb=" O   PHE L   5 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLY L   7 " --> pdb=" O   GLU N   8 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 19 through 20
      removed outlier: 6.068A  pdb=" N   ALA B  19 " --> pdb=" O   TYR D  20 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   ALA D  19 " --> pdb=" O   TYR F  20 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ALA F  19 " --> pdb=" O   TYR H  20 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ALA H  19 " --> pdb=" O   TYR L  20 " (cutoff:3.500A)
      removed outlier: 6.069A  pdb=" N   ALA L  19 " --> pdb=" O   TYR N  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 23 through 29
      removed outlier: 8.303A  pdb=" N   LYS B  24 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY D  27 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA B  26 " --> pdb=" O   GLY D  27 " (cutoff:3.500A)
      removed outlier: 10.812A  pdb=" N   LYS D  29 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP B  28 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   LYS D  24 " --> pdb=" O   GLU F  25 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY F  27 " --> pdb=" O   LYS D  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA D  26 " --> pdb=" O   GLY F  27 " (cutoff:3.500A)
      removed outlier: 10.811A  pdb=" N   LYS F  29 " --> pdb=" O   ALA D  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP D  28 " --> pdb=" O   LYS F  29 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   LYS F  24 " --> pdb=" O   GLU H  25 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   GLY H  27 " --> pdb=" O   LYS F  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA F  26 " --> pdb=" O   GLY H  27 " (cutoff:3.500A)
      removed outlier: 10.812A  pdb=" N   LYS H  29 " --> pdb=" O   ALA F  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP F  28 " --> pdb=" O   LYS H  29 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   LYS H  24 " --> pdb=" O   GLU L  25 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY L  27 " --> pdb=" O   LYS H  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA H  26 " --> pdb=" O   GLY L  27 " (cutoff:3.500A)
      removed outlier: 10.811A  pdb=" N   LYS L  29 " --> pdb=" O   ALA H  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP H  28 " --> pdb=" O   LYS L  29 " (cutoff:3.500A)
      removed outlier: 8.303A  pdb=" N   LYS L  24 " --> pdb=" O   GLU N  25 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   GLY N  27 " --> pdb=" O   LYS L  24 " (cutoff:3.500A)
      removed outlier: 9.219A  pdb=" N   ALA L  26 " --> pdb=" O   GLY N  27 " (cutoff:3.500A)
      removed outlier: 10.811A  pdb=" N   LYS N  29 " --> pdb=" O   ALA L  26 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   TRP L  28 " --> pdb=" O   LYS N  29 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 38
    Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 46
      removed outlier: 6.689A  pdb=" N   GLN B  45 " --> pdb=" O   ARG D  46 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN D  45 " --> pdb=" O   ARG F  46 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN F  45 " --> pdb=" O   ARG H  46 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN H  45 " --> pdb=" O   ARG L  46 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   GLN L  45 " --> pdb=" O   ARG N  46 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 53
      removed outlier: 6.513A  pdb=" N   TRP B  52 " --> pdb=" O   ALA D  53 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TRP D  52 " --> pdb=" O   ALA F  53 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TRP F  52 " --> pdb=" O   ALA H  53 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   TRP H  52 " --> pdb=" O   ALA L  53 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   TRP L  52 " --> pdb=" O   ALA N  53 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'B' and resid 57 through 58
      removed outlier: 6.726A  pdb=" N   ILE B  57 " --> pdb=" O   SER D  58 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE D  57 " --> pdb=" O   SER F  58 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE F  57 " --> pdb=" O   SER H  58 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE H  57 " --> pdb=" O   SER L  58 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ILE L  57 " --> pdb=" O   SER N  58 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 68
      removed outlier: 6.645A  pdb=" N   GLU B  66 " --> pdb=" O   PHE D  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU D  66 " --> pdb=" O   PHE F  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU F  66 " --> pdb=" O   PHE H  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU H  66 " --> pdb=" O   PHE L  67 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   GLU L  66 " --> pdb=" O   PHE N  67 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    50 hydrogen bonds defined for protein.
    150 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: 0.98

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1924
        1.34 -     1.45: 1742
        1.45 -     1.57: 3090
        1.57 -     1.69: 0
        1.69 -     1.80: 48
  Bond restraints: 6804
  Sorted by residual:
  bond pdb=" N   PHE I  10 "
       pdb=" CA  PHE I  10 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.19e-02 7.06e+03 9.15e+00
  bond pdb=" N   PHE L  10 "
       pdb=" CA  PHE L  10 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.19e-02 7.06e+03 9.15e+00
  bond pdb=" N   PHE G  10 "
       pdb=" CA  PHE G  10 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.19e-02 7.06e+03 9.15e+00
  bond pdb=" N   PHE H  10 "
       pdb=" CA  PHE H  10 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.19e-02 7.06e+03 9.15e+00
  bond pdb=" N   PHE A  10 "
       pdb=" CA  PHE A  10 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.19e-02 7.06e+03 9.13e+00
  ... (remaining 6799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 7298
        1.48 -     2.97: 1342
        2.97 -     4.45: 358
        4.45 -     5.93: 74
        5.93 -     7.42: 36
  Bond angle restraints: 9108
  Sorted by residual:
  angle pdb=" C   ARG N  61 "
        pdb=" CA  ARG N  61 "
        pdb=" CB  ARG N  61 "
      ideal   model   delta    sigma   weight residual
     110.19  102.77    7.42 1.62e+00 3.81e-01 2.10e+01
  angle pdb=" C   ARG M  61 "
        pdb=" CA  ARG M  61 "
        pdb=" CB  ARG M  61 "
      ideal   model   delta    sigma   weight residual
     110.19  102.77    7.42 1.62e+00 3.81e-01 2.10e+01
  angle pdb=" C   ARG I  61 "
        pdb=" CA  ARG I  61 "
        pdb=" CB  ARG I  61 "
      ideal   model   delta    sigma   weight residual
     110.19  102.78    7.41 1.62e+00 3.81e-01 2.09e+01
  angle pdb=" C   ARG L  61 "
        pdb=" CA  ARG L  61 "
        pdb=" CB  ARG L  61 "
      ideal   model   delta    sigma   weight residual
     110.19  102.78    7.41 1.62e+00 3.81e-01 2.09e+01
  angle pdb=" C   ARG D  61 "
        pdb=" CA  ARG D  61 "
        pdb=" CB  ARG D  61 "
      ideal   model   delta    sigma   weight residual
     110.19  102.78    7.41 1.62e+00 3.81e-01 2.09e+01
  ... (remaining 9103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.26: 3396
       12.26 -    24.53: 216
       24.53 -    36.79: 48
       36.79 -    49.05: 12
       49.05 -    61.31: 36
  Dihedral angle restraints: 3708
    sinusoidal: 1464
      harmonic: 2244
  Sorted by residual:
  dihedral pdb=" CB  LYS C  56 "
           pdb=" CG  LYS C  56 "
           pdb=" CD  LYS C  56 "
           pdb=" CE  LYS C  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -105.88   45.88     3      1.50e+01 4.44e-03 8.24e+00
  dihedral pdb=" CB  LYS D  56 "
           pdb=" CG  LYS D  56 "
           pdb=" CD  LYS D  56 "
           pdb=" CE  LYS D  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -105.88   45.88     3      1.50e+01 4.44e-03 8.24e+00
  dihedral pdb=" CB  LYS A  56 "
           pdb=" CG  LYS A  56 "
           pdb=" CD  LYS A  56 "
           pdb=" CE  LYS A  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -105.87   45.87     3      1.50e+01 4.44e-03 8.24e+00
  ... (remaining 3705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 272
       0.037 -    0.074: 232
       0.074 -    0.111: 192
       0.111 -    0.148: 36
       0.148 -    0.185: 12
  Chirality restraints: 744
  Sorted by residual:
  chirality pdb=" CA  MET A  23 "
            pdb=" N   MET A  23 "
            pdb=" C   MET A  23 "
            pdb=" CB  MET A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  MET B  23 "
            pdb=" N   MET B  23 "
            pdb=" C   MET B  23 "
            pdb=" CB  MET B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  MET H  23 "
            pdb=" N   MET H  23 "
            pdb=" C   MET H  23 "
            pdb=" CB  MET H  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.51e-01
  ... (remaining 741 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  27 "   -0.014 2.00e-02 2.50e+03   2.80e-02 7.83e+00
        pdb=" C   GLY A  27 "    0.048 2.00e-02 2.50e+03
        pdb=" O   GLY A  27 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   TRP A  28 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  27 "    0.014 2.00e-02 2.50e+03   2.80e-02 7.83e+00
        pdb=" C   GLY B  27 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLY B  27 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TRP B  28 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY H  27 "    0.014 2.00e-02 2.50e+03   2.79e-02 7.79e+00
        pdb=" C   GLY H  27 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLY H  27 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TRP H  28 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 2920
        2.93 -     3.42: 5626
        3.42 -     3.91: 11936
        3.91 -     4.41: 13810
        4.41 -     4.90: 25954
  Nonbonded interactions: 60246
  Sorted by model distance:
  nonbonded pdb=" O   ALA I  60 "
            pdb=" OG  SER M  63 "
     model   vdw
     2.432 3.040
  nonbonded pdb=" O   ALA L  60 "
            pdb=" OG  SER N  63 "
     model   vdw
     2.432 3.040
  nonbonded pdb=" O   ALA F  60 "
            pdb=" OG  SER H  63 "
     model   vdw
     2.432 3.040
  nonbonded pdb=" O   ALA E  60 "
            pdb=" OG  SER G  63 "
     model   vdw
     2.432 3.040
  nonbonded pdb=" O   ALA B  60 "
            pdb=" OG  SER D  63 "
     model   vdw
     2.432 3.040
  ... (remaining 60241 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

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:             1.690
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.770
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
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      :  0.010   0.047   6804  Z= 0.638
  Angle     :  1.358   7.415   9108  Z= 0.931
  Chirality :  0.068   0.185    744
  Planarity :  0.010   0.068   1236
  Dihedral  : 11.622  61.312   2316
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.32 (0.14), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.28 (0.11), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  46 
 TYR   0.010   0.002   TYR M  34 
 PHE   0.012   0.004   PHE C  35 
 TRP   0.012   0.003   TRP A  17 
 HIS   0.002   0.001   HIS B  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00992 ( 6804)
  covalent geometry    : angle       1.35759 ( 9108)
  hydrogen bonds       : bond        0.04973 (   50)
  hydrogen bonds       : angle       6.36626 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 368
  time to evaluate  : 0.270 
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: symmetry clash
REVERT: A   46 ARG cc_start: 0.7039 (tpt90) cc_final: 0.6395 (ttp80)
REVERT: B   46 ARG cc_start: 0.7028 (tpt90) cc_final: 0.6389 (ttp80)
REVERT: C   33 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7425 (mttm)
REVERT: D   33 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7430 (mttm)
REVERT: G   40 ASN cc_start: 0.7669 (m-40) cc_final: 0.7350 (m110)
REVERT: H   40 ASN cc_start: 0.7675 (m-40) cc_final: 0.7355 (m110)
REVERT: I   15 ASP cc_start: 0.7361 (m-30) cc_final: 0.7090 (m-30)
REVERT: L   15 ASP cc_start: 0.7357 (m-30) cc_final: 0.7086 (m-30)
REVERT: M    5 PHE cc_start: 0.7722 (m-10) cc_final: 0.6257 (p90)
REVERT: M   41 TYR cc_start: 0.7100 (m-80) cc_final: 0.6058 (p90)
REVERT: M   46 ARG cc_start: 0.7694 (tpt90) cc_final: 0.7302 (tpm170)
REVERT: N    5 PHE cc_start: 0.7726 (m-10) cc_final: 0.6257 (p90)
REVERT: N   41 TYR cc_start: 0.7101 (m-80) cc_final: 0.6059 (p90)
REVERT: N   46 ARG cc_start: 0.7693 (tpt90) cc_final: 0.7302 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 368
  average time/residue: 0.1201
  time to fit residues: 53.7046
Evaluate side-chains
  214 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  11 GLN
B  11 GLN
C  45 GLN
D  45 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.133697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.120343 restraints weight = 12989.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.123760 restraints weight = 5882.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.126031 restraints weight = 3386.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.127600 restraints weight = 2217.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.128716 restraints weight = 1580.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6804  Z= 0.153
  Angle     :  0.582   4.534   9108  Z= 0.334
  Chirality :  0.047   0.143    744
  Planarity :  0.005   0.051   1236
  Dihedral  :  4.587  15.850    900
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.97 %
    Favored  : 81.94 %
  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: -4.12 (0.15), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.11), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  61 
 TYR   0.016   0.002   TYR C  34 
 PHE   0.028   0.002   PHE E  10 
 TRP   0.016   0.002   TRP M  17 
 HIS   0.001   0.000   HIS C  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6804)
  covalent geometry    : angle       0.58198 ( 9108)
  hydrogen bonds       : bond        0.03264 (   50)
  hydrogen bonds       : angle       6.62677 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 248
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 ASN cc_start: 0.8090 (p0) cc_final: 0.7827 (p0)
REVERT: A   45 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7564 (mm-40)
REVERT: A   46 ARG cc_start: 0.7736 (tpt90) cc_final: 0.6303 (ttp80)
REVERT: B   40 ASN cc_start: 0.8062 (p0) cc_final: 0.7794 (p0)
REVERT: B   45 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7583 (mm-40)
REVERT: B   46 ARG cc_start: 0.7739 (tpt90) cc_final: 0.6306 (ttp80)
REVERT: C   22 ASP cc_start: 0.8500 (t0) cc_final: 0.7925 (t0)
REVERT: C   62 GLU cc_start: 0.8011 (tt0) cc_final: 0.7577 (tm-30)
REVERT: D   22 ASP cc_start: 0.8493 (t0) cc_final: 0.7924 (t0)
REVERT: D   62 GLU cc_start: 0.7982 (tt0) cc_final: 0.7575 (tm-30)
REVERT: E   17 TRP cc_start: 0.9185 (m100) cc_final: 0.8727 (m100)
REVERT: E   25 GLU cc_start: 0.7979 (mm-30) cc_final: 0.6762 (mm-30)
REVERT: E   34 TYR cc_start: 0.8443 (m-80) cc_final: 0.7872 (m-80)
REVERT: E   35 PHE cc_start: 0.9209 (t80) cc_final: 0.8588 (t80)
REVERT: E   45 GLN cc_start: 0.8802 (mt0) cc_final: 0.8224 (mt0)
REVERT: E   57 ILE cc_start: 0.9277 (mm) cc_final: 0.8982 (mm)
REVERT: F   17 TRP cc_start: 0.9182 (m100) cc_final: 0.8728 (m100)
REVERT: F   25 GLU cc_start: 0.7954 (mm-30) cc_final: 0.6747 (mm-30)
REVERT: F   34 TYR cc_start: 0.8445 (m-80) cc_final: 0.7880 (m-80)
REVERT: F   35 PHE cc_start: 0.9212 (t80) cc_final: 0.8590 (t80)
REVERT: F   45 GLN cc_start: 0.8795 (mt0) cc_final: 0.8227 (mt0)
REVERT: F   57 ILE cc_start: 0.9278 (mm) cc_final: 0.8989 (mm)
REVERT: G   15 ASP cc_start: 0.7909 (m-30) cc_final: 0.7513 (m-30)
REVERT: G   41 TYR cc_start: 0.7960 (m-80) cc_final: 0.7743 (m-80)
REVERT: G   42 ASP cc_start: 0.8728 (m-30) cc_final: 0.8365 (m-30)
REVERT: G   45 GLN cc_start: 0.8424 (mt0) cc_final: 0.7749 (mp10)
REVERT: H   15 ASP cc_start: 0.7918 (m-30) cc_final: 0.7530 (m-30)
REVERT: H   41 TYR cc_start: 0.7953 (m-80) cc_final: 0.7738 (m-80)
REVERT: H   42 ASP cc_start: 0.8716 (m-30) cc_final: 0.8360 (m-30)
REVERT: H   45 GLN cc_start: 0.8436 (mt0) cc_final: 0.7768 (mp10)
REVERT: I   15 ASP cc_start: 0.7959 (m-30) cc_final: 0.7601 (m-30)
REVERT: I   22 ASP cc_start: 0.8521 (t0) cc_final: 0.8318 (t0)
REVERT: I   33 LYS cc_start: 0.7709 (mtmm) cc_final: 0.6916 (mtmt)
REVERT: I   45 GLN cc_start: 0.8456 (mt0) cc_final: 0.8034 (mt0)
REVERT: I   55 GLU cc_start: 0.8377 (tp30) cc_final: 0.7906 (tp30)
REVERT: I   57 ILE cc_start: 0.9233 (mm) cc_final: 0.8968 (mm)
REVERT: L   15 ASP cc_start: 0.7956 (m-30) cc_final: 0.7600 (m-30)
REVERT: L   33 LYS cc_start: 0.7729 (mtmm) cc_final: 0.6951 (mtmt)
REVERT: L   45 GLN cc_start: 0.8444 (mt0) cc_final: 0.8033 (mt0)
REVERT: L   55 GLU cc_start: 0.8369 (tp30) cc_final: 0.7914 (tp30)
REVERT: L   57 ILE cc_start: 0.9230 (mm) cc_final: 0.8967 (mm)
REVERT: M   41 TYR cc_start: 0.7480 (m-80) cc_final: 0.6097 (p90)
REVERT: M   46 ARG cc_start: 0.8174 (tpt90) cc_final: 0.7295 (tpm170)
REVERT: N   41 TYR cc_start: 0.7477 (m-80) cc_final: 0.6102 (p90)
REVERT: N   46 ARG cc_start: 0.8172 (tpt90) cc_final: 0.7295 (tpm170)
  outliers start: 12
  outliers final: 8
  residues processed: 254
  average time/residue: 0.0806
  time to fit residues: 26.8810
Evaluate side-chains
  236 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 228
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain F residue   63 SER
Chi-restraints excluded: chain G residue   63 SER
Chi-restraints excluded: chain H residue   63 SER
Chi-restraints excluded: chain M residue   63 SER
Chi-restraints excluded: chain N residue   63 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0170
   chunk 8 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 58 optimal weight:    0.2980
   chunk 9 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.8624

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

Flipped N/Q/H residues before XYZ refinement:
** M  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.119889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.106552 restraints weight = 13414.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.109734 restraints weight = 5942.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.111729 restraints weight = 3463.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.113186 restraints weight = 2335.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.114073 restraints weight = 1716.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.6018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   6804  Z= 0.276
  Angle     :  0.578   4.118   9108  Z= 0.337
  Chirality :  0.044   0.127    744
  Planarity :  0.004   0.044   1236
  Dihedral  :  4.756  18.057    900
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.32 %
    Favored  : 82.29 %
  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: -4.07 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.09 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I  61 
 TYR   0.019   0.002   TYR C  34 
 PHE   0.018   0.002   PHE L  10 
 TRP   0.038   0.003   TRP D  17 
 HIS   0.003   0.001   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 6804)
  covalent geometry    : angle       0.57774 ( 9108)
  hydrogen bonds       : bond        0.03029 (   50)
  hydrogen bonds       : angle       6.25425 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 232
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7236 (pm20)
REVERT: A   22 ASP cc_start: 0.8281 (t0) cc_final: 0.7976 (t0)
REVERT: A   23 MET cc_start: 0.6333 (mmm) cc_final: 0.5422 (ptt)
REVERT: A   33 LYS cc_start: 0.8452 (mtmm) cc_final: 0.7432 (tttt)
REVERT: A   40 ASN cc_start: 0.7942 (p0) cc_final: 0.7729 (p0)
REVERT: A   46 ARG cc_start: 0.7972 (tpt90) cc_final: 0.6677 (ttp80)
REVERT: B    8 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7233 (pm20)
REVERT: B   22 ASP cc_start: 0.8274 (t0) cc_final: 0.7967 (t0)
REVERT: B   23 MET cc_start: 0.6331 (mmm) cc_final: 0.5414 (ptt)
REVERT: B   33 LYS cc_start: 0.8448 (mtmm) cc_final: 0.7428 (tttt)
REVERT: B   40 ASN cc_start: 0.7955 (p0) cc_final: 0.7742 (p0)
REVERT: B   46 ARG cc_start: 0.7983 (tpt90) cc_final: 0.6677 (ttp80)
REVERT: C   17 TRP cc_start: 0.9069 (m100) cc_final: 0.8630 (m100)
REVERT: C   22 ASP cc_start: 0.8497 (t0) cc_final: 0.8066 (t0)
REVERT: C   23 MET cc_start: 0.8096 (mmm) cc_final: 0.7459 (mmt)
REVERT: C   25 GLU cc_start: 0.4907 (tm-30) cc_final: 0.4623 (tm-30)
REVERT: C   33 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8150 (mtmt)
REVERT: C   62 GLU cc_start: 0.8093 (tt0) cc_final: 0.7754 (tm-30)
REVERT: D   17 TRP cc_start: 0.9062 (m100) cc_final: 0.8668 (m100)
REVERT: D   22 ASP cc_start: 0.8490 (t0) cc_final: 0.8056 (t0)
REVERT: D   23 MET cc_start: 0.8091 (mmm) cc_final: 0.7458 (mmt)
REVERT: D   25 GLU cc_start: 0.4910 (tm-30) cc_final: 0.4622 (tm-30)
REVERT: D   33 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8146 (mtmt)
REVERT: D   62 GLU cc_start: 0.8083 (tt0) cc_final: 0.7759 (tm-30)
REVERT: E   17 TRP cc_start: 0.9318 (m100) cc_final: 0.8611 (m100)
REVERT: E   22 ASP cc_start: 0.8230 (t0) cc_final: 0.7588 (t0)
REVERT: E   34 TYR cc_start: 0.8650 (m-80) cc_final: 0.8416 (m-80)
REVERT: E   45 GLN cc_start: 0.8621 (mt0) cc_final: 0.8379 (mt0)
REVERT: E   59 ASP cc_start: 0.7988 (m-30) cc_final: 0.7626 (m-30)
REVERT: F   17 TRP cc_start: 0.9320 (m100) cc_final: 0.8610 (m100)
REVERT: F   22 ASP cc_start: 0.8215 (t0) cc_final: 0.7580 (t0)
REVERT: F   34 TYR cc_start: 0.8655 (m-80) cc_final: 0.8425 (m-80)
REVERT: F   45 GLN cc_start: 0.8610 (mt0) cc_final: 0.8366 (mt0)
REVERT: F   59 ASP cc_start: 0.7978 (m-30) cc_final: 0.7618 (m-30)
REVERT: G   23 MET cc_start: 0.7858 (mmp) cc_final: 0.7424 (mmt)
REVERT: G   45 GLN cc_start: 0.8602 (mt0) cc_final: 0.8315 (mt0)
REVERT: G   65 GLN cc_start: 0.8518 (mt0) cc_final: 0.7836 (mp10)
REVERT: H   15 ASP cc_start: 0.8123 (m-30) cc_final: 0.7923 (m-30)
REVERT: H   23 MET cc_start: 0.7860 (mmp) cc_final: 0.7430 (mmt)
REVERT: H   45 GLN cc_start: 0.8603 (mt0) cc_final: 0.8316 (mt0)
REVERT: H   65 GLN cc_start: 0.8516 (mt0) cc_final: 0.7848 (mp10)
REVERT: I    8 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: I   45 GLN cc_start: 0.8441 (mt0) cc_final: 0.8194 (mt0)
REVERT: I   46 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.7094 (tpt-90)
REVERT: I   55 GLU cc_start: 0.8220 (tp30) cc_final: 0.7815 (tm-30)
REVERT: I   57 ILE cc_start: 0.9432 (mm) cc_final: 0.9126 (mm)
REVERT: L    8 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8119 (mt-10)
REVERT: L   45 GLN cc_start: 0.8437 (mt0) cc_final: 0.8192 (mt0)
REVERT: L   46 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.7098 (tpt-90)
REVERT: L   55 GLU cc_start: 0.8229 (tp30) cc_final: 0.7815 (tm-30)
REVERT: L   57 ILE cc_start: 0.9432 (mm) cc_final: 0.9125 (mm)
REVERT: M   45 GLN cc_start: 0.8156 (mt0) cc_final: 0.7413 (mp10)
REVERT: N   45 GLN cc_start: 0.8153 (mt0) cc_final: 0.7415 (mp10)
  outliers start: 8
  outliers final: 2
  residues processed: 236
  average time/residue: 0.0851
  time to fit residues: 26.2327
Evaluate side-chains
  226 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 224
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 22 optimal weight:    0.3980
   chunk 48 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.124473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.110268 restraints weight = 13426.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.113643 restraints weight = 5949.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.115509 restraints weight = 3465.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.117009 restraints weight = 2420.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.117985 restraints weight = 1806.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.6400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6804  Z= 0.145
  Angle     :  0.513   4.364   9108  Z= 0.294
  Chirality :  0.044   0.154    744
  Planarity :  0.003   0.041   1236
  Dihedral  :  4.266  16.666    900
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 16.84 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.99 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG I  61 
 TYR   0.014   0.001   TYR C  41 
 PHE   0.013   0.001   PHE H   2 
 TRP   0.015   0.001   TRP I  17 
 HIS   0.001   0.000   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6804)
  covalent geometry    : angle       0.51324 ( 9108)
  hydrogen bonds       : bond        0.02424 (   50)
  hydrogen bonds       : angle       5.99569 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 234
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8450 (mtmm) cc_final: 0.7517 (tttt)
REVERT: A   45 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8267 (mm-40)
REVERT: B   33 LYS cc_start: 0.8454 (mtmm) cc_final: 0.7514 (tttt)
REVERT: B   45 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8269 (mm-40)
REVERT: C   23 MET cc_start: 0.7783 (mmm) cc_final: 0.6710 (ptt)
REVERT: C   45 GLN cc_start: 0.8904 (mt0) cc_final: 0.7957 (mp10)
REVERT: C   62 GLU cc_start: 0.8065 (tt0) cc_final: 0.7697 (tm-30)
REVERT: D   23 MET cc_start: 0.7785 (mmm) cc_final: 0.6711 (ptt)
REVERT: D   45 GLN cc_start: 0.8907 (mt0) cc_final: 0.7959 (mp10)
REVERT: D   62 GLU cc_start: 0.8052 (tt0) cc_final: 0.7691 (tm-30)
REVERT: E    8 GLU cc_start: 0.8658 (mt-10) cc_final: 0.7851 (mt-10)
REVERT: E   17 TRP cc_start: 0.9233 (m100) cc_final: 0.8792 (m100)
REVERT: E   22 ASP cc_start: 0.8309 (t0) cc_final: 0.8108 (t0)
REVERT: E   34 TYR cc_start: 0.8633 (m-80) cc_final: 0.8387 (m-80)
REVERT: E   45 GLN cc_start: 0.8536 (mt0) cc_final: 0.8168 (mt0)
REVERT: F    8 GLU cc_start: 0.8679 (mt-10) cc_final: 0.7886 (mt-10)
REVERT: F   17 TRP cc_start: 0.9241 (m100) cc_final: 0.8793 (m100)
REVERT: F   22 ASP cc_start: 0.8317 (t0) cc_final: 0.8114 (t0)
REVERT: F   34 TYR cc_start: 0.8626 (m-80) cc_final: 0.8374 (m-80)
REVERT: F   45 GLN cc_start: 0.8528 (mt0) cc_final: 0.8167 (mt0)
REVERT: G    8 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7855 (mt-10)
REVERT: G   22 ASP cc_start: 0.8280 (t0) cc_final: 0.7976 (t0)
REVERT: G   23 MET cc_start: 0.8179 (mmt) cc_final: 0.7973 (mmt)
REVERT: G   33 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7609 (mttp)
REVERT: G   45 GLN cc_start: 0.8453 (mt0) cc_final: 0.8121 (mt0)
REVERT: G   46 ARG cc_start: 0.8205 (tpt170) cc_final: 0.6823 (tpt170)
REVERT: G   55 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7299 (tm-30)
REVERT: G   57 ILE cc_start: 0.9325 (mm) cc_final: 0.8882 (mm)
REVERT: G   62 GLU cc_start: 0.8019 (tt0) cc_final: 0.7434 (tt0)
REVERT: H    8 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7845 (mt-10)
REVERT: H   15 ASP cc_start: 0.7900 (m-30) cc_final: 0.7696 (m-30)
REVERT: H   22 ASP cc_start: 0.8287 (t0) cc_final: 0.7983 (t0)
REVERT: H   23 MET cc_start: 0.8185 (mmt) cc_final: 0.7984 (mmt)
REVERT: H   33 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7611 (mttp)
REVERT: H   45 GLN cc_start: 0.8452 (mt0) cc_final: 0.8118 (mt0)
REVERT: H   46 ARG cc_start: 0.8186 (tpt170) cc_final: 0.6828 (tpt170)
REVERT: H   55 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7294 (tm-30)
REVERT: H   57 ILE cc_start: 0.9323 (mm) cc_final: 0.8882 (mm)
REVERT: H   62 GLU cc_start: 0.8024 (tt0) cc_final: 0.7436 (tt0)
REVERT: I   45 GLN cc_start: 0.8527 (mt0) cc_final: 0.8263 (mt0)
REVERT: I   57 ILE cc_start: 0.9417 (mm) cc_final: 0.9162 (mm)
REVERT: L   15 ASP cc_start: 0.8119 (m-30) cc_final: 0.7775 (m-30)
REVERT: L   33 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7482 (mtmt)
REVERT: L   45 GLN cc_start: 0.8518 (mt0) cc_final: 0.8255 (mt0)
REVERT: L   57 ILE cc_start: 0.9413 (mm) cc_final: 0.9157 (mm)
REVERT: M   45 GLN cc_start: 0.8112 (mt0) cc_final: 0.7409 (mp10)
REVERT: N   45 GLN cc_start: 0.8106 (mt0) cc_final: 0.7396 (mp10)
  outliers start: 4
  outliers final: 4
  residues processed: 238
  average time/residue: 0.0763
  time to fit residues: 24.2035
Evaluate side-chains
  222 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 218
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain F residue   63 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 57 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0020
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  40 ASN
L  40 ASN
** M  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.125645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.111963 restraints weight = 13595.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.115298 restraints weight = 6027.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.117331 restraints weight = 3515.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.118741 restraints weight = 2362.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.119786 restraints weight = 1739.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.6725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6804  Z= 0.141
  Angle     :  0.513   4.256   9108  Z= 0.297
  Chirality :  0.044   0.148    744
  Planarity :  0.003   0.029   1236
  Dihedral  :  4.161  18.820    900
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 19.79 %
    Favored  : 78.82 %
  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: -3.98 (0.16), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.12), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  61 
 TYR   0.013   0.001   TYR C  34 
 PHE   0.011   0.001   PHE G   2 
 TRP   0.036   0.002   TRP C  17 
 HIS   0.001   0.000   HIS G  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6804)
  covalent geometry    : angle       0.51269 ( 9108)
  hydrogen bonds       : bond        0.02445 (   50)
  hydrogen bonds       : angle       5.73746 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 232
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8154 (mt-10) cc_final: 0.6953 (pm20)
REVERT: A   33 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7573 (tttt)
REVERT: A   45 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8352 (mm-40)
REVERT: B    8 GLU cc_start: 0.8158 (mt-10) cc_final: 0.6955 (pm20)
REVERT: B   33 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7575 (tttt)
REVERT: B   45 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8347 (mm-40)
REVERT: C   42 ASP cc_start: 0.8715 (m-30) cc_final: 0.8309 (m-30)
REVERT: C   45 GLN cc_start: 0.8927 (mt0) cc_final: 0.7889 (mp10)
REVERT: C   62 GLU cc_start: 0.7932 (tt0) cc_final: 0.7509 (tm-30)
REVERT: D   42 ASP cc_start: 0.8729 (m-30) cc_final: 0.8317 (m-30)
REVERT: D   45 GLN cc_start: 0.8924 (mt0) cc_final: 0.7886 (mp10)
REVERT: D   62 GLU cc_start: 0.7924 (tt0) cc_final: 0.7503 (tm-30)
REVERT: E   17 TRP cc_start: 0.9242 (m100) cc_final: 0.8996 (m100)
REVERT: E   34 TYR cc_start: 0.8606 (m-80) cc_final: 0.8344 (m-80)
REVERT: E   45 GLN cc_start: 0.8592 (mt0) cc_final: 0.8193 (mt0)
REVERT: F   17 TRP cc_start: 0.9203 (m100) cc_final: 0.8939 (m100)
REVERT: F   34 TYR cc_start: 0.8617 (m-80) cc_final: 0.8343 (m-80)
REVERT: F   45 GLN cc_start: 0.8582 (mt0) cc_final: 0.8186 (mt0)
REVERT: G    8 GLU cc_start: 0.8631 (mt-10) cc_final: 0.7868 (mt-10)
REVERT: G   22 ASP cc_start: 0.8306 (t0) cc_final: 0.8029 (t0)
REVERT: G   23 MET cc_start: 0.8072 (mmt) cc_final: 0.7843 (mmt)
REVERT: G   33 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7632 (mptt)
REVERT: G   45 GLN cc_start: 0.8499 (mt0) cc_final: 0.8141 (mt0)
REVERT: G   46 ARG cc_start: 0.8094 (tpt170) cc_final: 0.6746 (tpt170)
REVERT: G   55 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7282 (tm-30)
REVERT: G   57 ILE cc_start: 0.9334 (mm) cc_final: 0.8932 (mm)
REVERT: H    8 GLU cc_start: 0.8646 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: H   15 ASP cc_start: 0.7799 (m-30) cc_final: 0.6987 (m-30)
REVERT: H   22 ASP cc_start: 0.8318 (t0) cc_final: 0.8027 (t0)
REVERT: H   33 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7737 (mptt)
REVERT: H   45 GLN cc_start: 0.8496 (mt0) cc_final: 0.8137 (mt0)
REVERT: H   46 ARG cc_start: 0.8079 (tpt170) cc_final: 0.6741 (tpt170)
REVERT: H   55 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7263 (tm-30)
REVERT: H   57 ILE cc_start: 0.9333 (mm) cc_final: 0.8933 (mm)
REVERT: I   45 GLN cc_start: 0.8551 (mt0) cc_final: 0.8326 (mt0)
REVERT: I   55 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: I   57 ILE cc_start: 0.9390 (mm) cc_final: 0.9150 (mm)
REVERT: L   15 ASP cc_start: 0.8015 (m-30) cc_final: 0.7738 (m-30)
REVERT: L   33 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7703 (mtmt)
REVERT: L   45 GLN cc_start: 0.8547 (mt0) cc_final: 0.8322 (mt0)
REVERT: L   55 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: L   57 ILE cc_start: 0.9389 (mm) cc_final: 0.9151 (mm)
  outliers start: 8
  outliers final: 4
  residues processed: 236
  average time/residue: 0.0765
  time to fit residues: 23.7782
Evaluate side-chains
  226 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 222
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain E residue   63 SER
Chi-restraints excluded: chain F residue   63 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0570
   chunk 54 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  40 ASN
L  40 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.127219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.113201 restraints weight = 13383.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.116614 restraints weight = 5925.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.118656 restraints weight = 3442.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.120098 restraints weight = 2351.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.121142 restraints weight = 1753.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.6896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6804  Z= 0.132
  Angle     :  0.508   5.334   9108  Z= 0.294
  Chirality :  0.043   0.146    744
  Planarity :  0.003   0.030   1236
  Dihedral  :  4.090  18.621    900
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 20.83 %
    Favored  : 78.12 %
  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: -3.92 (0.17), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.98 (0.13), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I  61 
 TYR   0.014   0.001   TYR E  34 
 PHE   0.009   0.001   PHE H   2 
 TRP   0.045   0.002   TRP L  17 
 HIS   0.001   0.000   HIS B  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6804)
  covalent geometry    : angle       0.50783 ( 9108)
  hydrogen bonds       : bond        0.02352 (   50)
  hydrogen bonds       : angle       5.67836 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 237
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7518 (tttt)
REVERT: A   45 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8334 (mm-40)
REVERT: A   57 ILE cc_start: 0.8467 (mm) cc_final: 0.8177 (mt)
REVERT: B   33 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7520 (tttt)
REVERT: B   45 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8343 (mm-40)
REVERT: B   57 ILE cc_start: 0.8472 (mm) cc_final: 0.8183 (mt)
REVERT: C    8 GLU cc_start: 0.8612 (tt0) cc_final: 0.8403 (tt0)
REVERT: C   45 GLN cc_start: 0.8906 (mt0) cc_final: 0.7952 (mp10)
REVERT: C   62 GLU cc_start: 0.7935 (tt0) cc_final: 0.7464 (tm-30)
REVERT: D    8 GLU cc_start: 0.8619 (tt0) cc_final: 0.8405 (tt0)
REVERT: D   45 GLN cc_start: 0.8907 (mt0) cc_final: 0.7913 (mp10)
REVERT: D   62 GLU cc_start: 0.7936 (tt0) cc_final: 0.7463 (tm-30)
REVERT: E   17 TRP cc_start: 0.9256 (m100) cc_final: 0.8974 (m100)
REVERT: E   34 TYR cc_start: 0.8418 (m-80) cc_final: 0.8195 (m-80)
REVERT: E   45 GLN cc_start: 0.8654 (mt0) cc_final: 0.8415 (mt0)
REVERT: F   17 TRP cc_start: 0.9241 (m100) cc_final: 0.8900 (m100)
REVERT: F   34 TYR cc_start: 0.8404 (m-80) cc_final: 0.8152 (m-80)
REVERT: F   45 GLN cc_start: 0.8648 (mt0) cc_final: 0.8412 (mt0)
REVERT: G   22 ASP cc_start: 0.8479 (t0) cc_final: 0.8029 (t0)
REVERT: G   23 MET cc_start: 0.8181 (mmt) cc_final: 0.7916 (mmt)
REVERT: G   45 GLN cc_start: 0.8532 (mt0) cc_final: 0.8183 (mt0)
REVERT: G   55 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7318 (tm-30)
REVERT: G   65 GLN cc_start: 0.8399 (mt0) cc_final: 0.7947 (mp10)
REVERT: H   15 ASP cc_start: 0.7685 (m-30) cc_final: 0.7476 (m-30)
REVERT: H   22 ASP cc_start: 0.8377 (t0) cc_final: 0.8051 (t0)
REVERT: H   30 ASP cc_start: 0.8092 (p0) cc_final: 0.7752 (p0)
REVERT: H   45 GLN cc_start: 0.8532 (mt0) cc_final: 0.8185 (mt0)
REVERT: H   55 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7311 (tm-30)
REVERT: H   65 GLN cc_start: 0.8407 (mt0) cc_final: 0.7946 (mp10)
REVERT: I    8 GLU cc_start: 0.7744 (tt0) cc_final: 0.7454 (tt0)
REVERT: I   42 ASP cc_start: 0.8720 (m-30) cc_final: 0.8510 (m-30)
REVERT: I   45 GLN cc_start: 0.8464 (mt0) cc_final: 0.8127 (mt0)
REVERT: I   46 ARG cc_start: 0.8038 (tpt-90) cc_final: 0.7438 (tpt-90)
REVERT: I   55 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7705 (tm-30)
REVERT: L   15 ASP cc_start: 0.8157 (m-30) cc_final: 0.7847 (m-30)
REVERT: L   33 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7736 (mtmt)
REVERT: L   42 ASP cc_start: 0.8717 (m-30) cc_final: 0.8508 (m-30)
REVERT: L   45 GLN cc_start: 0.8467 (mt0) cc_final: 0.8122 (mt0)
REVERT: L   46 ARG cc_start: 0.8035 (tpt-90) cc_final: 0.7432 (tpt-90)
REVERT: L   55 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: M   22 ASP cc_start: 0.5889 (p0) cc_final: 0.5631 (p0)
REVERT: M   33 LYS cc_start: 0.7321 (mtmm) cc_final: 0.7082 (mmmt)
REVERT: N   22 ASP cc_start: 0.5884 (p0) cc_final: 0.5606 (p0)
  outliers start: 6
  outliers final: 0
  residues processed: 237
  average time/residue: 0.0769
  time to fit residues: 23.8125
Evaluate side-chains
  224 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
I  40 ASN
L  40 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.122279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.107975 restraints weight = 13357.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.111122 restraints weight = 6197.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.113290 restraints weight = 3724.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.114814 restraints weight = 2557.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.115780 restraints weight = 1914.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.7135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   6804  Z= 0.245
  Angle     :  0.565   5.634   9108  Z= 0.326
  Chirality :  0.044   0.162    744
  Planarity :  0.003   0.026   1236
  Dihedral  :  4.586  23.414    900
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 20.31 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.00 (0.17), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.13), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  61 
 TYR   0.018   0.001   TYR D  34 
 PHE   0.011   0.002   PHE G   2 
 TRP   0.044   0.003   TRP L  17 
 HIS   0.001   0.001   HIS H  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 6804)
  covalent geometry    : angle       0.56530 ( 9108)
  hydrogen bonds       : bond        0.02789 (   50)
  hydrogen bonds       : angle       5.83942 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 231
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7526 (tttt)
REVERT: A   40 ASN cc_start: 0.7376 (p0) cc_final: 0.7051 (p0)
REVERT: A   45 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8450 (mm-40)
REVERT: B   33 LYS cc_start: 0.8281 (mtmm) cc_final: 0.7537 (tttt)
REVERT: B   40 ASN cc_start: 0.7380 (p0) cc_final: 0.7049 (p0)
REVERT: B   45 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8454 (mm-40)
REVERT: C   45 GLN cc_start: 0.8982 (mt0) cc_final: 0.7941 (mt0)
REVERT: C   62 GLU cc_start: 0.8001 (tt0) cc_final: 0.7454 (tm-30)
REVERT: D   45 GLN cc_start: 0.8980 (mt0) cc_final: 0.7936 (mt0)
REVERT: D   62 GLU cc_start: 0.7998 (tt0) cc_final: 0.7451 (tm-30)
REVERT: E   17 TRP cc_start: 0.9389 (m100) cc_final: 0.9078 (m100)
REVERT: E   22 ASP cc_start: 0.8202 (t0) cc_final: 0.7721 (t0)
REVERT: E   34 TYR cc_start: 0.8600 (m-80) cc_final: 0.8381 (m-80)
REVERT: E   45 GLN cc_start: 0.8660 (mt0) cc_final: 0.8252 (mt0)
REVERT: E   46 ARG cc_start: 0.8150 (ttt90) cc_final: 0.7935 (ttt90)
REVERT: E   57 ILE cc_start: 0.9398 (mm) cc_final: 0.9003 (mm)
REVERT: F    8 GLU cc_start: 0.8554 (tt0) cc_final: 0.8305 (tt0)
REVERT: F   17 TRP cc_start: 0.9362 (m100) cc_final: 0.9082 (m100)
REVERT: F   34 TYR cc_start: 0.8571 (m-80) cc_final: 0.8305 (m-80)
REVERT: F   45 GLN cc_start: 0.8650 (mt0) cc_final: 0.8241 (mt0)
REVERT: F   46 ARG cc_start: 0.8155 (ttt90) cc_final: 0.7808 (ttt90)
REVERT: F   57 ILE cc_start: 0.9399 (mm) cc_final: 0.9004 (mm)
REVERT: G   22 ASP cc_start: 0.8451 (t0) cc_final: 0.8068 (t0)
REVERT: G   23 MET cc_start: 0.8390 (mmt) cc_final: 0.8124 (mmt)
REVERT: G   33 LYS cc_start: 0.7987 (mppt) cc_final: 0.7413 (mtmm)
REVERT: G   45 GLN cc_start: 0.8452 (mt0) cc_final: 0.8151 (mt0)
REVERT: G   55 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7375 (tm-30)
REVERT: H    8 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7495 (tt0)
REVERT: H   15 ASP cc_start: 0.7969 (m-30) cc_final: 0.7636 (m-30)
REVERT: H   45 GLN cc_start: 0.8461 (mt0) cc_final: 0.8156 (mt0)
REVERT: H   46 ARG cc_start: 0.7509 (tpt170) cc_final: 0.6757 (tpt170)
REVERT: H   55 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7374 (tm-30)
REVERT: I   45 GLN cc_start: 0.8577 (mt0) cc_final: 0.8339 (mt0)
REVERT: I   55 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7839 (tm-30)
REVERT: L   15 ASP cc_start: 0.8003 (m-30) cc_final: 0.7623 (m-30)
REVERT: L   33 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7288 (mtmt)
REVERT: L   45 GLN cc_start: 0.8608 (mt0) cc_final: 0.8370 (mt0)
REVERT: L   55 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7844 (tm-30)
REVERT: M   33 LYS cc_start: 0.7439 (mtmm) cc_final: 0.7201 (mmmt)
  outliers start: 7
  outliers final: 6
  residues processed: 235
  average time/residue: 0.0726
  time to fit residues: 22.6581
Evaluate side-chains
  232 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 226
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain E residue   62 GLU
Chi-restraints excluded: chain F residue   62 GLU
Chi-restraints excluded: chain I residue   40 ASN
Chi-restraints excluded: chain L residue   40 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 62 optimal weight:    0.2980
   chunk 53 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
I  40 ASN
L  40 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.123019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.108560 restraints weight = 13501.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.111803 restraints weight = 6292.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.114004 restraints weight = 3769.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.115537 restraints weight = 2583.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.116625 restraints weight = 1930.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.7251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6804  Z= 0.197
  Angle     :  0.585   6.886   9108  Z= 0.333
  Chirality :  0.045   0.157    744
  Planarity :  0.003   0.030   1236
  Dihedral  :  4.433  19.639    900
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 21.35 %
    Favored  : 77.95 %
  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: -3.97 (0.17), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.02 (0.13), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG I  61 
 TYR   0.015   0.001   TYR D  34 
 PHE   0.010   0.001   PHE G   2 
 TRP   0.033   0.002   TRP L  17 
 HIS   0.001   0.000   HIS B  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6804)
  covalent geometry    : angle       0.58507 ( 9108)
  hydrogen bonds       : bond        0.02618 (   50)
  hydrogen bonds       : angle       5.67514 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 237
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7566 (tttt)
REVERT: A   40 ASN cc_start: 0.7299 (p0) cc_final: 0.6970 (p0)
REVERT: A   41 TYR cc_start: 0.8115 (m-10) cc_final: 0.7877 (m-80)
REVERT: A   45 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8483 (mm-40)
REVERT: B   33 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7678 (tttt)
REVERT: B   40 ASN cc_start: 0.7293 (p0) cc_final: 0.6956 (p0)
REVERT: B   41 TYR cc_start: 0.8115 (m-10) cc_final: 0.7873 (m-80)
REVERT: B   45 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8491 (mm-40)
REVERT: C   45 GLN cc_start: 0.8983 (mt0) cc_final: 0.7969 (mt0)
REVERT: C   62 GLU cc_start: 0.7945 (tt0) cc_final: 0.7374 (tm-30)
REVERT: D   45 GLN cc_start: 0.8987 (mt0) cc_final: 0.7966 (mt0)
REVERT: D   62 GLU cc_start: 0.7934 (tt0) cc_final: 0.7374 (tm-30)
REVERT: E   17 TRP cc_start: 0.9339 (m100) cc_final: 0.9105 (m100)
REVERT: E   34 TYR cc_start: 0.8632 (m-80) cc_final: 0.8399 (m-80)
REVERT: E   45 GLN cc_start: 0.8681 (mt0) cc_final: 0.8464 (mt0)
REVERT: F   17 TRP cc_start: 0.9342 (m100) cc_final: 0.9091 (m100)
REVERT: F   34 TYR cc_start: 0.8603 (m-80) cc_final: 0.8339 (m-80)
REVERT: F   45 GLN cc_start: 0.8654 (mt0) cc_final: 0.8443 (mt0)
REVERT: G   22 ASP cc_start: 0.8418 (t0) cc_final: 0.8052 (t0)
REVERT: G   45 GLN cc_start: 0.8515 (mt0) cc_final: 0.8195 (mt0)
REVERT: G   55 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: H   15 ASP cc_start: 0.7850 (m-30) cc_final: 0.7365 (m-30)
REVERT: H   33 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8130 (mmtm)
REVERT: H   45 GLN cc_start: 0.8508 (mt0) cc_final: 0.8182 (mt0)
REVERT: H   55 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: I   45 GLN cc_start: 0.8633 (mt0) cc_final: 0.8365 (mt0)
REVERT: I   46 ARG cc_start: 0.7960 (tpt-90) cc_final: 0.7750 (tpt170)
REVERT: I   55 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: I   61 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7507 (mtt-85)
REVERT: L   33 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7791 (mtmt)
REVERT: L   45 GLN cc_start: 0.8584 (mt0) cc_final: 0.8326 (mt0)
REVERT: L   55 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: L   62 GLU cc_start: 0.8229 (tt0) cc_final: 0.7842 (tm-30)
REVERT: M   33 LYS cc_start: 0.7484 (mtmm) cc_final: 0.7266 (mmmt)
  outliers start: 4
  outliers final: 2
  residues processed: 237
  average time/residue: 0.0720
  time to fit residues: 22.7387
Evaluate side-chains
  236 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 234
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   62 GLU
Chi-restraints excluded: chain F residue   62 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0070
   chunk 51 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 34 optimal weight:    0.2980
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  40 ASN
L  40 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.127635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.113801 restraints weight = 13270.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.117171 restraints weight = 6013.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.119259 restraints weight = 3499.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.120789 restraints weight = 2369.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.121806 restraints weight = 1744.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.7476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6804  Z= 0.134
  Angle     :  0.569   6.938   9108  Z= 0.323
  Chirality :  0.045   0.161    744
  Planarity :  0.003   0.030   1236
  Dihedral  :  4.170  16.531    900
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 21.88 %
    Favored  : 76.91 %
  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: -3.87 (0.17), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.13), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  46 
 TYR   0.012   0.001   TYR D  34 
 PHE   0.008   0.001   PHE G   2 
 TRP   0.031   0.002   TRP L  17 
 HIS   0.001   0.000   HIS E  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6804)
  covalent geometry    : angle       0.56879 ( 9108)
  hydrogen bonds       : bond        0.02519 (   50)
  hydrogen bonds       : angle       5.35965 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 231
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7961 (tt0) cc_final: 0.7169 (pm20)
REVERT: A   33 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7628 (tttt)
REVERT: A   40 ASN cc_start: 0.7720 (p0) cc_final: 0.7328 (p0)
REVERT: A   41 TYR cc_start: 0.7852 (m-10) cc_final: 0.7579 (m-80)
REVERT: B    8 GLU cc_start: 0.7978 (tt0) cc_final: 0.7187 (pm20)
REVERT: B   33 LYS cc_start: 0.8178 (mtmm) cc_final: 0.7345 (tttt)
REVERT: B   40 ASN cc_start: 0.7729 (p0) cc_final: 0.7337 (p0)
REVERT: B   41 TYR cc_start: 0.7853 (m-10) cc_final: 0.7570 (m-80)
REVERT: C   45 GLN cc_start: 0.8919 (mt0) cc_final: 0.8261 (mp10)
REVERT: C   62 GLU cc_start: 0.7919 (tt0) cc_final: 0.7366 (tm-30)
REVERT: D   45 GLN cc_start: 0.8920 (mt0) cc_final: 0.8264 (mp10)
REVERT: D   62 GLU cc_start: 0.7912 (tt0) cc_final: 0.7364 (tm-30)
REVERT: E   33 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8240 (mmtm)
REVERT: E   34 TYR cc_start: 0.8563 (m-80) cc_final: 0.8346 (m-80)
REVERT: E   45 GLN cc_start: 0.8594 (mt0) cc_final: 0.8294 (mt0)
REVERT: F    8 GLU cc_start: 0.8752 (tt0) cc_final: 0.8448 (tt0)
REVERT: F   17 TRP cc_start: 0.9298 (m100) cc_final: 0.9088 (m100)
REVERT: F   34 TYR cc_start: 0.8492 (m-80) cc_final: 0.8250 (m-80)
REVERT: F   45 GLN cc_start: 0.8579 (mt0) cc_final: 0.8283 (mt0)
REVERT: G   22 ASP cc_start: 0.8421 (t0) cc_final: 0.8137 (t0)
REVERT: G   33 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7261 (mttp)
REVERT: G   45 GLN cc_start: 0.8484 (mt0) cc_final: 0.8167 (mt0)
REVERT: G   55 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7608 (tm-30)
REVERT: H    8 GLU cc_start: 0.8519 (tt0) cc_final: 0.7646 (tt0)
REVERT: H   33 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7881 (mmtm)
REVERT: H   45 GLN cc_start: 0.8491 (mt0) cc_final: 0.8160 (mt0)
REVERT: H   46 ARG cc_start: 0.7563 (tpt170) cc_final: 0.7091 (tpt170)
REVERT: H   55 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7619 (tm-30)
REVERT: I   45 GLN cc_start: 0.8504 (mt0) cc_final: 0.8217 (mt0)
REVERT: I   55 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: I   61 ARG cc_start: 0.7995 (mtt-85) cc_final: 0.7744 (mmt180)
REVERT: L   45 GLN cc_start: 0.8516 (mt0) cc_final: 0.8255 (mt0)
REVERT: L   55 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7691 (tm-30)
REVERT: L   61 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7714 (mmt180)
REVERT: M   57 ILE cc_start: 0.8107 (mm) cc_final: 0.7799 (pt)
REVERT: M   58 SER cc_start: 0.9139 (m) cc_final: 0.8716 (p)
REVERT: N   57 ILE cc_start: 0.8117 (mm) cc_final: 0.7810 (pt)
REVERT: N   58 SER cc_start: 0.9141 (m) cc_final: 0.8712 (p)
  outliers start: 7
  outliers final: 3
  residues processed: 234
  average time/residue: 0.0791
  time to fit residues: 24.2951
Evaluate side-chains
  231 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 228
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain I residue   40 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 47 optimal weight:    0.7980
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** C  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  40 ASN
L  40 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.128491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.114310 restraints weight = 13255.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.117722 restraints weight = 6074.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.119879 restraints weight = 3560.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.121417 restraints weight = 2431.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.122476 restraints weight = 1800.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.7548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6804  Z= 0.155
  Angle     :  0.604   9.172   9108  Z= 0.338
  Chirality :  0.045   0.153    744
  Planarity :  0.003   0.032   1236
  Dihedral  :  4.156  16.715    900
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 23.26 %
    Favored  : 75.87 %
  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: -3.87 (0.18), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.13), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  46 
 TYR   0.018   0.001   TYR H  41 
 PHE   0.007   0.001   PHE H   2 
 TRP   0.029   0.001   TRP L  17 
 HIS   0.001   0.000   HIS D  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6804)
  covalent geometry    : angle       0.60381 ( 9108)
  hydrogen bonds       : bond        0.03036 (   50)
  hydrogen bonds       : angle       5.22352 (  150)

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

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

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

  1608 Ramachandran restraints generated.
    804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 235
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.7167 (tt0) cc_final: 0.6670 (pm20)
REVERT: A   33 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7360 (tttt)
REVERT: A   41 TYR cc_start: 0.7874 (m-10) cc_final: 0.7609 (m-80)
REVERT: A   46 ARG cc_start: 0.7803 (tpt90) cc_final: 0.6717 (ttp80)
REVERT: B    8 GLU cc_start: 0.7141 (tt0) cc_final: 0.6653 (pm20)
REVERT: B   33 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7350 (tttt)
REVERT: B   41 TYR cc_start: 0.7870 (m-10) cc_final: 0.7602 (m-80)
REVERT: B   46 ARG cc_start: 0.7796 (tpt90) cc_final: 0.6765 (ttp80)
REVERT: C   62 GLU cc_start: 0.7918 (tt0) cc_final: 0.7324 (tm-30)
REVERT: D   62 GLU cc_start: 0.7928 (tt0) cc_final: 0.7325 (tm-30)
REVERT: E   34 TYR cc_start: 0.8602 (m-80) cc_final: 0.8394 (m-80)
REVERT: E   45 GLN cc_start: 0.8618 (mt0) cc_final: 0.8339 (mt0)
REVERT: E   46 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7801 (ttt90)
REVERT: E   57 ILE cc_start: 0.9250 (mm) cc_final: 0.8823 (mm)
REVERT: F   17 TRP cc_start: 0.9312 (m100) cc_final: 0.9089 (m100)
REVERT: F   33 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7889 (mtpt)
REVERT: F   45 GLN cc_start: 0.8603 (mt0) cc_final: 0.8325 (mt0)
REVERT: F   46 ARG cc_start: 0.7994 (ttt90) cc_final: 0.7688 (ttt90)
REVERT: F   57 ILE cc_start: 0.9260 (mm) cc_final: 0.8829 (mm)
REVERT: G   45 GLN cc_start: 0.8503 (mt0) cc_final: 0.8178 (mt0)
REVERT: G   55 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7573 (tm-30)
REVERT: H    8 GLU cc_start: 0.8527 (tt0) cc_final: 0.7658 (tt0)
REVERT: H   15 ASP cc_start: 0.7568 (m-30) cc_final: 0.6654 (m-30)
REVERT: H   33 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7899 (mptt)
REVERT: H   45 GLN cc_start: 0.8518 (mt0) cc_final: 0.8187 (mt0)
REVERT: H   46 ARG cc_start: 0.7602 (tpt170) cc_final: 0.7149 (tpt170)
REVERT: H   55 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7594 (tm-30)
REVERT: I   45 GLN cc_start: 0.8500 (mt0) cc_final: 0.8233 (mt0)
REVERT: I   55 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7670 (tm-30)
REVERT: I   61 ARG cc_start: 0.8014 (mtt-85) cc_final: 0.7760 (mmt180)
REVERT: L   33 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7487 (mmtt)
REVERT: L   45 GLN cc_start: 0.8544 (mt0) cc_final: 0.8283 (mt0)
REVERT: L   55 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7708 (tm-30)
REVERT: L   61 ARG cc_start: 0.8039 (mtt-85) cc_final: 0.7758 (mmt180)
REVERT: M   57 ILE cc_start: 0.8034 (mm) cc_final: 0.7778 (pt)
REVERT: M   58 SER cc_start: 0.9115 (m) cc_final: 0.8702 (p)
REVERT: N   57 ILE cc_start: 0.8045 (mm) cc_final: 0.7782 (pt)
REVERT: N   58 SER cc_start: 0.9115 (m) cc_final: 0.8690 (p)
  outliers start: 5
  outliers final: 4
  residues processed: 239
  average time/residue: 0.0823
  time to fit residues: 25.4651
Evaluate side-chains
  234 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 229
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain F residue   33 LYS
Chi-restraints excluded: chain I residue   40 ASN
Chi-restraints excluded: chain L residue   40 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 25 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0870
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  40 ASN
L  40 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.127993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.114328 restraints weight = 13247.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.117622 restraints weight = 6222.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.119768 restraints weight = 3722.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.121273 restraints weight = 2517.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.122187 restraints weight = 1856.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.7630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6804  Z= 0.152
  Angle     :  0.607   8.596   9108  Z= 0.340
  Chirality :  0.046   0.157    744
  Planarity :  0.003   0.030   1236
  Dihedral  :  4.184  16.849    900
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 23.09 %
    Favored  : 76.04 %
  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: -3.87 (0.18), residues: 804
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.14), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  18 
 TYR   0.020   0.002   TYR I  41 
 PHE   0.009   0.001   PHE I  10 
 TRP   0.057   0.002   TRP I  17 
 HIS   0.001   0.000   HIS B  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 6804)
  covalent geometry    : angle       0.60743 ( 9108)
  hydrogen bonds       : bond        0.03423 (   50)
  hydrogen bonds       : angle       5.23679 (  150)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1198.88 seconds
wall clock time: 21 minutes 18.81 seconds (1278.81 seconds total)